From Sina.Madani at vumc.org  Thu Feb  1 11:51:52 2018
From: Sina.Madani at vumc.org (Madani, Sina)
Date: Thu, 1 Feb 2018 19:51:52 +0000
Subject: [bioontology-support] search by id in a subtree -> sparql
 service in VA similar to BioPortal
In-Reply-To: <6590516A-9AA6-4161-9122-142483B1D4A2@stanford.edu>
References: <103B3C18EAB4F444A941714214A04B8159418D83@ITS-HCWNEM105.ds.vanderbilt.edu>
 <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu>
 <6590516A-9AA6-4161-9122-142483B1D4A2@stanford.edu>
Message-ID: <103B3C18EAB4F444A941714214A04B8159419920@ITS-HCWNEM105.ds.vanderbilt.edu>

Hi John,

Thank you for getting back to me. Yes, I meant similar functionality like the sparql end point at the Stanford instance.
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.
We are evaluating your appliance for search/browse and visualization purposes for our order sets catalogue, with mappings to standard terminologies, at this point.

Thanks!
Sina

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Wednesday, January 31, 2018 6:50 PM
To: Michael Dorf
Cc: support at bioontology.org; Madani, Sina
Subject: Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal

Sina,

(Changing the topic line to focus on the SPARQL question that I'm addressing here.)

The exact answer to your last question may depend on what you mean by "similar to the BioPortal web site".

On BioPortal we have the 'front-end beta SPARQL query UI' set up at http://sparql.bioontology.org<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>. 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.

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.)

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.

I know the technical folks are thinking about your other questions, I'm not going to try to guess at those answers!

John




On Jan 31, 2018, at 3:05 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=C7B0qSamo%2BQz%2F1zW3G41kA3FzLCGJlKPYhMdXu7G8NU%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'"]


_______________________________________________
bioontology-support mailing list
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

-------------- next part --------------
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From jgraybeal at stanford.edu  Thu Feb  1 23:27:56 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 2 Feb 2018 07:27:56 +0000
Subject: [bioontology-support] search by id in a subtree -> sparql
 service in VA similar to BioPortal
In-Reply-To: <103B3C18EAB4F444A941714214A04B8159419920@ITS-HCWNEM105.ds.vanderbilt.edu>
References: <103B3C18EAB4F444A941714214A04B8159418D83@ITS-HCWNEM105.ds.vanderbilt.edu>
 <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu>
 <6590516A-9AA6-4161-9122-142483B1D4A2@stanford.edu>
 <103B3C18EAB4F444A941714214A04B8159419920@ITS-HCWNEM105.ds.vanderbilt.edu>
Message-ID: <4F631481-F89E-4A1D-B934-64CE1BB398E1@stanford.edu>

Hi Sina,

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.

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!)

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!).

I think we'll be able to come back to you with more thoughts soon, hopefully by the weekend.

John


On Feb 1, 2018, at 11:51 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi John,

Thank you for getting back to me. Yes, I meant similar functionality like the sparql end point at the Stanford instance.
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.
We are evaluating your appliance for search/browse and visualization purposes for our order sets catalogue, with mappings to standard terminologies, at this point.

Thanks!
Sina

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Wednesday, January 31, 2018 6:50 PM
To: Michael Dorf
Cc: support at bioontology.org<mailto:support at bioontology.org>; Madani, Sina
Subject: Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal

Sina,

(Changing the topic line to focus on the SPARQL question that I'm addressing here.)

The exact answer to your last question may depend on what you mean by "similar to the BioPortal web site".

On BioPortal we have the 'front-end beta SPARQL query UI' set up at http://sparql.bioontology.org<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>. 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.

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.)

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.

I know the technical folks are thinking about your other questions, I'm not going to try to guess at those answers!

John




On Jan 31, 2018, at 3:05 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=C7B0qSamo%2BQz%2F1zW3G41kA3FzLCGJlKPYhMdXu7G8NU%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'"]


_______________________________________________
bioontology-support mailing list
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

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


-------------- next part --------------
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From Sina.Madani at vumc.org  Fri Feb  2 05:25:23 2018
From: Sina.Madani at vumc.org (Madani, Sina)
Date: Fri, 2 Feb 2018 13:25:23 +0000
Subject: [bioontology-support] search by id in a subtree -> sparql
 service in VA similar to BioPortal
In-Reply-To: <4F631481-F89E-4A1D-B934-64CE1BB398E1@stanford.edu>
References: <103B3C18EAB4F444A941714214A04B8159418D83@ITS-HCWNEM105.ds.vanderbilt.edu>
 <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu>
 <6590516A-9AA6-4161-9122-142483B1D4A2@stanford.edu>
 <103B3C18EAB4F444A941714214A04B8159419920@ITS-HCWNEM105.ds.vanderbilt.edu>
 <4F631481-F89E-4A1D-B934-64CE1BB398E1@stanford.edu>
Message-ID: <18FE2944-380A-4473-B1CF-FD0E0EDA154D@vumc.org>

Thank you, John for the response.
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.

Thanks again for looking into this

Sina

From: John Graybeal <jgraybeal at stanford.edu>
Date: Friday, February 2, 2018 at 2:28 AM
To: "Madani, Sina" <Sina.Madani at vumc.org>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal

Hi Sina,

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.

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!)

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!).

I think we'll be able to come back to you with more thoughts soon, hopefully by the weekend.

John


On Feb 1, 2018, at 11:51 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi John,

Thank you for getting back to me. Yes, I meant similar functionality like the sparql end point at the Stanford instance.
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.
We are evaluating your appliance for search/browse and visualization purposes for our order sets catalogue, with mappings to standard terminologies, at this point.

Thanks!
Sina

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Wednesday, January 31, 2018 6:50 PM
To: Michael Dorf
Cc: support at bioontology.org<mailto:support at bioontology.org>; Madani, Sina
Subject: Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal

Sina,

(Changing the topic line to focus on the SPARQL question that I'm addressing here.)

The exact answer to your last question may depend on what you mean by "similar to the BioPortal web site".

On BioPortal we have the 'front-end beta SPARQL query UI' set up at http://sparql.bioontology.org<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>. 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.

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.)

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.

I know the technical folks are thinking about your other questions, I'm not going to try to guess at those answers!

John




On Jan 31, 2018, at 3:05 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=C7B0qSamo%2BQz%2F1zW3G41kA3FzLCGJlKPYhMdXu7G8NU%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'"]


_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support<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>

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

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

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From jgraybeal at stanford.edu  Fri Feb  2 11:36:38 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 2 Feb 2018 19:36:38 +0000
Subject: [bioontology-support] search by id in a subtree -> sparql
 service in VA similar to BioPortal
In-Reply-To: <18FE2944-380A-4473-B1CF-FD0E0EDA154D@vumc.org>
References: <103B3C18EAB4F444A941714214A04B8159418D83@ITS-HCWNEM105.ds.vanderbilt.edu>
 <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu>
 <6590516A-9AA6-4161-9122-142483B1D4A2@stanford.edu>
 <103B3C18EAB4F444A941714214A04B8159419920@ITS-HCWNEM105.ds.vanderbilt.edu>
 <4F631481-F89E-4A1D-B934-64CE1BB398E1@stanford.edu>
 <18FE2944-380A-4473-B1CF-FD0E0EDA154D@vumc.org>
Message-ID: <21138D6D-7969-4A6C-9BE0-FC63148E6631@stanford.edu>

Ah, sorry, I misunderstood what you had done earlier. I'm guessing we are likely to run into the same issue, we will keep you apprised.

john

On Feb 2, 2018, at 5:25 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Thank you, John for the response.
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.

Thanks again for looking into this

Sina

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Friday, February 2, 2018 at 2:28 AM
To: "Madani, Sina" <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal

Hi Sina,

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.

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!)

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!).

I think we'll be able to come back to you with more thoughts soon, hopefully by the weekend.

John


On Feb 1, 2018, at 11:51 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi John,

Thank you for getting back to me. Yes, I meant similar functionality like the sparql end point at the Stanford instance.
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.
We are evaluating your appliance for search/browse and visualization purposes for our order sets catalogue, with mappings to standard terminologies, at this point.

Thanks!
Sina

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Wednesday, January 31, 2018 6:50 PM
To: Michael Dorf
Cc: support at bioontology.org<mailto:support at bioontology.org>; Madani, Sina
Subject: Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal

Sina,

(Changing the topic line to focus on the SPARQL question that I'm addressing here.)

The exact answer to your last question may depend on what you mean by "similar to the BioPortal web site".

On BioPortal we have the 'front-end beta SPARQL query UI' set up at http://sparql.bioontology.org<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>. 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.

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.)

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.

I know the technical folks are thinking about your other questions, I'm not going to try to guess at those answers!

John




On Jan 31, 2018, at 3:05 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=C7B0qSamo%2BQz%2F1zW3G41kA3FzLCGJlKPYhMdXu7G8NU%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'"]


_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support<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>

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

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

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


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From Monica.O'Neill at calvarymater.org.au  Sun Feb  4 18:51:17 2018
From: Monica.O'Neill at calvarymater.org.au (O'Neill, Monica)
Date: Mon, 5 Feb 2018 02:51:17 +0000
Subject: [bioontology-support] Using biomedical ontology feature in REDCap
Message-ID: <B1BF633C57B39640B1F0B99035AE8186DE7ACA8C@CMN-EXCH4.mater.health.nsw.gov.au>

Hello,

I am an administrator of REDCap for my institution. I am very keen to employ the biomedical ontology functionality within REDCap for use in our clinical trials, but I am having some technical issues.

When I copy-paste the API token from my account with NCBO (username: monicaoneill), REDCap tells me this is not a valid token. I searched the online REDCap community and found others experienced the same error (see image below), which turned out to be because of security settings at their institution. I contacted Yelena Fridgant to ask for more details but she was unable to assist any further other than remembering she asked her IT Department to "whitelist" the website.

I have been in contact with Alberto Varas (cc'd) from my institutions IT department, who made every attempt to figure out which URL specifically needed "whitelisting". Are you able to help in this regard? I would be happy to provide you with more information if you need it, just let Alberto and myself know.

[cid:image001.png at 01D39E86.7F568820]

Many thanks in advance,
Monica O'Neill
Data Manager |Clinical Cancer Research Network
monica.o'neill at calvarymater.org.au<mailto:monica.o'neill at calvarymater.org.au>

Monday, Tuesday and Wednesday
Calvary Mater Newcastle
Due to hot-desking arrangements, please contact via email

Thursday and Friday
John Hunter Hospital
Tel 02 4923 6397 | Fax 02 4921 4274

This message is intended for the addressee and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of the Calvary Mater Newcastle or NSW Health.
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From jgraybeal at stanford.edu  Mon Feb  5 10:30:08 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 5 Feb 2018 18:30:08 +0000
Subject: [bioontology-support] Using biomedical ontology feature in
	REDCap
In-Reply-To: <B1BF633C57B39640B1F0B99035AE8186DE7ACA8C@CMN-EXCH4.mater.health.nsw.gov.au>
References: <B1BF633C57B39640B1F0B99035AE8186DE7ACA8C@CMN-EXCH4.mater.health.nsw.gov.au>
Message-ID: <E6DDA5D8-8DCE-4FE3-8BF4-DC5375E780F6@stanford.edu>

Hi Monica,

Thanks for doing most of this investigation for us! I will confirm what you have already found, but can give you one more test you can perform.

If you look at the URL for any query from the http://data.bioontology.org/documentation, for example something like http://data.bioontology.org/search?q=melanoma, you can try it in your browser. Probably it won't work, assuming you haven't entered your API key in a query before. To do so, complete the query like so:
 http://data.bioontology.org/search?q=melanoma&apikey=YOUR_API_KEY_HERE

If that still doesn't work, your browser is probably also behind some firewall that has to be opened to allow access to BioPortal. But if it *does* work, then you have confirmed your API key works, and now you have to get the firewall opened that is in front of the REDCap machine.)

This step of 'whitelisting' the BioPortal site is something that your IT department has to do?we can not help with that, sorry. Please have your IT person contact us if he or she is having some difficulty.

John



On Feb 4, 2018, at 6:51 PM, O'Neill, Monica <Monica.O'Neill at calvarymater.org.au<mailto:Monica.O'Neill at calvarymater.org.au>> wrote:

Hello,

I am an administrator of REDCap for my institution. I am very keen to employ the biomedical ontology functionality within REDCap for use in our clinical trials, but I am having some technical issues.

When I copy-paste the API token from my account with NCBO (username: monicaoneill), REDCap tells me this is not a valid token. I searched the online REDCap community and found others experienced the same error (see image below), which turned out to be because of security settings at their institution. I contacted Yelena Fridgant to ask for more details but she was unable to assist any further other than remembering she asked her IT Department to ?whitelist? the website.

I have been in contact with Alberto Varas (cc?d) from my institutions IT department, who made every attempt to figure out which URL specifically needed ?whitelisting?. Are you able to help in this regard? I would be happy to provide you with more information if you need it, just let Alberto and myself know.

<image001.png>

Many thanks in advance,
Monica O'Neill
Data Manager |Clinical Cancer Research Network
monica.o'neill at calvarymater.org.au<mailto:monica.o'neill at calvarymater.org.au>

Monday, Tuesday and Wednesday
Calvary Mater Newcastle
Due to hot-desking arrangements, please contact via email

Thursday and Friday
John Hunter Hospital
Tel 02 4923 6397 | Fax 02 4921 4274

This message is intended for the addressee and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of the Calvary Mater Newcastle or NSW Health. _______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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From vendetti at stanford.edu  Mon Feb  5 18:04:34 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 6 Feb 2018 02:04:34 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Elspeth Bruford
In-Reply-To: <5a6af5f5c10ac_31e03f97d78abf845169e@ncbo-prd-app-09.stanford.edu.mail>
References: <5a6af5f5c10ac_31e03f97d78abf845169e@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <603DF807-2AD5-41CB-81D5-5D24A048F145@stanford.edu>

Hello Dr. Bruford,


On Jan 26, 2018, at 1:33 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Elspeth Bruford

Email: hgnc at genenames.org<mailto:hgnc at genenames.org>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FHUGO

Feedback:

Hi, I'd like to request a few changes to the page you have for HGNC, https://bioportal.bioontology.org/ontologies/HUGO.

The main one would be that we really aren't "HUGO", we're one of the committees that work under the auspices of HUGO, while HUGO itself has a number of activities that have nothing to do with us (see www.hugo-international.org/<http://www.hugo-international.org/>). We're the HGNC (HUGO Gene Nomenclature Committee), so please can you it be updated to HGNC, presumably you can still alias with HUGO if you wish in case anyone is confused.

Ontology acronyms are unique identifiers / unmodifiable in our system. What we could do is create a new ontology entry with the desired HGNC acronym, and copy over the data from HUGO. You could look it over to make sure everything appears OK, then we could delete the HUGO entry. Let us know if you?d like us to proceed with that.


Also, if you could change the visible email address to hgnc at genenames.org<mailto:hgnc at genenames.org> as opposed to my personal work address that would be helpful. Thank you.

I modified the visible email address as requested.

Kind regards,
Jennifer

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From hpan at rti.org  Mon Feb  5 20:18:01 2018
From: hpan at rti.org (Pan, Huaqin (Helen))
Date: Tue, 6 Feb 2018 04:18:01 +0000
Subject: [bioontology-support] Help with Submission
In-Reply-To: <A2118F05-0F67-404A-A407-40E476BBA3C8@stanford.edu>
References: <DM2PR07MB146831270FE485F737287F10AE810@DM2PR07MB1468.namprd07.prod.outlook.com>
 <B8615F3E-9427-4BD5-A0D5-77D57DAD8E3D@stanford.edu>
 <D81B02B4-C624-4C6C-9753-0567DEC95D22@stanford.edu>
 <CY1PR0701MB14038EB9731C2691E3204DE1D6870@CY1PR0701MB1403.namprd07.prod.outlook.com>
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 <72A93DA6-DF31-4328-BD86-54F7AC380965@stanford.edu>
 <SN1PR07MB1518425380F982FBBAFE26A5D6EC0@SN1PR07MB1518.namprd07.prod.outlook.com>
 <A5ED5903-C0B8-4C78-AAF5-8861A57E00EF@stanford.edu>
 <ABA15D8F-3367-475C-8D62-7DB78FB5AACE@stanford.edu>
 <CY1PR0701MB174130275A8D7B504E6D29AFD6E10@CY1PR0701MB1741.namprd07.prod.outlook.com>
 <A2118F05-0F67-404A-A407-40E476BBA3C8@stanford.edu>
Message-ID: <CY1PR0701MB1741C3FE8F1B99827A9FCA71D6FD0@CY1PR0701MB1741.namprd07.prod.outlook.com>

Hi Jennifer, John, and Samson,

I submitted 2 versions in private.

  *   Subclass version ? nice hierarchical display,

http://purl.bioontology.org/ontology/LUNGMAP-MOUSE

  *   part-of version ? the right relations with part-of and subclass,

http://purl.bioontology.org/ontology/LUNGMAP-MOUSE_P

Would you please advise? The right implementation (part-of version)at our project site is in https://lungmap.net/breath-ontology-browser/.

Thank you!
Helen


From: Samson Tu [mailto:swt at stanford.edu]
Sent: Thursday, January 25, 2018 11:04 PM
To: Pan, Huaqin (Helen) <hpan at rti.org>
Cc: Samson Tu <swt at stanford.edu>; John Graybeal <jgraybeal at stanford.edu>; Jennifer Leigh Vendetti <vendetti at stanford.edu>; NCBO User Support <support at bioontology.org>
Subject: Re: [bioontology-support] Help with Submission

Hi,

I?d endorse John?s advocacy of ?mak[ing] the ontology correct (i.e., do not misrepresent partOf relationships as subclasses.)." Where you have ?part-of? relation in your domain, don?t modeled it as ?subclass_of.? Perhaps you want to create a third version where ?part-of? is never modeled as ?subclass_of?.

The next version of Protege (which may become available in February) will display relationships other than subclass-of. In the current version of Protege, there is an Individual Hierarchy plugin that you can install that can display object-property assertions as hierarchies at the individual level. It may not be what you need, but I am mentioning it just in case.

With best regards,
Samson

On Jan 25, 2018, at 3:12 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer and John,

Thank you both for your advice! I will submit both versions as private first, and choose the ?correct? one to make public.

John, I appreciate your suggestion in the last paragraph. Yes, I didn?t do that (have both ?part-of? AND ?subclass?). In version 1, I don?t have ?part-of?. In version 2 where I have ?part-of?, it?s either ?part-of? or ?subclass_of?, not BOTH.

Best regards,
Helen

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Wednesday, January 24, 2018 10:59 PM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>; NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] Help with Submission

I might add a few thoughts to Jennifer's summary.

My bias in such things is to make the ontology correct (i.e., do not misrepresent partOf relationships as subclasses, because it messes up any inferencing that people may want to do (and maybe quite important research, too). It's better to 'force' the tools to improve than to create improper data artifacts, even if it is painful.

Re the visualization, I understand the Protege team may be working on an improved visual presentation of tree hierarchies, partly to address this issue?I just saw a note to that effect in another list, but haven't asked the team. If that's the case, we would definitely see if leveraging that code for BioPortal could be possible, though it wouldn't happen quickly.

Regarding the proposed idea to publish them privately at first?since you don't know which one you'll make public, you won't know which one to give the correct acronym. I'd give them both 'fake' acronyms, then republish the one you like publicly under the correct acronym. (We could delete the private ones afterwards, that would be best for BioPortal.)

And finally, a really bad suggestion given my bias above: if you basically _added_ a subclass relation for each partOf relation, if the ontology parsed (not sure if it could), you'd have both worlds?a hierarchical view and still being able to see the partOf relations. But I really hope you don't do that.

John


On Jan 24, 2018, at 5:18 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Helen,




On Jan 22, 2018, at 1:59 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Jennifer,

I am working on another project that developed an ontology that I will submit soon. It?s currently available at our project site, https://lungmap.net/breath-ontology-browser/.

Here is my questions. Due to the fact that owl/Prot?g? display the hierarchical relation only for ?subclass-of?, not ?part-of?, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal.


My expertise is on the software development side of things with regard to BioPortal. It?s difficult for me to comment on which version of your ontology the biomedical community might find more useful.






  *   Version 1 with exclusive ?subclass_of? ? Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of ?part-of? and ?subclass_of?
  *   Version 2 with mix of ?part-of? and ?subclass_of? ? Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of ?part-of? and ?subclass_of?

We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for ?part-of?.


One option I can suggest would be for you to create two separate ontology entries in BioPortal for your versions 1 and 2 above. You could initially make the viewing restriction ?private?, which would give you the opportunity to view them and decide which seems better for your needs / use cases. After you?ve made your decision, we could remove whichever one you decide not to publish, and change the viewing restriction of your preferred ontology to ?public?.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From support at bioontology.org  Tue Feb  6 03:06:31 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 06 Feb 2018 03:06:31 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Laia Subirats
Message-ID: <5a798c37cc686_4b993fd36da90bc0585a3@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Mon Feb  5 19:28:30 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 05 Feb 2018 19:28:30 -0800
Subject: [bioontology-support] [BioPortal] Feedback from fpylin
Message-ID: <5a7920de3724e_6f7f3f997336445c720b7@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Tue Feb  6 11:03:33 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 6 Feb 2018 19:03:33 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Laia Subirats
In-Reply-To: <5a798c37cc686_4b993fd36da90bc0585a3@ncbo-prd-app-08.stanford.edu.mail>
References: <5a798c37cc686_4b993fd36da90bc0585a3@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <3CF3D7EC-3B2C-437F-A2C7-66E6591E3B0D@stanford.edu>

Hi Laia,

I just tested this functionality and can confirm that I?m seeing some sort of issue on our site with the lost password page. Sincere apologies for the inconvenience. I?m looking into it now and will report back.

Kind regards,
Jennifer



On Feb 6, 2018, at 3:06 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Laia Subirats

Email: laia.subirats at gmail.com<mailto:laia.subirats at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Flogin%3Fredirect%3Dhttps%253A%252F%252Fbioportal.bioontology.org<http://252Fbioportal.bioontology.org>%252Flogin%252Fsend_pass

Feedback:

Dear Mr/Mrs,
I am trying to upload a new version of an ontology but I do not remember my password. I am trying to recover it but I do not receive any email. I wonder what I can do.
Yours faithfully,

Laia Subirats

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From support at bioontology.org  Tue Feb  6 11:51:20 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 06 Feb 2018 11:51:20 -0800
Subject: [bioontology-support] [BioPortal] Feedback from carrie irvine
Message-ID: <5a7a0738c32dc_5a1f3ff4be69c7f47973@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Tue Feb  6 14:40:23 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 6 Feb 2018 22:40:23 +0000
Subject: [bioontology-support] [BioPortal] Feedback from carrie irvine
In-Reply-To: <5a7a0738c32dc_5a1f3ff4be69c7f47973@ncbo-prd-app-08.stanford.edu.mail>
References: <5a7a0738c32dc_5a1f3ff4be69c7f47973@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <4847A754-AF13-4AC2-9806-A8A2B2822FDE@stanford.edu>

Hello Carrie,

I queried our system for an account associated with your email address (carrie_irvine at urmc.rochester.edu<http://urmc.rochester.edu>), and didn?t find any results. Is it possible you signed up for an account with a different email address?

Kind regards,
Jennifer



On Feb 6, 2018, at 11:51 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: carrie irvine

Email: carrie_irvine at urmc.rochester.edu<mailto:carrie_irvine at urmc.rochester.edu>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Flost_pass

Feedback:

Hello - I cannot find my account name associated with my email. can you provide this to me to I can reset my password.

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From Carrie_Irvine at URMC.Rochester.edu  Wed Feb  7 06:20:10 2018
From: Carrie_Irvine at URMC.Rochester.edu (Irvine, Carrie)
Date: Wed, 7 Feb 2018 14:20:10 +0000
Subject: [bioontology-support] [BioPortal] Feedback from carrie irvine
In-Reply-To: <4847A754-AF13-4AC2-9806-A8A2B2822FDE@stanford.edu>
References: <5a7a0738c32dc_5a1f3ff4be69c7f47973@ncbo-prd-app-08.stanford.edu.mail>
 <4847A754-AF13-4AC2-9806-A8A2B2822FDE@stanford.edu>
Message-ID: <8c9a9036e418489690dac14f4b9de6d6@EXMBXSDC03.urmc-sh.rochester.edu>

Hi Jennifer,

Strange, I am pretty sure I did not signup with another account.  We will just request another token.  Thanks for your help

Carrie Irvine, MS
Manager of Software Development for Research
Research and Academic Information Technology
Saunders Research Building ? 4th Floor, Room 240
Clinical and Translational Science Institute
University of Rochester Medical Center
265 Crittenden Blvd.
Box CU420639
Rochester, NY 14642

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, February 06, 2018 5:40 PM
To: support at bioontology.org
Cc: Irvine, Carrie <Carrie_Irvine at URMC.Rochester.edu>
Subject: Re: [bioontology-support] [BioPortal] Feedback from carrie irvine

Hello Carrie,

I queried our system for an account associated with your email address (carrie_irvine at urmc.rochester.edu<http://urmc.rochester.edu>), and didn?t find any results. Is it possible you signed up for an account with a different email address?

Kind regards,
Jennifer




On Feb 6, 2018, at 11:51 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: carrie irvine
Email: carrie_irvine at urmc.rochester.edu<mailto:carrie_irvine at urmc.rochester.edu>
Location: https%3A%2F%2Fbioportal.bioontology.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__2Fbioportal.bioontology.org&d=DwMGaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=q415wRSOZmV0I1W8H5OLbZjn2fLIobhFfhIcAY7hg9w&m=ydvpPwCArZ_KZgJW9h7RWNrgNNAP9HY5lxDtf8-KZok&s=exXNz9YbPt5R1tpf7R6HzgzLTmHZMdgPzqQmAG_jEVE&e=>%2Flost_pass

Feedback:
Hello - I cannot find my account name associated with my email. can you provide this to me to I can reset my password.

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support<https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwQGaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=q415wRSOZmV0I1W8H5OLbZjn2fLIobhFfhIcAY7hg9w&m=ydvpPwCArZ_KZgJW9h7RWNrgNNAP9HY5lxDtf8-KZok&s=AuxekyutGwZ2gHLtR6yTqQAA_UhdwFXWdwFNWjR6lUk&e=>

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From support at bioontology.org  Wed Feb  7 06:26:32 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 07 Feb 2018 06:26:32 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Luis Gonzalez
Message-ID: <5a7b0c9894d75_7d8d3fd3dd64ff287791@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Wed Feb  7 02:24:35 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 07 Feb 2018 02:24:35 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Paul Schofield
Message-ID: <5a7ad3e3eab10_14223f92afffbf00859df@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Wed Feb  7 13:15:03 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 7 Feb 2018 21:15:03 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Laia Subirats
In-Reply-To: <3CF3D7EC-3B2C-437F-A2C7-66E6591E3B0D@stanford.edu>
References: <5a798c37cc686_4b993fd36da90bc0585a3@ncbo-prd-app-08.stanford.edu.mail>
 <3CF3D7EC-3B2C-437F-A2C7-66E6591E3B0D@stanford.edu>
Message-ID: <C3B39A48-B59D-42BD-A374-F341375C04CE@stanford.edu>

Hi Laia,

A recent code change caused the issue you had with the lost password page. I committed a fix and released it to our production environment. I?ve tested the lost password page and everything appears to be functioning well.

Apologies again for the inconvenience.

Kind regards,
Jennifer



On Feb 6, 2018, at 11:03 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Laia,

I just tested this functionality and can confirm that I?m seeing some sort of issue on our site with the lost password page. Sincere apologies for the inconvenience. I?m looking into it now and will report back.

Kind regards,
Jennifer



On Feb 6, 2018, at 3:06 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Laia Subirats

Email: laia.subirats at gmail.com<mailto:laia.subirats at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Flogin%3Fredirect%3Dhttps%253A%252F%252Fbioportal.bioontology.org<http://252fbioportal.bioontology.org/>%252Flogin%252Fsend_pass

Feedback:

Dear Mr/Mrs,
I am trying to upload a new version of an ontology but I do not remember my password. I am trying to recover it but I do not receive any email. I wonder what I can do.
Yours faithfully,

Laia Subirats

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From vendetti at stanford.edu  Wed Feb  7 13:29:49 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 7 Feb 2018 21:29:49 +0000
Subject: [bioontology-support] [BioPortal] Feedback from fpylin
In-Reply-To: <5a7920de3724e_6f7f3f997336445c720b7@ncbo-prd-app-08.stanford.edu.mail>
References: <5a7920de3724e_6f7f3f997336445c720b7@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <8635F5F3-CBDD-4EEA-8D14-E535487D2EFF@stanford.edu>

Hello Frank,


On Feb 5, 2018, at 7:28 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

I am encountering difficulties uploading our work, CCTOO, to the bioportal. A entry has been created but uploading of OBO file has failed. Is there a method to enable update/re-uploading of file? Many thanks for your help.



I looked at the log files for the ontology submission you uploaded. There was an error during the indexing process. I reprocessed the submission, and it?s now fully available in BioPortal.

Apologies for that delay.

Kind regards,
Jennifer

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From vendetti at stanford.edu  Wed Feb  7 14:16:40 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 7 Feb 2018 22:16:40 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Luis Gonzalez
In-Reply-To: <5a7b0c9894d75_7d8d3fd3dd64ff287791@ncbo-prd-app-08.stanford.edu.mail>
References: <5a7b0c9894d75_7d8d3fd3dd64ff287791@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <185E9515-8D48-4EFE-A048-40F6D5D72EFE@stanford.edu>

Hello Luis,

Apologies - there appears to have been a problem during the processing of your latest submission. I reprocessed the submission, which is now fully available in BioPortal.

Kind regards,
Jennifer



On Feb 7, 2018, at 6:26 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Luis Gonzalez

Email: lagonzalezmo at unal.edu.co<mailto:lagonzalezmo at unal.edu.co>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500

Feedback:

Hi,

I cannot access my ontology (Collembola Anatomy Ontology). I want to make some changes. Thank you

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From vendetti at stanford.edu  Wed Feb  7 15:19:48 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 7 Feb 2018 23:19:48 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Paul Schofield
In-Reply-To: <5a7ad3e3eab10_14223f92afffbf00859df@ncbo-prd-app-08.stanford.edu.mail>
References: <5a7ad3e3eab10_14223f92afffbf00859df@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <62A211F2-CBF5-40E0-9D87-80243D6E8354@stanford.edu>

Hi Paul,

I?m not entirely sure how MPATH got into a state where the system was repeatedly creating submissions that erred out. However, I removed the corrupt submissions, and reprocessed the latest one with your updated URL that points to your GitHub location.

Everything seems to be accessible w/out issue in BioPortal now.

Kind regards,
Jennifer



On Feb 7, 2018, at 2:24 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Paul Schofield

Email: pns12 at cam.ac.uk<mailto:pns12 at cam.ac.uk>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:

I have recently corrected the URL from which MPATH uploads but seeing an "uploaded, Error, Rdf" flag. Would be grateful for guidance as to what might be going wrong please!
Many thanks! Paul

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From laia.subirats at gmail.com  Thu Feb  8 01:16:30 2018
From: laia.subirats at gmail.com (Laia Subirats)
Date: Thu, 8 Feb 2018 10:16:30 +0100
Subject: [bioontology-support] [BioPortal] Feedback from Laia Subirats
In-Reply-To: <C3B39A48-B59D-42BD-A374-F341375C04CE@stanford.edu>
References: <5a798c37cc686_4b993fd36da90bc0585a3@ncbo-prd-app-08.stanford.edu.mail>
 <3CF3D7EC-3B2C-437F-A2C7-66E6591E3B0D@stanford.edu>
 <C3B39A48-B59D-42BD-A374-F341375C04CE@stanford.edu>
Message-ID: <CAHaRLjtPVfALEwQ0vFgb=PSjMpmnzpfL26+dcgNZ9aqjouDvVg@mail.gmail.com>

Thank you Jennifer,

Now works perfectly.

Kind regards,

Laia

On Wed, Feb 7, 2018 at 10:15 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi Laia,
>
> A recent code change caused the issue you had with the lost password page.
> I committed a fix and released it to our production environment. I?ve
> tested the lost password page and everything appears to be functioning well.
>
> Apologies again for the inconvenience.
>
> Kind regards,
> Jennifer
>
>
>
> On Feb 6, 2018, at 11:03 AM, Jennifer Leigh Vendetti <
> vendetti at stanford.edu> wrote:
>
> Hi Laia,
>
> I just tested this functionality and can confirm that I?m seeing some sort
> of issue on our site with the lost password page. Sincere apologies for the
> inconvenience. I?m looking into it now and will report back.
>
> Kind regards,
> Jennifer
>
>
>
> On Feb 6, 2018, at 3:06 AM, support at bioontology.org wrote:
>
> Name: Laia Subirats
>
> Email: laia.subirats at gmail.com <laia.subirats at gmail.com>
>
> Location: https%3A%2F%2Fbioportal.bioontology.org
> <http://2fbioportal.bioontology.org/>%2Flogin%
> 3Fredirect%3Dhttps%253A%252F%252Fbioportal.bioontology.org
> <http://252fbioportal.bioontology.org/>%252Flogin%252Fsend_pass
>
>
> *Feedback:*
>
> Dear Mr/Mrs,
> I am trying to upload a new version of an ontology but I do not remember
> my password. I am trying to recover it but I do not receive any email. I
> wonder what I can do.
> Yours faithfully,
>
> Laia Subirats
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>


-- 
Laia Subirats
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From support at bioontology.org  Thu Feb  8 03:38:16 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 08 Feb 2018 03:38:16 -0800
Subject: [bioontology-support] [BioPortal] Feedback from mferrerb
Message-ID: <5a7c36a8dcc15_5d1b3fc6b6512b9414662@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Thu Feb  8 12:57:04 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 8 Feb 2018 20:57:04 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mferrerb
In-Reply-To: <5a7c36a8dcc15_5d1b3fc6b6512b9414662@ncbo-prd-app-08.stanford.edu.mail>
References: <5a7c36a8dcc15_5d1b3fc6b6512b9414662@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <ACC959A4-A447-400E-870F-6D4C17061649@stanford.edu>

Hello Minerva,

I would love to see if there are any responses from the research community. It might help if you describe a task you are trying to accomplish; it may be that BioPortal does not directly contribute to your needs.

(I can say our BioPortal team does not have the domain background to help, sorry.)

John


On Feb 8, 2018, at 3:38 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: mferrerb

Email: Minerva.FerrerBuitrago at UGent.be<mailto:Minerva.FerrerBuitrago at UGent.be>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FEDAM%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fedamontology.org<http://252Fedamontology.org>%252Foperation_0315

Feedback:

How can I start using bioontology for Gene expression RNA-seq analysis?

_______________________________________________
bioontology-support mailing list
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


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From support at bioontology.org  Thu Feb  8 16:18:35 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 08 Feb 2018 16:18:35 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Simon Cox
Message-ID: <5a7ce8dbefb76_35ef3f7efc3f93043478d@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Feb  8 17:54:21 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 9 Feb 2018 01:54:21 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Simon Cox
In-Reply-To: <5a7ce8dbefb76_35ef3f7efc3f93043478d@ncbo-prd-app-08.stanford.edu.mail>
References: <5a7ce8dbefb76_35ef3f7efc3f93043478d@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <59609BCE-24EC-44EF-88AE-DE61B0BF0958@stanford.edu>

Hello Simon,


On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Simon Cox

Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FTIME

Feedback:

I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

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From jgraybeal at stanford.edu  Thu Feb  8 21:35:19 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 9 Feb 2018 05:35:19 +0000
Subject: [bioontology-support] labels for Time ontology
Message-ID: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,


On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Simon Cox

Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:

I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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


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From Simon.Cox at csiro.au  Thu Feb  8 21:49:10 2018
From: Simon.Cox at csiro.au (Simon.Cox at csiro.au)
Date: Fri, 9 Feb 2018 05:49:10 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
Message-ID: <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,



On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

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From swt at stanford.edu  Fri Feb  9 10:59:24 2018
From: swt at stanford.edu (Samson Tu)
Date: Fri, 9 Feb 2018 18:59:24 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
 <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
Message-ID: <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>

Hi,

I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,
Samson


On Feb 8, 2018, at 9:49 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,



On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From vendetti at stanford.edu  Fri Feb  9 11:22:34 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 9 Feb 2018 19:22:34 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
 <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
 <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
Message-ID: <D5F38910-6D0E-4EBA-A87E-128AFFA78E61@stanford.edu>

Hello All,

It was my suspicion as well that this particular axiom might be causing the issue. Here?s a screenshot in the Protege ontology editor that shows rdfs:Literal appearing in the class tree:


[cid:EB52426F-2ABA-4606-B22A-3242A94C6F35 at stanford.edu]


I removed this axiom and uploaded the modified version of the ontology to our private staging environment. Without that axiom, the ontology is processed without errors in BioPortal:


[cid:E1072C3A-BED3-43D5-AA50-B4FF9AAD7332 at stanford.edu]



Simon - any chance an updated version of the ontology could be provided to us?

Kind regards,
Jennifer



On Feb 9, 2018, at 10:59 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

Hi,

I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,
Samson


On Feb 8, 2018, at 9:49 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,



On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From Simon.Cox at csiro.au  Sat Feb 10 22:10:49 2018
From: Simon.Cox at csiro.au (Simon.Cox at csiro.au)
Date: Sun, 11 Feb 2018 06:10:49 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
 <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
 <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
Message-ID: <6d6184f83a494502a3cbc8c4e1202c37@exch1-mel.nexus.csiro.au>

I don?t think you are correct.
The RDFS Spec is quite explicit on this [1]: ?Each instance of rdfs:Datatype is a subclass of rdfs:Literal.?

The offending lines in the OWL-Time rdf are

xsd:dateTimeStamp
  rdf:type rdfs:Datatype ;              #i.e xsd:dateTimeStamp is an instance of rdfs:Datatype
  rdfs:label "dateTimeStamp" ;
  rdfs:subClassOf rdfs:Literal ;     #... and is a subclass of rdfs:Literal
.

I guess the explanation in the RDFS spec means that the sub-class axiom is strictly not needed, since it is an entailment of typing axiom anyway, but it should not cause a conforming processor to throw an error.

[1] https://www.w3.org/TR/rdf-schema/#ch_datatype

From: Samson Tu [mailto:swt at stanford.edu]
Sent: Saturday, 10 February, 2018 05:59
To: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au>
Cc: Samson Tu <swt at stanford.edu>; John Graybeal <jgraybeal at stanford.edu>; bioontology-support at lists.stanford.edu
Subject: Re: [bioontology-support] labels for Time ontology

Hi,

I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,
Samson


On Feb 8, 2018, at 9:49 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,




On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
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From Simon.Cox at csiro.au  Sat Feb 10 22:34:44 2018
From: Simon.Cox at csiro.au (Simon.Cox at csiro.au)
Date: Sun, 11 Feb 2018 06:34:44 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <D5F38910-6D0E-4EBA-A87E-128AFFA78E61@stanford.edu>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
 <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
 <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
 <D5F38910-6D0E-4EBA-A87E-128AFFA78E61@stanford.edu>
Message-ID: <85294a58bfd344b19bd795ae2b204519@exch1-mel.nexus.csiro.au>

As I just commented in response to Samson, I think we?ve probably hot one of those places where OWL processors have made some assumptions inconsistent with the original RDFS definitions. The RDFS Spec is quite explicit on this [1]: ?Each instance of rdfs:Datatype is a subclass of rdfs:Literal.? so while the subclass axiom is arguably redundant, there should not be an error thrown.

However, I can suggest that it is removed from the official ontology.

Simon

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Saturday, 10 February, 2018 06:23
To: bioontology-support at lists.stanford.edu
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au>; John Graybeal <jgraybeal at stanford.edu>; Samson Tu <swt at stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

Hello All,

It was my suspicion as well that this particular axiom might be causing the issue. Here?s a screenshot in the Protege ontology editor that shows rdfs:Literal appearing in the class tree:


[cid:image001.png at 01D3A35B.E5890530]


I removed this axiom and uploaded the modified version of the ontology to our private staging environment. Without that axiom, the ontology is processed without errors in BioPortal:


[cid:image002.png at 01D3A35B.E5890530]



Simon - any chance an updated version of the ontology could be provided to us?

Kind regards,
Jennifer




On Feb 9, 2018, at 10:59 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

Hi,

I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,
Samson


On Feb 8, 2018, at 9:49 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,




On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From swt at stanford.edu  Sun Feb 11 08:43:18 2018
From: swt at stanford.edu (Samson Tu)
Date: Sun, 11 Feb 2018 16:43:18 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <6d6184f83a494502a3cbc8c4e1202c37@exch1-mel.nexus.csiro.au>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
 <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
 <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
 <6d6184f83a494502a3cbc8c4e1202c37@exch1-mel.nexus.csiro.au>
Message-ID: <C0BD3869-F3A9-4226-946F-0AF4D1B205B3@stanford.edu>

The OWL 2 spec makes a distinction between datatype and class:

"Datatypes are entities that refer to sets of data values. Thus, datatypes are analogous to classes, the main difference being that the former contain data values such as strings and numbers, rather than individuals.? [1]

Maybe the issue is whether the Time ontology is meant to be an RDF schema or an OWL ontology. These are two different specifications.

The OWL API loads the ontology didn?t throw an error. It?s the Bioportal hierarchy display code that had problem. I agree that the Bioportal hierarchy display code should be more forgiving. Maybe that should be an issue  tracker item.

With best regards,
Samson

[1] https://www.w3.org/TR/owl2-syntax/#Datatypes


On Feb 10, 2018, at 10:10 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

I don?t think you are correct.
The RDFS Spec is quite explicit on this [1]: ?Each instance of rdfs:Datatype is a subclass of rdfs:Literal.?

The offending lines in the OWL-Time rdf are

xsd:dateTimeStamp
  rdf:type rdfs:Datatype ;              #i.e xsd:dateTimeStamp is an instance of rdfs:Datatype
  rdfs:label "dateTimeStamp" ;
  rdfs:subClassOf rdfs:Literal ;     #... and is a subclass of rdfs:Literal
.

I guess the explanation in the RDFS spec means that the sub-class axiom is strictly not needed, since it is an entailment of typing axiom anyway, but it should not cause a conforming processor to throw an error.

[1] https://www.w3.org/TR/rdf-schema/#ch_datatype

From: Samson Tu [mailto:swt at stanford.edu]
Sent: Saturday, 10 February, 2018 05:59
To: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Cc: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>; John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

Hi,

I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,
Samson


On Feb 8, 2018, at 9:49 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,




On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From Simon.Cox at csiro.au  Sun Feb 11 13:09:19 2018
From: Simon.Cox at csiro.au (Simon.Cox at csiro.au)
Date: Sun, 11 Feb 2018 21:09:19 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <C0BD3869-F3A9-4226-946F-0AF4D1B205B3@stanford.edu>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
 <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
 <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
 <6d6184f83a494502a3cbc8c4e1202c37@exch1-mel.nexus.csiro.au>,
 <C0BD3869-F3A9-4226-946F-0AF4D1B205B3@stanford.edu>
Message-ID: <a0886ec84be74b6faa7d5595bbce158d@exch1-mel.nexus.csiro.au>

> The OWL 2 spec makes a distinction between datatype and class:

Yes. And that's also partly why owl:Class != rdfs:Class.
But I don't think that's the issue here.
It's about how a datatype is formally defined.

RDFS says that all datatypes are subclasses of rdfs:Literal which makes complete sense.
I think there may be a question whether that should be captured using the rdfs:subClassOf axiom.
Else this is where Bioportal might be too fierce.

Anyway, the inclusion of a definition of xsd:dateTimeStamp in this ontology is not necessary since it is defined elsewhere (in the xsd spec) so I will see if we can get it removed from the RDF sources.

Simon

________________________________
From: Samson Tu <swt at stanford.edu>
Sent: Sunday, 11 February 2018 4:43:18 PM
To: Cox, Simon (L&W, Clayton)
Cc: Samson Tu; John Graybeal; bioontology-support at lists.stanford.edu
Subject: Re: [bioontology-support] labels for Time ontology

The OWL 2 spec makes a distinction between datatype and class:

"Datatypes are entities that refer to sets of data values. Thus, datatypes are analogous to classes, the main difference being that the former contain data values such as strings and numbers, rather than individuals.? [1]

Maybe the issue is whether the Time ontology is meant to be an RDF schema or an OWL ontology. These are two different specifications.

The OWL API loads the ontology didn?t throw an error. It?s the Bioportal hierarchy display code that had problem. I agree that the Bioportal hierarchy display code should be more forgiving. Maybe that should be an issue  tracker item.

With best regards,
Samson

[1] https://www.w3.org/TR/owl2-syntax/#Datatypes


On Feb 10, 2018, at 10:10 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

I don?t think you are correct.
The RDFS Spec is quite explicit on this [1]: ?Each instance of rdfs:Datatype is a subclass of rdfs:Literal.?

The offending lines in the OWL-Time rdf are

xsd:dateTimeStamp
  rdf:type rdfs:Datatype ;              #i.e xsd:dateTimeStamp is an instance of rdfs:Datatype
  rdfs:label "dateTimeStamp" ;
  rdfs:subClassOf rdfs:Literal ;     #... and is a subclass of rdfs:Literal
.

I guess the explanation in the RDFS spec means that the sub-class axiom is strictly not needed, since it is an entailment of typing axiom anyway, but it should not cause a conforming processor to throw an error.

[1] https://www.w3.org/TR/rdf-schema/#ch_datatype

From: Samson Tu [mailto:swt at stanford.edu]
Sent: Saturday, 10 February, 2018 05:59
To: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Cc: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>; John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

Hi,

I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,
Samson


On Feb 8, 2018, at 9:49 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,




On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From jgraybeal at stanford.edu  Sun Feb 11 13:40:34 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Sun, 11 Feb 2018 21:40:34 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <a0886ec84be74b6faa7d5595bbce158d@exch1-mel.nexus.csiro.au>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
 <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
 <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
 <6d6184f83a494502a3cbc8c4e1202c37@exch1-mel.nexus.csiro.au>
 <C0BD3869-F3A9-4226-946F-0AF4D1B205B3@stanford.edu>
 <a0886ec84be74b6faa7d5595bbce158d@exch1-mel.nexus.csiro.au>
Message-ID: <32C6DC30-005B-46EF-8A30-A6FF61031C64@stanford.edu>

perhaps we should do a quick test with that change in BioPortal, to see if it behaves better.

john

On Feb 11, 2018, at 1:09 PM, Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au> wrote:

> The OWL 2 spec makes a distinction between datatype and class:

Yes. And that's also partly why owl:Class != rdfs:Class.
But I don't think that's the issue here.
It's about how a datatype is formally defined.

RDFS says that all datatypes are subclasses of rdfs:Literal which makes complete sense.
I think there may be a question whether that should be captured using the rdfs:subClassOf axiom.
Else this is where Bioportal might be too fierce.

Anyway, the inclusion of a definition of xsd:dateTimeStamp in this ontology is not necessary since it is defined elsewhere (in the xsd spec) so I will see if we can get it removed from the RDF sources.

Simon

________________________________
From: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>
Sent: Sunday, 11 February 2018 4:43:18 PM
To: Cox, Simon (L&W, Clayton)
Cc: Samson Tu; John Graybeal; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

The OWL 2 spec makes a distinction between datatype and class:

"Datatypes are entities that refer to sets of data values. Thus, datatypes are analogous to classes, the main difference being that the former contain data values such as strings and numbers, rather than individuals.? [1]

Maybe the issue is whether the Time ontology is meant to be an RDF schema or an OWL ontology. These are two different specifications.

The OWL API loads the ontology didn?t throw an error. It?s the Bioportal hierarchy display code that had problem. I agree that the Bioportal hierarchy display code should be more forgiving. Maybe that should be an issue  tracker item.

With best regards,
Samson

[1] https://www.w3.org/TR/owl2-syntax/#Datatypes


On Feb 10, 2018, at 10:10 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

I don?t think you are correct.
The RDFS Spec is quite explicit on this [1]: ?Each instance of rdfs:Datatype is a subclass of rdfs:Literal.?

The offending lines in the OWL-Time rdf are

xsd:dateTimeStamp
  rdf:type rdfs:Datatype ;              #i.e xsd:dateTimeStamp is an instance of rdfs:Datatype
  rdfs:label "dateTimeStamp" ;
  rdfs:subClassOf rdfs:Literal ;     #... and is a subclass of rdfs:Literal
.

I guess the explanation in the RDFS spec means that the sub-class axiom is strictly not needed, since it is an entailment of typing axiom anyway, but it should not cause a conforming processor to throw an error.

[1] https://www.w3.org/TR/rdf-schema/#ch_datatype

From: Samson Tu [mailto:swt at stanford.edu]
Sent: Saturday, 10 February, 2018 05:59
To: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Cc: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>; John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

Hi,

I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,
Samson


On Feb 8, 2018, at 9:49 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,




On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
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


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From support at bioontology.org  Sat Feb 10 09:43:46 2018
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 10 Feb 2018 09:43:46 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Andrey Fedorov
Message-ID: <5a7f2f529c525_7c683f89f27fdef4796fb@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Sun Feb 11 14:53:29 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Sun, 11 Feb 2018 22:53:29 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Andrey Fedorov
In-Reply-To: <5a7f2f529c525_7c683f89f27fdef4796fb@ncbo-prd-app-08.stanford.edu.mail>
References: <5a7f2f529c525_7c683f89f27fdef4796fb@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <D9F38B5C-4BCF-42DF-AC3E-2C930169ACCC@stanford.edu>

Andrey,

To answer this question in a useful way (not just "yes"), we'd need to hear more details about your use case, including the exact queries you're trying to answer, and when and for how long it has seemed slow.

Many of the queries can be expected to take seconds to tens of seconds, because they have to perform a lot of computations and/or transmit a lot of data. (When I look at the class list in DICOM, it seems to take a while, but it's sending information about more than 3000 terms over my slow DSL...)

So if you can post some example queries (or indicate what web page you're trying to access), and tell us your expectations in terms of response time, we can tell whether we need to troubleshoot something, and if so, what.  Thanks!

John

On Feb 10, 2018, at 9:43 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Andrey Fedorov

Email: andrey.fedorov at gmail.com<mailto:andrey.fedorov at gmail.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FDCM%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fdicom.nema.org<http://252Fdicom.nema.org>%252Fresources%252Fontology%252FDCM%252F113206

Feedback:

Can anything be done to make BioPortal queries faster? It literally takes seconds to get a response.

_______________________________________________
bioontology-support mailing list
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


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From Monica.O'Neill at calvarymater.org.au  Sun Feb 11 16:20:58 2018
From: Monica.O'Neill at calvarymater.org.au (O'Neill, Monica)
Date: Mon, 12 Feb 2018 00:20:58 +0000
Subject: [bioontology-support] Using biomedical ontology feature in
 REDCap
In-Reply-To: <E6DDA5D8-8DCE-4FE3-8BF4-DC5375E780F6@stanford.edu>
References: <B1BF633C57B39640B1F0B99035AE8186DE7ACA8C@CMN-EXCH4.mater.health.nsw.gov.au>
 <E6DDA5D8-8DCE-4FE3-8BF4-DC5375E780F6@stanford.edu>
Message-ID: <B1BF633C57B39640B1F0B99035AE8186DE7ADE50@CMN-EXCH4.mater.health.nsw.gov.au>

Thank you John for getting back to me so quickly.

Our browser is indeed behind a firewall. My issue is that I cannot find the specific URL that my IT department has to whitelist. My IT department conducted many tests to monitor traffic and where exactly the firewall was blocking access, but couldn?t find anything. They suggested I get in contact with someone like yourself, who may know exactly what URL address redcap is trying to access when you first try to enable the bioontology feature in redcap.

Does that make more sense? Unfortunately I am not from an IT background so I can?t be more specific.

Much appreciated ? I look forward to using your ontologies!

Monica O'Neill
Data Manager |Clinical Cancer Research Network
Email: monica.o'neill at calvarymater.org.au<mailto:monica.o'neill at calvarymater.org.au>
Please note I work a 7 day fortnight

Monday, Tuesday and Wednesday
Calvary Mater Newcastle
Due to hot-desking arrangements, please contact via email

Every second Friday
John Hunter Hospital
Tel 02 4923 6397 | Fax 02 4921 4274

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Tuesday, 6 February 2018 5:30 AM
To: O'Neill, Monica
Cc: support at bioontology.org; Alberto.varas at hnehealth.nsw.gov.au
Subject: Re: [bioontology-support] Using biomedical ontology feature in REDCap

Hi Monica,

Thanks for doing most of this investigation for us! I will confirm what you have already found, but can give you one more test you can perform.

If you look at the URL for any query from the http://data.bioontology.org/documentation, for example something like http://data.bioontology.org/search?q=melanoma, you can try it in your browser. Probably it won't work, assuming you haven't entered your API key in a query before. To do so, complete the query like so:
 http://data.bioontology.org/search?q=melanoma&apikey=YOUR_API_KEY_HERE

If that still doesn't work, your browser is probably also behind some firewall that has to be opened to allow access to BioPortal. But if it *does* work, then you have confirmed your API key works, and now you have to get the firewall opened that is in front of the REDCap machine.)

This step of 'whitelisting' the BioPortal site is something that your IT department has to do?we can not help with that, sorry. Please have your IT person contact us if he or she is having some difficulty.

John



On Feb 4, 2018, at 6:51 PM, O'Neill, Monica <Monica.O'Neill at calvarymater.org.au<mailto:Monica.O'Neill at calvarymater.org.au>> wrote:

Hello,

I am an administrator of REDCap for my institution. I am very keen to employ the biomedical ontology functionality within REDCap for use in our clinical trials, but I am having some technical issues.

When I copy-paste the API token from my account with NCBO (username: monicaoneill), REDCap tells me this is not a valid token. I searched the online REDCap community and found others experienced the same error (see image below), which turned out to be because of security settings at their institution. I contacted Yelena Fridgant to ask for more details but she was unable to assist any further other than remembering she asked her IT Department to ?whitelist? the website.

I have been in contact with Alberto Varas (cc?d) from my institutions IT department, who made every attempt to figure out which URL specifically needed ?whitelisting?. Are you able to help in this regard? I would be happy to provide you with more information if you need it, just let Alberto and myself know.

<image001.png>

Many thanks in advance,
Monica O'Neill
Data Manager |Clinical Cancer Research Network
monica.o'neill at calvarymater.org.au<mailto:monica.o'neill at calvarymater.org.au>

Monday, Tuesday and Wednesday
Calvary Mater Newcastle
Due to hot-desking arrangements, please contact via email

Thursday and Friday
John Hunter Hospital
Tel 02 4923 6397 | Fax 02 4921 4274

This message is intended for the addressee and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of the Calvary Mater Newcastle or NSW Health. _______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


This message is intended for the addressee and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of the Calvary Mater Newcastle or NSW Health.
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From support at bioontology.org  Mon Feb 12 07:23:47 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 12 Feb 2018 07:23:47 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Kellie Fay
Message-ID: <5a81b1833d4e_45f73fbd96341014668f0@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Mon Feb 12 12:26:35 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 12 Feb 2018 20:26:35 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Kellie Fay
In-Reply-To: <5a81b1833d4e_45f73fbd96341014668f0@ncbo-prd-app-08.stanford.edu.mail>
References: <5a81b1833d4e_45f73fbd96341014668f0@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <D14969BD-E404-4680-8747-1658D5CCFCF9@stanford.edu>

Hello Fay,

Can you please contact me offline to discuss the details of your use case?

BioPortal processes hundreds of thousands of API requests daily, most of them successfully and without outages (according to our independent API monitors). While it is a research system, we are proud of availability numbers typically over 99.5%.

We have often found that if a specific external query engine asks a large number of complex queries, or a whole lot of somewhat complex queries in a short period of time, that can cause the system to become non-responsive. In this context, I note that the Recommender queries are quite expensive in terms of their computational load on BioPortal.

If we can work with the originators to tune the request pattern, we usually see BioPortal return to 100% up time, and they are able to get the data that they need. Alternatively, if our system just can't support the requests, we can give you advice on other ways you could implement the same capability yourself.

Thanks for your request, and I look forward to working with you to address your needs.

John


On Feb 12, 2018, at 7:23 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Kellie Fay

Email: fay.kellie at epa.gov<mailto:fay.kellie at epa.gov>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Frecommender

Feedback:

This site provides a very useful service and we have developed an ontology mapping tool which makes use of the web services feature. Unfortunately, this site is down or crashes too frequently to be very useful in this capacity. In most cases, the query is terminated because BioPortal goes offline. Is there a plan to fix this issue?

_______________________________________________
bioontology-support mailing list
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


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From andrey.fedorov at gmail.com  Mon Feb 12 13:32:11 2018
From: andrey.fedorov at gmail.com (Andrey Fedorov)
Date: Mon, 12 Feb 2018 16:32:11 -0500
Subject: [bioontology-support] [BioPortal] Feedback from Andrey Fedorov
In-Reply-To: <D9F38B5C-4BCF-42DF-AC3E-2C930169ACCC@stanford.edu>
References: <5a7f2f529c525_7c683f89f27fdef4796fb@ncbo-prd-app-08.stanford.edu.mail>
 <D9F38B5C-4BCF-42DF-AC3E-2C930169ACCC@stanford.edu>
Message-ID: <CAMw6MkcAxMwnRoTKxrMSHYq20xaT+kognvC-zjwnQ4OBx-5uqA@mail.gmail.com>

John, thank you for the reply. I will see if I can do more
comprehensive profiling.

I also cc David Clunie, who has also always been mentioning how slow
BioPortal is. Perhaps he can chime in.

On Sun, Feb 11, 2018 at 5:53 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
> Andrey,
>
> To answer this question in a useful way (not just "yes"), we'd need to hear
> more details about your use case, including the exact queries you're trying
> to answer, and when and for how long it has seemed slow.
>
> Many of the queries can be expected to take seconds to tens of seconds,
> because they have to perform a lot of computations and/or transmit a lot of
> data. (When I look at the class list in DICOM, it seems to take a while, but
> it's sending information about more than 3000 terms over my slow DSL...)
>
> So if you can post some example queries (or indicate what web page you're
> trying to access), and tell us your expectations in terms of response time,
> we can tell whether we need to troubleshoot something, and if so, what.
> Thanks!
>
> John
>
> On Feb 10, 2018, at 9:43 AM, support at bioontology.org wrote:
>
> Name: Andrey Fedorov
>
> Email: andrey.fedorov at gmail.com
>
> Location:
> http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDCM%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fdicom.nema.org%252Fresources%252Fontology%252FDCM%252F113206
>
>
> Feedback:
>
> Can anything be done to make BioPortal queries faster? It literally takes
> seconds to get a response.
>
>
> _______________________________________________
> bioontology-support mailing list
> 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
>
>

From gabriellavs at yahoo.com.br  Mon Feb 12 13:38:44 2018
From: gabriellavs at yahoo.com.br (Gabriela Santos)
Date: Mon, 12 Feb 2018 21:38:44 +0000 (UTC)
Subject: [bioontology-support] Annotator tool
References: <146490406.6525438.1518471524117.ref@mail.yahoo.com>
Message-ID: <146490406.6525438.1518471524117@mail.yahoo.com>

Hi,
I'm working with semantic annotation and I'm looking for a tool that can help me. I used BioPortal's Annotator online tool and would like to know if Annotator also writes PDF documents.
Thank you,Gabriela.
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From vendetti at stanford.edu  Mon Feb 12 15:33:35 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 12 Feb 2018 23:33:35 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Andrey Fedorov
In-Reply-To: <CAMw6MkcAxMwnRoTKxrMSHYq20xaT+kognvC-zjwnQ4OBx-5uqA@mail.gmail.com>
References: <5a7f2f529c525_7c683f89f27fdef4796fb@ncbo-prd-app-08.stanford.edu.mail>
 <D9F38B5C-4BCF-42DF-AC3E-2C930169ACCC@stanford.edu>
 <CAMw6MkcAxMwnRoTKxrMSHYq20xaT+kognvC-zjwnQ4OBx-5uqA@mail.gmail.com>
Message-ID: <37CFB969-7A9A-486F-85EB-3B67A2809D09@stanford.edu>

Hello Andrey,

It?s unclear to me from your initial post if you?re specifically referring just to the DCM ontology. I downloaded / examined this ontology and it?s worth noting that it?s an unusual one due to the almost complete lack of any hierarchical structure in the class tree. There are 3,866 classes with only one SubClassOf axiom. In other words, this ontology appears to be a flat list of classes, with only one class appearing as a subclass of another.

It?s not particularly surprising that the initial page load time for this ontology is somewhat slow. In order to construct a class tree, BioPortal has to retrieve class data for 3,865 root level classes. However, after the initial page load, the class data is cached and subsequent navigation to other classes in the tree is fast. I clicked on several other classes in the tree and the Chrome developer console shows load times less than a second.

I compared the load times of the underlying REST call for constructing the initial class tree between DCM and a much larger ontology - SNOMEDCT at 327K classes. Chrome developer console shows a load time for SNOMEDCT of 456ms compared to 7.5s for DCM. This is again due to the lack of any hierarchy / very large number of root level classes in DCM.

If on the other hand, you?re referring to programmatic access to class data, the more expedient method is via the REST API. Issuing a REST call for the class information you listed below:

http://data.bioontology.org/ontologies/DCM/classes/http%3A%2F%2Fdicom.nema.org%2Fresources%2Fontology%2FDCM%2F113206?apikey=32688b66-537e-45b7-badc-ce525bebca4d<http://data.bioontology.org/ontologies/DCM/classes/http://dicom.nema.org/resources/ontology/DCM/113206?apikey=32688b66-537e-45b7-badc-ce525bebca4d>

...completes in roughly 743ms on the first uncached attempt, then roughly 75ms on subsequent cached retrievals. You can also retrieve all classes for DCM with the classes endpoint, which implements paging:

http://data.bioontology.org/ontologies/DCM/classes

Kind regards,
Jennifer



On Feb 12, 2018, at 1:32 PM, Andrey Fedorov <andrey.fedorov at gmail.com<mailto:andrey.fedorov at gmail.com>> wrote:

John, thank you for the reply. I will see if I can do more
comprehensive profiling.

I also cc David Clunie, who has also always been mentioning how slow
BioPortal is. Perhaps he can chime in.

On Sun, Feb 11, 2018 at 5:53 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:
Andrey,

To answer this question in a useful way (not just "yes"), we'd need to hear
more details about your use case, including the exact queries you're trying
to answer, and when and for how long it has seemed slow.

Many of the queries can be expected to take seconds to tens of seconds,
because they have to perform a lot of computations and/or transmit a lot of
data. (When I look at the class list in DICOM, it seems to take a while, but
it's sending information about more than 3000 terms over my slow DSL...)

So if you can post some example queries (or indicate what web page you're
trying to access), and tell us your expectations in terms of response time,
we can tell whether we need to troubleshoot something, and if so, what.
Thanks!

John

On Feb 10, 2018, at 9:43 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Andrey Fedorov

Email: andrey.fedorov at gmail.com<mailto:andrey.fedorov at gmail.com>

Location:
http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDCM%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fdicom.nema.org%252Fresources%252Fontology%252FDCM%252F113206


Feedback:

Can anything be done to make BioPortal queries faster? It literally takes
seconds to get a response.


_______________________________________________
bioontology-support mailing list
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


_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From support at bioontology.org  Mon Feb 12 17:53:17 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 12 Feb 2018 17:53:17 -0800
Subject: [bioontology-support] [BioPortal] Feedback from elmar bucher
Message-ID: <5a82450d1407f_7e9c3fbdf38ead28696d6@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Mon Feb 12 19:18:21 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 13 Feb 2018 03:18:21 +0000
Subject: [bioontology-support] [BioPortal] Feedback from elmar bucher
In-Reply-To: <5a82450d1407f_7e9c3fbdf38ead28696d6@ncbo-prd-app-08.stanford.edu.mail>
References: <5a82450d1407f_7e9c3fbdf38ead28696d6@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <EED13012-E40D-4FAD-AEE5-FD956886AFA3@stanford.edu>

Apologies Elmar. Those PURLs should be restored now.

Kind regards,
Jennifer



On Feb 12, 2018, at 5:53 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: elmar bucher

Email: buchere at ohsu.edu<mailto:buchere at ohsu.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500%3Fp%3Dclasses%26conceptid%3Droot

Feedback:

dear BioPortal,

i am really appreciate your resource.
however, the following BioPortal purl links are broken:
+ http://purl.bioontology.org/ontology/DOID
+ http://purl.bioontology.org/ontology/OBI
+ http://purl.bioontology.org/ontology/UBERON

could they be fixed?
thank you very much, Elmar Bucher

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From support at bioontology.org  Tue Feb 13 00:52:20 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 13 Feb 2018 00:52:20 -0800
Subject: [bioontology-support] [BioPortal] Feedback from ulfschwarz
Message-ID: <5a82a744cc60e_320e3f8150a3561863984@ncbo-prd-app-08.stanford.edu.mail>

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From michel.dumontier at gmail.com  Tue Feb 13 00:59:53 2018
From: michel.dumontier at gmail.com (Michel Dumontier)
Date: Tue, 13 Feb 2018 09:59:53 +0100
Subject: [bioontology-support] ontology mappings
Message-ID: <CALcEXf7QwWDC_DBRVfRq+dQ5vdKUxdRNgy54f=UdLh+KJgXj6A@mail.gmail.com>

Hi!
  Can you point me to public documentation that describes how my ontology
(SIO) can be annotated with mappings that can be recognized by the
BioPortal system?
  thanks!
m.

-- 
Michel Dumontier
Distinguished Professor of Data Science
Maastricht University
http://dumontierlab.com
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From dclunie at dclunie.com  Tue Feb 13 05:08:28 2018
From: dclunie at dclunie.com (=?UTF-8?Q?David_Clunie?=)
Date: Tue, 13 Feb 2018 13:08:28 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Andrey Fedorov
In-Reply-To: <37CFB969-7A9A-486F-85EB-3B67A2809D09@stanford.edu>
References: <5a7f2f529c525_7c683f89f27fdef4796fb@ncbo-prd-app-08.stanford.edu.mail> 
 <D9F38B5C-4BCF-42DF-AC3E-2C930169ACCC@stanford.edu> 
 <CAMw6MkcAxMwnRoTKxrMSHYq20xaT+kognvC-zjwnQ4OBx-5uqA@mail.gmail.com> 
 <37CFB969-7A9A-486F-85EB-3B67A2809D09@stanford.edu> 
 <961733e8-70f6-641b-deb8-9ee7eebb5fce@dclunie.com>
Message-ID: <010001618f47e349-c4b0592f-f92a-4f0c-bc8c-0652dc43bf9c-000000@email.amazonses.com>

Hi Jennifer

Thanks for explaining why the DCM "ontology" loads more
slowly initially. In this day and age, loading a flat
list of just under 4,000 entries shouldn't take noticeable
time, IMHO, but I understand that your implementation may not
be optimized for this pattern, and 7 seconds is not that
bad for the first response if it is cached afterwards.

However, through the web browser, if I "jump to" a term
after having loaded the top level, say "Segmentation", it
takes quite a few seconds to actually load the class and
quite a few seconds more to "jump to" it in the list.
Again I understand that this may be lack of optimization
for the "large flat list" case (choice of data structure,
size of nodes, indexing/insertion mechanism, re-sending the
list for the user interface frame rather than moving around
in what was already sent if content unchanged, etc.).

On the other hand, if I search for a term across all ontologies,
e.g., "Segmentation" it is pretty fast and finds the DCM class(es).
I assume this is because it a different index is used.

One of these days we may make the DCM ontology into
a proper ontology, but mostly it is used as a grab bag
of independent concepts that are used when we can't find
concepts in a "real" ontology like SNOMED, LOINC, FMA or
NCIt, so it doesn't have a meaningful class "hierarchy" (yet),
and building one hasn't been a priority for us (in DICOM). I
have considered various mechanical ways to do this (e.g., using
the context group (value set) labels as pseudo-classes to
produce at least a two level hierarchy), but I haven't got
very far with that yet.

I haven't used the REST API myself.

The only other data point for speed is the RSNA's RadLex
term browser (http://www.radlex.org/) which is sometimes glacial,
and they attribute that to poor performance of Bioportal,
but I have no direct evidence of that myself, and the alleged
slowness does not manifest when using the Bioportal web
browser directly.

E.g., search for "spiculation" from the top level in the RadLex
ontology in Bioportal and compare that with doing the same at
www.radlex.org ... I just tried it again and the latter just
says "Loading" forever, which is not uncommon.

David

On 2/12/18 6:33 PM, Jennifer Leigh Vendetti wrote:
> Hello Andrey,
> 
> It?s unclear to me from your initial post if you?re specifically referring just to the DCM ontology. I downloaded / examined this ontology and it?s worth noting that it?s an unusual one due to the almost complete lack of any hierarchical structure in the class tree. There are 3,866 classes with only one SubClassOf axiom. In other words, this ontology appears to be a flat list of classes, with only one class appearing as a subclass of another.?
> 
> It?s not particularly surprising that the initial page load time for this ontology is somewhat slow. In order to construct a class tree, BioPortal has to retrieve class data for 3,865 root level classes. However, after the initial page load, the class data is cached and subsequent navigation to other classes in the tree is fast. I clicked on several other classes in the tree and the Chrome developer console shows load times less than a second.
> 
> I compared the load times of the underlying REST call for constructing the initial class tree between DCM and a much larger ontology - SNOMEDCT at 327K classes. Chrome developer console shows a load time for SNOMEDCT of 456ms compared to 7.5s for DCM. This is again due to the lack of any hierarchy / very large number of root level classes in DCM.
> 
> If on the other hand, you?re referring to programmatic access to class data, the more expedient method is via the REST API. Issuing a REST call for the class information you listed below:
> 
> http://data.bioontology.org/ontologies/DCM/classes/http%3A%2F%2Fdicom.nema.org%2Fresources%2Fontology%2FDCM%2F113206?apikey=32688b66-537e-45b7-badc-ce525bebca4d <http://data.bioontology.org/ontologies/DCM/classes/http://dicom.nema.org/resources/ontology/DCM/113206?apikey=32688b66-537e-45b7-badc-ce525bebca4d>
> 
> ...completes in roughly 743ms on the first uncached attempt, then roughly 75ms on subsequent cached retrievals. You can also retrieve all classes for DCM with the classes endpoint, which implements paging:
> 
> http://data.bioontology.org/ontologies/DCM/classes
> 
> Kind regards,
> Jennifer
> 
> 
> 
>> On Feb 12, 2018, at 1:32 PM, Andrey Fedorov <andrey.fedorov at gmail.com <mailto:andrey.fedorov at gmail.com>> wrote:
>>
>> John, thank you for the reply. I will see if I can do more
>> comprehensive profiling.
>>
>> I also cc David Clunie, who has also always been mentioning how slow
>> BioPortal is. Perhaps he can chime in.
>>
>> On Sun, Feb 11, 2018 at 5:53 PM, John Graybeal <jgraybeal at stanford.edu <mailto:jgraybeal at stanford.edu>> wrote:
>>> Andrey,
>>>
>>> To answer this question in a useful way (not just "yes"), we'd need to hear
>>> more details about your use case, including the exact queries you're trying
>>> to answer, and when and for how long it has seemed slow.
>>>
>>> Many of the queries can be expected to take seconds to tens of seconds,
>>> because they have to perform a lot of computations and/or transmit a lot of
>>> data. (When I look at the class list in DICOM, it seems to take a while, but
>>> it's sending information about more than 3000 terms over my slow DSL...)
>>>
>>> So if you can post some example queries (or indicate what web page you're
>>> trying to access), and tell us your expectations in terms of response time,
>>> we can tell whether we need to troubleshoot something, and if so, what.
>>> Thanks!
>>>
>>> John
>>>
>>> On Feb 10, 2018, at 9:43 AM, support at bioontology.org <mailto:support at bioontology.org> wrote:
>>>
>>> Name: Andrey Fedorov
>>>
>>> Email: andrey.fedorov at gmail.com <mailto:andrey.fedorov at gmail.com>
>>>
>>> Location:
>>> http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDCM%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fdicom.nema.org%252Fresources%252Fontology%252FDCM%252F113206
>>>
>>>
>>> Feedback:
>>>
>>> Can anything be done to make BioPortal queries faster? It literally takes
>>> seconds to get a response.
>>>
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> 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
>>>
>>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 


From buchere at ohsu.edu  Mon Feb 12 23:02:17 2018
From: buchere at ohsu.edu (Elmar Bucher)
Date: Tue, 13 Feb 2018 07:02:17 +0000
Subject: [bioontology-support] [BioPortal] Feedback from elmar bucher
In-Reply-To: <EED13012-E40D-4FAD-AEE5-FD956886AFA3@stanford.edu>
References: <5a82450d1407f_7e9c3fbdf38ead28696d6@ncbo-prd-app-08.stanford.edu.mail>,
 <EED13012-E40D-4FAD-AEE5-FD956886AFA3@stanford.edu>
Message-ID: <B1158654EBBA614D8F0B460047CB9444CC7A1D63@EXMB09.ohsu.edu>

Dear Jennifer,

Now it works perfectly.
Thank you for fixing the problem that fast!

Best, Elmar


________________________________
From: Jennifer Leigh Vendetti [vendetti at stanford.edu]
Sent: Monday, February 12, 2018 7:18 PM
To: NCBO User Support
Cc: Elmar Bucher
Subject: Re: [bioontology-support] [BioPortal] Feedback from elmar bucher

Apologies Elmar. Those PURLs should be restored now.

Kind regards,
Jennifer



On Feb 12, 2018, at 5:53 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: elmar bucher

Email: buchere at ohsu.edu<mailto:buchere at ohsu.edu>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500%3Fp%3Dclasses%26conceptid%3Droot

Feedback:

dear BioPortal,

i am really appreciate your resource.
however, the following BioPortal purl links are broken:
+ http://purl.bioontology.org/ontology/DOID
+ http://purl.bioontology.org/ontology/OBI
+ http://purl.bioontology.org/ontology/UBERON

could they be fixed?
thank you very much, Elmar Bucher

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From vendetti at stanford.edu  Tue Feb 13 09:19:00 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 13 Feb 2018 17:19:00 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ulfschwarz
In-Reply-To: <5a82a744cc60e_320e3f8150a3561863984@ncbo-prd-app-08.stanford.edu.mail>
References: <5a82a744cc60e_320e3f8150a3561863984@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <D038F4F3-80B1-4116-AF9D-E496BD429A46@stanford.edu>

Hello Ulf,


On Feb 13, 2018, at 12:52 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FTES%2Fsubmissions%2Fnew

Feedback:

Hi,

I would like to upload an ontology. However I cannot fill in the required administrators field. There seems to be a preselection for which administrators I try to fill in are not found.

You can add administrators from the edit ontology page. For your ontology, the URL would be:

http://bioportal.bioontology.org/ontologies/TES/edit

I noticed that the administrators field is blank. I added your account name so that you have privileges to edit the ontology:


[cid:965AE2F3-A176-4697-982B-7763F224A447 at stanford.edu]

I?m not sure how it got into a state initially where there were no administrators listed. At any rate, you should be able to add other accounts now. What are the account names for the administrators you?re trying to add that aren?t found?

Kind regards,
Jennifer






What can I do?
Thanks for your help in advance.
Ulf

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From jonquet.lirmm at gmail.com  Tue Feb 13 11:00:06 2018
From: jonquet.lirmm at gmail.com (Clement Jonquet)
Date: Tue, 13 Feb 2018 11:00:06 -0800
Subject: [bioontology-support] ontology mappings
In-Reply-To: <CALcEXf7QwWDC_DBRVfRq+dQ5vdKUxdRNgy54f=UdLh+KJgXj6A@mail.gmail.com>
References: <CALcEXf7QwWDC_DBRVfRq+dQ5vdKUxdRNgy54f=UdLh+KJgXj6A@mail.gmail.com>
Message-ID: <ECEEBB3F-FFA4-4203-B35C-B85F197ACC90@gmail.com>

Hi Michel, 

NCBO and us do not have a lot of documentation about mappings. A small technical explanation is here: 
https://github.com/agroportal/documentation/wiki/Mappings <https://github.com/agroportal/documentation/wiki/Mappings>

On the "recognized?? point: 
BioPortal does not automatically extract/recognize mappings that would be in described inside the ontologies. Except if the class explicitly uses the same URI or has a CUI property described properly (as documented in the link). 

If an ontology file contains "mappings" represented with SKOS matching properties or owl:sameAs or any other specific property (e.g., OBO-XREF), those mappings will not be extracted by AgroPortal. 

It sounds weird, but there are multiple historical reasons for this including the fact that at the beginning of the NCBO project, one would not always expect the mapped ontologies to be ? already ? in BioPortal. This situation is not always true, but now there is a strong chance  the mapped ontologies are already on BioPortal. 
Within AgroPortal we removed that constraint a couple of years ago (external mappings) and will start soon working (again) on mappings with Elcio (CC) who just join us at LIRMM.

As of now, I would recommend to use SKOS properties inside you SIO file to represent mappings. Those would be considered by the new parser for sure.

Bye
Clement


> Le 13 f?vr. 2018 ? 00:59, Michel Dumontier <michel.dumontier at gmail.com> a ?crit :
> 
> Hi!
>   Can you point me to public documentation that describes how my ontology (SIO) can be annotated with mappings that can be recognized by the BioPortal system?
>   thanks!
> m.
> 
> -- 
> Michel Dumontier
> Distinguished Professor of Data Science
> Maastricht University
> http://dumontierlab.com <http://dumontierlab.com/>_______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From jgraybeal at stanford.edu  Tue Feb 13 14:11:03 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 13 Feb 2018 22:11:03 +0000
Subject: [bioontology-support] ontology mappings
In-Reply-To: <ECEEBB3F-FFA4-4203-B35C-B85F197ACC90@gmail.com>
References: <CALcEXf7QwWDC_DBRVfRq+dQ5vdKUxdRNgy54f=UdLh+KJgXj6A@mail.gmail.com>
 <ECEEBB3F-FFA4-4203-B35C-B85F197ACC90@gmail.com>
Message-ID: <8CB38F79-36B6-4F48-9EBA-AEB31DB098A6@stanford.edu>

On the perhaps-broader subject of how to put mappings for an ontology into BioPortal, the answer is 'via the API'. (If you have just a few, you can do so via the UI at https://bioportal.bioontology.org/help#Viewing_and_editing_mappings .)

Example code for creating API mappings is at
  https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/CreateMapping.java

A past thread on how to do this is at
  http://ncbo-support.2288202.n4.nabble.com/Uploading-a-Mapping-td4653220.html#a4653222
It mentions the general info on running the above sample code:
  https://github.com/ncbo/ncbo_rest_sample_code/tree/master/java

Links that might be useful:
  https://www.bioontology.org/wiki/index.php/BioPortal_Mappings
  http://data.bioontology.org/documentation#Mapping    -- the actual API documentation

Sorry we do not have more better documentation!

John


On Feb 13, 2018, at 11:00 AM, Clement Jonquet <jonquet.lirmm at gmail.com<mailto:jonquet.lirmm at gmail.com>> wrote:

Hi Michel,

NCBO and us do not have a lot of documentation about mappings. A small technical explanation is here:
https://github.com/agroportal/documentation/wiki/Mappings

On the "recognized?? point:
BioPortal does not automatically extract/recognize mappings that would be in described inside the ontologies. Except if the class explicitly uses the same URI or has a CUI property described properly (as documented in the link).

If an ontology file contains "mappings" represented with SKOS matching properties or owl:sameAs or any other specific property (e.g., OBO-XREF), those mappings will not be extracted by AgroPortal.

It sounds weird, but there are multiple historical reasons for this including the fact that at the beginning of the NCBO project, one would not always expect the mapped ontologies to be ? already ? in BioPortal. This situation is not always true, but now there is a strong chance  the mapped ontologies are already on BioPortal.
Within AgroPortal we removed that constraint a couple of years ago (external mappings) and will start soon working (again) on mappings with Elcio (CC) who just join us at LIRMM.

As of now, I would recommend to use SKOS properties inside you SIO file to represent mappings. Those would be considered by the new parser for sure.

Bye
Clement


Le 13 f?vr. 2018 ? 00:59, Michel Dumontier <michel.dumontier at gmail.com<mailto:michel.dumontier at gmail.com>> a ?crit :

Hi!
  Can you point me to public documentation that describes how my ontology (SIO) can be annotated with mappings that can be recognized by the BioPortal system?
  thanks!
m.

--
Michel Dumontier
Distinguished Professor of Data Science
Maastricht University
http://dumontierlab.com<http://dumontierlab.com/>
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
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


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From Simon.Cox at csiro.au  Tue Feb 13 14:24:14 2018
From: Simon.Cox at csiro.au (Simon.Cox at csiro.au)
Date: Tue, 13 Feb 2018 22:24:14 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <32C6DC30-005B-46EF-8A30-A6FF61031C64@stanford.edu>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
 <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
 <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
 <6d6184f83a494502a3cbc8c4e1202c37@exch1-mel.nexus.csiro.au>
 <C0BD3869-F3A9-4226-946F-0AF4D1B205B3@stanford.edu>
 <a0886ec84be74b6faa7d5595bbce158d@exch1-mel.nexus.csiro.au>
 <32C6DC30-005B-46EF-8A30-A6FF61031C64@stanford.edu>
Message-ID: <e8501906b8d1436c85cb70d492742658@exch1-mel.nexus.csiro.au>

The RDF representation of the OWL-Time ontology has been updated, removing the declaration of xsd:DateTimeStamp.
See https://www.w3.org/2006/time

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Monday, 12 February, 2018 08:41
To: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au>
Cc: Samson Tu <swt at stanford.edu>; bioontology-support at lists.stanford.edu
Subject: Re: [bioontology-support] labels for Time ontology

perhaps we should do a quick test with that change in BioPortal, to see if it behaves better.

john

On Feb 11, 2018, at 1:09 PM, Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au> wrote:

> The OWL 2 spec makes a distinction between datatype and class:

Yes. And that's also partly why owl:Class != rdfs:Class.
But I don't think that's the issue here.
It's about how a datatype is formally defined.

RDFS says that all datatypes are subclasses of rdfs:Literal which makes complete sense.
I think there may be a question whether that should be captured using the rdfs:subClassOf axiom.
Else this is where Bioportal might be too fierce.

Anyway, the inclusion of a definition of xsd:dateTimeStamp in this ontology is not necessary since it is defined elsewhere (in the xsd spec) so I will see if we can get it removed from the RDF sources.

Simon
________________________________
From: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>
Sent: Sunday, 11 February 2018 4:43:18 PM
To: Cox, Simon (L&W, Clayton)
Cc: Samson Tu; John Graybeal; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

The OWL 2 spec makes a distinction between datatype and class:

"Datatypes are entities that refer to sets of data values. Thus, datatypes are analogous to classes, the main difference being that the former contain data values such as strings and numbers, rather than individuals.? [1]

Maybe the issue is whether the Time ontology is meant to be an RDF schema or an OWL ontology. These are two different specifications.

The OWL API loads the ontology didn?t throw an error. It?s the Bioportal hierarchy display code that had problem. I agree that the Bioportal hierarchy display code should be more forgiving. Maybe that should be an issue  tracker item.

With best regards,
Samson

[1] https://www.w3.org/TR/owl2-syntax/#Datatypes


On Feb 10, 2018, at 10:10 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

I don?t think you are correct.
The RDFS Spec is quite explicit on this [1]: ?Each instance of rdfs:Datatype is a subclass of rdfs:Literal.?

The offending lines in the OWL-Time rdf are

xsd:dateTimeStamp
  rdf:type rdfs:Datatype ;              #i.e xsd:dateTimeStamp is an instance of rdfs:Datatype
  rdfs:label "dateTimeStamp" ;
  rdfs:subClassOf rdfs:Literal ;     #... and is a subclass of rdfs:Literal
.

I guess the explanation in the RDFS spec means that the sub-class axiom is strictly not needed, since it is an entailment of typing axiom anyway, but it should not cause a conforming processor to throw an error.

[1] https://www.w3.org/TR/rdf-schema/#ch_datatype

From: Samson Tu [mailto:swt at stanford.edu]
Sent: Saturday, 10 February, 2018 05:59
To: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Cc: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>; John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

Hi,

I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,
Samson


On Feb 8, 2018, at 9:49 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,



On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
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

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From ulf.schwarz at ifomis.uni-saarland.de  Wed Feb 14 04:13:13 2018
From: ulf.schwarz at ifomis.uni-saarland.de (Ulf Schwarz)
Date: Wed, 14 Feb 2018 13:13:13 +0100
Subject: [bioontology-support] [BioPortal] Feedback from ulfschwarz
In-Reply-To: <D038F4F3-80B1-4116-AF9D-E496BD429A46@stanford.edu>
References: <5a82a744cc60e_320e3f8150a3561863984@ncbo-prd-app-08.stanford.edu.mail>
 <D038F4F3-80B1-4116-AF9D-E496BD429A46@stanford.edu>
Message-ID: <CABfB3ii7SgOaS8+eAZDOX94takJ7AJ0_7BvoLCz-PO7fs_1YBQ@mail.gmail.com>

Thanks a lot for your help.
ulfschwarz could now be added to the administrator field.
I tried to upload the ontology vdot (acronym vdot_core) from a URL and an
error message appeared saying that you are notified about the problem.
I am not sure what happens now.

Best,

Ulf

2018-02-13 18:19 GMT+01:00 Jennifer Leigh Vendetti <vendetti at stanford.edu>:

> Hello Ulf,
>
>
> On Feb 13, 2018, at 12:52 AM, support at bioontology.org wrote:
>
> Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%
> 2FTES%2Fsubmissions%2Fnew
>
>
> *Feedback:*
>
> Hi,
>
> I would like to upload an ontology. However I cannot fill in the required
> administrators field. There seems to be a preselection for which
> administrators I try to fill in are not found.
>
>
> You can add administrators from the edit ontology page. For your ontology,
> the URL would be:
>
> http://bioportal.bioontology.org/ontologies/TES/edit
>
> I noticed that the administrators field is blank. I added your account
> name so that you have privileges to edit the ontology:
>
>
>
> I?m not sure how it got into a state initially where there were no
> administrators listed. At any rate, you should be able to add other
> accounts now. What are the account names for the administrators you?re
> trying to add that aren?t found?
>
> Kind regards,
> Jennifer
>
>
>
>
>
> What can I do?
> Thanks for your help in advance.
> Ulf
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
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From Sina.Madani at vumc.org  Wed Feb 14 11:33:47 2018
From: Sina.Madani at vumc.org (Madani, Sina)
Date: Wed, 14 Feb 2018 19:33:47 +0000
Subject: [bioontology-support] search by id in a subtree
In-Reply-To: <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu>
References: <103B3C18EAB4F444A941714214A04B8159418D83@ITS-HCWNEM105.ds.vanderbilt.edu>
 <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu>
Message-ID: <AA85DAE0-92F1-4EF7-8E33-3F726AE9C0F6@vumc.org>

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'"]



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From vendetti at stanford.edu  Wed Feb 14 15:05:21 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 14 Feb 2018 23:05:21 +0000
Subject: [bioontology-support] labels for Time ontology
In-Reply-To: <e8501906b8d1436c85cb70d492742658@exch1-mel.nexus.csiro.au>
References: <07C2C6B4-94E6-47B0-8032-E59052A84DEE@stanford.edu>
 <a2021b1d00c6480f945ef0e75f9384ff@exch1-mel.nexus.csiro.au>
 <CCF91ADC-255B-4928-B8FE-CA51EE989825@stanford.edu>
 <6d6184f83a494502a3cbc8c4e1202c37@exch1-mel.nexus.csiro.au>
 <C0BD3869-F3A9-4226-946F-0AF4D1B205B3@stanford.edu>
 <a0886ec84be74b6faa7d5595bbce158d@exch1-mel.nexus.csiro.au>
 <32C6DC30-005B-46EF-8A30-A6FF61031C64@stanford.edu>
 <e8501906b8d1436c85cb70d492742658@exch1-mel.nexus.csiro.au>
Message-ID: <02620BD2-BD90-444A-8216-476D85C15524@stanford.edu>

Hi Simon,

Thanks! BioPortal picked up the new version overnight. Initially it failed to parse in our production environment due to a subtlety that I didn?t account for the other day when I was doing some testing in our staging environment. It looks like when the ontology was originally submitted to us, there were some property overrides specified in the add/edit submission form:

Preferred Name Property: local:OWL-Time
Synonym Property: local:Time ontology in OWL

BioPortal doesn?t recognize the ?local:? syntax for property overrides - instead, a full URL is required. Apologies that this isn?t evident from the placeholder text on the form. We have an open issue in our tracker to add better validation for these fields.

I looked at the ontology content and it seems that it already adheres to standard practices for specifying preferred names (rdfs:label). BioPortal checks this property for preferred names, so the override doesn?t seem necessary. Also, it wasn?t clear to me what the override was meant to be for the synonym property. At any rate, I removed these overrides and reprocessed the ontology, which is now fully available in BioPortal, and via the REST API (http://data.bioontology.org/ontologies/TIME). The appearance of the class tree mimics what I see when I load the OWL file in the Protege ontology editing application. Let me know if you see anything awry.

Kind regards,
Jennifer



On Feb 13, 2018, at 2:24 PM, Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au> wrote:

The RDF representation of the OWL-Time ontology has been updated, removing the declaration of xsd:DateTimeStamp.
See https://www.w3.org/2006/time

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Monday, 12 February, 2018 08:41
To: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Cc: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

perhaps we should do a quick test with that change in BioPortal, to see if it behaves better.

john

On Feb 11, 2018, at 1:09 PM, Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au> wrote:

> The OWL 2 spec makes a distinction between datatype and class:

Yes. And that's also partly why owl:Class != rdfs:Class.
But I don't think that's the issue here.
It's about how a datatype is formally defined.

RDFS says that all datatypes are subclasses of rdfs:Literal which makes complete sense.
I think there may be a question whether that should be captured using the rdfs:subClassOf axiom.
Else this is where Bioportal might be too fierce.

Anyway, the inclusion of a definition of xsd:dateTimeStamp in this ontology is not necessary since it is defined elsewhere (in the xsd spec) so I will see if we can get it removed from the RDF sources.

Simon
________________________________
From: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>
Sent: Sunday, 11 February 2018 4:43:18 PM
To: Cox, Simon (L&W, Clayton)
Cc: Samson Tu; John Graybeal; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

The OWL 2 spec makes a distinction between datatype and class:

"Datatypes are entities that refer to sets of data values. Thus, datatypes are analogous to classes, the main difference being that the former contain data values such as strings and numbers, rather than individuals.? [1]

Maybe the issue is whether the Time ontology is meant to be an RDF schema or an OWL ontology. These are two different specifications.

The OWL API loads the ontology didn?t throw an error. It?s the Bioportal hierarchy display code that had problem. I agree that the Bioportal hierarchy display code should be more forgiving. Maybe that should be an issue  tracker item.

With best regards,
Samson

[1] https://www.w3.org/TR/owl2-syntax/#Datatypes


On Feb 10, 2018, at 10:10 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

I don?t think you are correct.
The RDFS Spec is quite explicit on this [1]: ?Each instance of rdfs:Datatype is a subclass of rdfs:Literal.?

The offending lines in the OWL-Time rdf are

xsd:dateTimeStamp
  rdf:type rdfs:Datatype ;              #i.e xsd:dateTimeStamp is an instance of rdfs:Datatype
  rdfs:label "dateTimeStamp" ;
  rdfs:subClassOf rdfs:Literal ;     #... and is a subclass of rdfs:Literal
.

I guess the explanation in the RDFS spec means that the sub-class axiom is strictly not needed, since it is an entailment of typing axiom anyway, but it should not cause a conforming processor to throw an error.

[1] https://www.w3.org/TR/rdf-schema/#ch_datatype

From: Samson Tu [mailto:swt at stanford.edu]
Sent: Saturday, 10 February, 2018 05:59
To: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Cc: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>; John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

Hi,

I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,
Samson


On Feb 8, 2018, at 9:49 PM, simon.cox at csiro.au<mailto:simon.cox at csiro.au> wrote:

John ? there are rdfs:label annotations on every class and property ? https://www.w3.org/2006/time ... So I?m not sure what the issue is? ? Simon

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Subject: labels for Time ontology

Simon,

(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)

John


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Simon,



On Feb 8, 2018, at 4:18 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don?t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn?t immediately obvious to me what the problem is. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/66

? so that we can spend some time debugging.

Kind regards,
Jennifer

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
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

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From jgraybeal at stanford.edu  Wed Feb 14 15:11:02 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 14 Feb 2018 23:11:02 +0000
Subject: [bioontology-support] search by id in a subtree
In-Reply-To: <AA85DAE0-92F1-4EF7-8E33-3F726AE9C0F6@vumc.org>
References: <103B3C18EAB4F444A941714214A04B8159418D83@ITS-HCWNEM105.ds.vanderbilt.edu>
 <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu>,
 <AA85DAE0-92F1-4EF7-8E33-3F726AE9C0F6@vumc.org>
Message-ID: <MWHPR0201MB3516333AA13FB37534A9CFD5DAF50@MWHPR0201MB3516.namprd02.prod.outlook.com>

I'm going to try to get this right, but I may need help from the professionals.


To my knowledge, BioPortal does not parse mappings that are contained within ontologies, so a linkage would not appear in that way. However, BioPortal does watch for the same IRI appearing in multiple ontologies, and will indicate the relationship between those two entities. (I don't *think* it uses the sameAs or exactMatch relations at that point either.)


It is possible to map any two classes that are within BioPortal ontologies. The most documentation we have on this was captured in a thread just yesterday; read to the last post of http://ncbo-support.2288202.n4.nabble.com/bioontology-support-ontology-mappings-td4656117.html for this information.


There is an issue in the AgroPortal github issues about adding the ability to the AgroPortal to parse mappings contained in ontologies (https://github.com/sifrproject/ncbo_annotator/issues/18). We stay in close communication with AgroPortal, and if that goes forward, we would be hoping to use the same approach. Unfortunately their handling of mappings is more general than BioPortal's right now, so it might not be an easy port. (Read: Don't hold your breath for BioPortal to have it soon.)


John


________________________________
From: bioontology-support <bioontology-support-bounces at lists.stanford.edu> on behalf of Madani, Sina <Sina.Madani at vumc.org>
Sent: Wednesday, February 14, 2018 11:33 AM
To: Michael Dorf; support at bioontology.org
Subject: Re: [bioontology-support] search by id in a subtree


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'"]




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From vendetti at stanford.edu  Wed Feb 14 15:16:24 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 14 Feb 2018 23:16:24 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ulfschwarz
In-Reply-To: <CABfB3ii7SgOaS8+eAZDOX94takJ7AJ0_7BvoLCz-PO7fs_1YBQ@mail.gmail.com>
References: <5a82a744cc60e_320e3f8150a3561863984@ncbo-prd-app-08.stanford.edu.mail>
 <D038F4F3-80B1-4116-AF9D-E496BD429A46@stanford.edu>
 <CABfB3ii7SgOaS8+eAZDOX94takJ7AJ0_7BvoLCz-PO7fs_1YBQ@mail.gmail.com>
Message-ID: <B130BA6B-BE2B-49CB-8365-5CF8B6A73B1E@stanford.edu>

Hi Ulf,

> On Feb 14, 2018, at 4:13 AM, Ulf Schwarz <ulf.schwarz at ifomis.uni-saarland.de> wrote:
> 
> Thanks a lot for your help.
> ulfschwarz could now be added to the administrator field.
> I tried to upload the ontology vdot (acronym vdot_core) from a URL and an error message appeared saying that you are notified about the problem.


I queried the system for any submissions for your ontology and didn?t find anything. I?m not sure what caused the internal server error you saw. Are you willing to give it another try? If it fails a second time, could you send me the URL you?re trying to enter? I can try to create a new submission here and see if the problem is reproducible.

Kind regards,
Jennifer


From mohamed.anani at live.com  Wed Feb 14 17:44:46 2018
From: mohamed.anani at live.com (Mohamed Anani)
Date: Thu, 15 Feb 2018 01:44:46 +0000
Subject: [bioontology-support] NCBO virtual appliance
Message-ID: <79D1CAF9-DB0F-42BE-B04B-36D22038FE2C@live.com>

Hello,
I would like to have access to the NCBO Virtual Appliance. I need to use the NCBO recommender for a research project at my school. Here is my account: mmanani1s

Thank you,
Mohammad Anani



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From c.chung at med.miami.edu  Thu Feb 15 07:24:46 2018
From: c.chung at med.miami.edu (Chung, Caty Elizabeth)
Date: Thu, 15 Feb 2018 15:24:46 +0000
Subject: [bioontology-support] BioPortal DTO license CC BY-SA 4.0
Message-ID: <SN2PR0701MB7654C72D249ABE12ED6D5F8B9F40@SN2PR0701MB765.namprd07.prod.outlook.com>

Hello,

The ontology file (http://drugtargetontology.org/dto/dto_complete.owl) has the license CC BY-SA 4.0 (<dc:license rdf:resource="https://creativecommons.org/licenses/by-sa/4.0/"/>)

On BioPortal (https://bioportal.bioontology.org/ontologies/DTO) I do not see the field (LICENSE INFORMATION) and value for the license.

Can you let me know why?

Caty


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From ulf.schwarz at ifomis.uni-saarland.de  Thu Feb 15 00:11:39 2018
From: ulf.schwarz at ifomis.uni-saarland.de (Ulf Schwarz)
Date: Thu, 15 Feb 2018 09:11:39 +0100
Subject: [bioontology-support] [BioPortal] Feedback from ulfschwarz
In-Reply-To: <B130BA6B-BE2B-49CB-8365-5CF8B6A73B1E@stanford.edu>
References: <5a82a744cc60e_320e3f8150a3561863984@ncbo-prd-app-08.stanford.edu.mail>
 <D038F4F3-80B1-4116-AF9D-E496BD429A46@stanford.edu>
 <CABfB3ii7SgOaS8+eAZDOX94takJ7AJ0_7BvoLCz-PO7fs_1YBQ@mail.gmail.com>
 <B130BA6B-BE2B-49CB-8365-5CF8B6A73B1E@stanford.edu>
Message-ID: <CABfB3iiEsEnaR9jzJ8EobfJ47g_=OgBL1yoQ=MJdmw_+=z2W=g@mail.gmail.com>

Hi Jennifer,




>
> I queried the system for any submissions for your ontology and didn?t find
> anything. I?m not sure what caused the internal server error you saw. Are
> you willing to give it another try? If it fails a second time, could you
> send me the URL you?re trying to enter? I can try to create a new
> submission here and see if the problem is reproducible.
>
> I tried it again it it failed with the same error message.
The URL I try to enter is:
www.ifomis.org/vdot/vdot_core.owl

Is it possible to delete previous ontology registration attempts? The
orginal name I intended to use is now blocked by a previous regsitration
attempt which was not successful but still appears under the submitted
ontologies field in settings.

Best regards,

Ulf
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From vendetti at stanford.edu  Thu Feb 15 11:15:13 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 15 Feb 2018 19:15:13 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ulfschwarz
In-Reply-To: <CABfB3iiEsEnaR9jzJ8EobfJ47g_=OgBL1yoQ=MJdmw_+=z2W=g@mail.gmail.com>
References: <5a82a744cc60e_320e3f8150a3561863984@ncbo-prd-app-08.stanford.edu.mail>
 <D038F4F3-80B1-4116-AF9D-E496BD429A46@stanford.edu>
 <CABfB3ii7SgOaS8+eAZDOX94takJ7AJ0_7BvoLCz-PO7fs_1YBQ@mail.gmail.com>
 <B130BA6B-BE2B-49CB-8365-5CF8B6A73B1E@stanford.edu>
 <CABfB3iiEsEnaR9jzJ8EobfJ47g_=OgBL1yoQ=MJdmw_+=z2W=g@mail.gmail.com>
Message-ID: <913C55D6-2C77-4D48-8C65-578F983A7DE1@stanford.edu>

Hi Ulf,

On Feb 15, 2018, at 12:11 AM, Ulf Schwarz <ulf.schwarz at ifomis.uni-saarland.de<mailto:ulf.schwarz at ifomis.uni-saarland.de>> wrote:



I queried the system for any submissions for your ontology and didn?t find anything. I?m not sure what caused the internal server error you saw. Are you willing to give it another try? If it fails a second time, could you send me the URL you?re trying to enter? I can try to create a new submission here and see if the problem is reproducible.

I tried it again it it failed with the same error message.
The URL I try to enter is:
www.ifomis.org/vdot/vdot_core.owl<http://www.ifomis.org/vdot/vdot_core.owl>

Is it possible to delete previous ontology registration attempts? The orginal name I intended to use is now blocked by a previous regsitration attempt which was not successful but still appears under the submitted ontologies field in settings.


Sorry - I?m not following. What ontology entry do you want us to delete? VDOT_CORE? TES?

Also, if you indicate which ontology you?d like to create a submission for with the URL you listed above, I can try to reproduce the error here.

Kind regards,
Jennifer
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From vendetti at stanford.edu  Thu Feb 15 11:51:01 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 15 Feb 2018 19:51:01 +0000
Subject: [bioontology-support] BioPortal DTO license CC BY-SA 4.0
In-Reply-To: <SN2PR0701MB7654C72D249ABE12ED6D5F8B9F40@SN2PR0701MB765.namprd07.prod.outlook.com>
References: <SN2PR0701MB7654C72D249ABE12ED6D5F8B9F40@SN2PR0701MB765.namprd07.prod.outlook.com>
Message-ID: <B3F2815E-FEB0-4EA8-829D-CEC6F547DC8F@stanford.edu>

Hello Caty,


On Feb 15, 2018, at 7:24 AM, Chung, Caty Elizabeth <c.chung at med.miami.edu<mailto:c.chung at med.miami.edu>> wrote:


Hello,

The ontology file (http://drugtargetontology.org/dto/dto_complete.owl) has the license CC BY-SA 4.0 (<dc:license rdf:resource="https://creativecommons.org/licenses/by-sa/4.0/"/>)

On BioPortal (https://bioportal.bioontology.org/ontologies/DTO) I do not see the field (LICENSE INFORMATION) and value for the license.

Can you let me know why?


Allowing end users to enter ontology license information via the BioPortal user interface is functionality we haven?t implemented. I?m not aware of a particular reason for this, other than we?re a small team and providing this functionality hasn?t hit the top of our priority list. For ontologies that do display license information (e.g., ontologies from the UMLS with download restrictions like SNOMEDCT, CPT, etc.) that license text has been manually added to a configuration file that's read by the user interface when the ontology summary pages are displayed.

If it?s critical to display license information for a particular ontology, there is the option of having us add it manually to our configuration file.

Kind regards,
Jennifer

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From c.chung at med.miami.edu  Thu Feb 15 12:28:51 2018
From: c.chung at med.miami.edu (Chung, Caty Elizabeth)
Date: Thu, 15 Feb 2018 20:28:51 +0000
Subject: [bioontology-support] BioPortal DTO license CC BY-SA 4.0
In-Reply-To: <B3F2815E-FEB0-4EA8-829D-CEC6F547DC8F@stanford.edu>
References: <SN2PR0701MB7654C72D249ABE12ED6D5F8B9F40@SN2PR0701MB765.namprd07.prod.outlook.com>,
 <B3F2815E-FEB0-4EA8-829D-CEC6F547DC8F@stanford.edu>
Message-ID: <SN2PR0701MB7657F3D6BFE469EF50C7A4BB9F40@SN2PR0701MB765.namprd07.prod.outlook.com>

Thank you Jennifer, it would be great if you could add the license for us: https://github.com/DrugTargetOntology/DTO/blob/master/LICENSE.md
Caty


________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Thursday, February 15, 2018 2:51:01 PM
To: Chung, Caty Elizabeth
Cc: support at bioontology.org
Subject: Re: [bioontology-support] BioPortal DTO license CC BY-SA 4.0

Hello Caty,


On Feb 15, 2018, at 7:24 AM, Chung, Caty Elizabeth <c.chung at med.miami.edu<mailto:c.chung at med.miami.edu>> wrote:


Hello,

The ontology file (http://drugtargetontology.org/dto/dto_complete.owl<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdrugtargetontology.org%2Fdto%2Fdto_complete.owl&data=02%7C01%7Cc.chung%40med.miami.edu%7C5a069016dd2342b2945408d574ad7d13%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C1%7C636543210867782524&sdata=8aHKkRT2CTOsB2h09EuyJV9Z026zzN6WQ%2B3F05vA%2BeY%3D&reserved=0>) has the license CC BY-SA 4.0 (<dc:license rdf:resource="https://creativecommons.org/licenses/by-sa/4.0<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcreativecommons.org%2Flicenses%2Fby-sa%2F4.0&data=02%7C01%7Cc.chung%40med.miami.edu%7C5a069016dd2342b2945408d574ad7d13%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C1%7C636543210867782524&sdata=szf4sV9Fh7CBwIRbuKMyD3JB6IDTiCyR929NudiOOX0%3D&reserved=0>/"/>)

On BioPortal (https://bioportal.bioontology.org/ontologies/DTO<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDTO&data=02%7C01%7Cc.chung%40med.miami.edu%7C5a069016dd2342b2945408d574ad7d13%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C1%7C636543210867782524&sdata=kJHtMACGarJoR%2B%2BpVizzgzn3m4rDFTeCse1K4hJSdeA%3D&reserved=0>) I do not see the field (LICENSE INFORMATION) and value for the license.

Can you let me know why?


Allowing end users to enter ontology license information via the BioPortal user interface is functionality we haven?t implemented. I?m not aware of a particular reason for this, other than we?re a small team and providing this functionality hasn?t hit the top of our priority list. For ontologies that do display license information (e.g., ontologies from the UMLS with download restrictions like SNOMEDCT, CPT, etc.) that license text has been manually added to a configuration file that's read by the user interface when the ontology summary pages are displayed.

If it?s critical to display license information for a particular ontology, there is the option of having us add it manually to our configuration file.

Kind regards,
Jennifer

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From jgraybeal at stanford.edu  Thu Feb 15 18:12:04 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 16 Feb 2018 02:12:04 +0000
Subject: [bioontology-support] Using biomedical ontology feature in
	REDCap
In-Reply-To: <B1BF633C57B39640B1F0B99035AE8186DE7ADE50@CMN-EXCH4.mater.health.nsw.gov.au>
References: <B1BF633C57B39640B1F0B99035AE8186DE7ACA8C@CMN-EXCH4.mater.health.nsw.gov.au>
 <E6DDA5D8-8DCE-4FE3-8BF4-DC5375E780F6@stanford.edu>
 <B1BF633C57B39640B1F0B99035AE8186DE7ADE50@CMN-EXCH4.mater.health.nsw.gov.au>
Message-ID: <6C11A346-8AB4-4B42-8026-7A6519F04DC5@stanford.edu>

It makes more sense, but the IT people should have all the information they need from the BioPortal side of things. If you follow the directions I previously gave from something outside the firewall (a browser on your cell phone, or your home machine) you should be able to verify that the API to BIoPortal works.

With that information, you can go to your IT department and say "This is the domain name I am trying to access from my here. It works on my home system. If you whitelist it, I should be able to access it from here."  They can look up the IP address from the domain name, and whitelist that, and you can verify that your browser now works for you. (If they can't figure out how to make it possible for your browser to access BioPortal, I am not sure how to help?no one has ever had that particular problem in my experience. I'll double-check with our DevOps person to make sure, but this is something that your IT department has to have the ability to address.)

That will not necessariy fix RedCAP. It seems that RedCAP is likely not able to access BioPortal at all, but I have no way to examine why that might be in your environment. You could try to contact the REDcap people to find out what *their* system actually accesses?I have no idea how the RedCAP code accesses BioPortal, and perhaps they are accessing another system first before accessing BioPortal, and that system needs to be whitelisted.  I am sorry I can't help you with that particular situation.

John


On Feb 11, 2018, at 4:20 PM, O'Neill, Monica <Monica.O'Neill at calvarymater.org.au<mailto:Monica.O'Neill at calvarymater.org.au>> wrote:

Thank you John for getting back to me so quickly.

Our browser is indeed behind a firewall. My issue is that I cannot find the specific URL that my IT department has to whitelist. My IT department conducted many tests to monitor traffic and where exactly the firewall was blocking access, but couldn?t find anything. They suggested I get in contact with someone like yourself, who may know exactly what URL address redcap is trying to access when you first try to enable the bioontology feature in redcap.

Does that make more sense? Unfortunately I am not from an IT background so I can?t be more specific.

Much appreciated ? I look forward to using your ontologies!

Monica O'Neill
Data Manager |Clinical Cancer Research Network
Email: monica.o'neill at calvarymater.org.au<mailto:monica.o'neill at calvarymater.org.au>
Please note I work a 7 day fortnight

Monday, Tuesday and Wednesday
Calvary Mater Newcastle
Due to hot-desking arrangements, please contact via email

Every second Friday
John Hunter Hospital
Tel 02 4923 6397 | Fax 02 4921 4274

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Tuesday, 6 February 2018 5:30 AM
To: O'Neill, Monica
Cc: support at bioontology.org<mailto:support at bioontology.org>; Alberto.varas at hnehealth.nsw.gov.au<mailto:Alberto.varas at hnehealth.nsw.gov.au>
Subject: Re: [bioontology-support] Using biomedical ontology feature in REDCap

Hi Monica,

Thanks for doing most of this investigation for us! I will confirm what you have already found, but can give you one more test you can perform.

If you look at the URL for any query from the http://data.bioontology.org/documentation, for example something like http://data.bioontology.org/search?q=melanoma, you can try it in your browser. Probably it won't work, assuming you haven't entered your API key in a query before. To do so, complete the query like so:
 http://data.bioontology.org/search?q=melanoma&apikey=YOUR_API_KEY_HERE

If that still doesn't work, your browser is probably also behind some firewall that has to be opened to allow access to BioPortal. But if it *does* work, then you have confirmed your API key works, and now you have to get the firewall opened that is in front of the REDCap machine.)

This step of 'whitelisting' the BioPortal site is something that your IT department has to do?we can not help with that, sorry. Please have your IT person contact us if he or she is having some difficulty.

John



On Feb 4, 2018, at 6:51 PM, O'Neill, Monica <Monica.O'Neill at calvarymater.org.au<mailto:Monica.O'Neill at calvarymater.org.au>> wrote:

Hello,

I am an administrator of REDCap for my institution. I am very keen to employ the biomedical ontology functionality within REDCap for use in our clinical trials, but I am having some technical issues.

When I copy-paste the API token from my account with NCBO (username: monicaoneill), REDCap tells me this is not a valid token. I searched the online REDCap community and found others experienced the same error (see image below), which turned out to be because of security settings at their institution. I contacted Yelena Fridgant to ask for more details but she was unable to assist any further other than remembering she asked her IT Department to ?whitelist? the website.

I have been in contact with Alberto Varas (cc?d) from my institutions IT department, who made every attempt to figure out which URL specifically needed ?whitelisting?. Are you able to help in this regard? I would be happy to provide you with more information if you need it, just let Alberto and myself know.

<image001.png>

Many thanks in advance,
Monica O'Neill
Data Manager |Clinical Cancer Research Network
monica.o'neill at calvarymater.org.au<mailto:monica.o'neill at calvarymater.org.au>

Monday, Tuesday and Wednesday
Calvary Mater Newcastle
Due to hot-desking arrangements, please contact via email

Thursday and Friday
John Hunter Hospital
Tel 02 4923 6397 | Fax 02 4921 4274

This message is intended for the addressee and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of the Calvary Mater Newcastle or NSW Health. _______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


This message is intended for the addressee and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of the Calvary Mater Newcastle or NSW Health.

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


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From jgraybeal at stanford.edu  Thu Feb 15 18:29:33 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 16 Feb 2018 02:29:33 +0000
Subject: [bioontology-support] search by id in a subtree -> sparql
 service in VA similar to BioPortal
In-Reply-To: <18FE2944-380A-4473-B1CF-FD0E0EDA154D@vumc.org>
References: <103B3C18EAB4F444A941714214A04B8159418D83@ITS-HCWNEM105.ds.vanderbilt.edu>
 <74171848-BE6D-47A4-87EB-46777D560C00@stanford.edu>
 <6590516A-9AA6-4161-9122-142483B1D4A2@stanford.edu>
 <103B3C18EAB4F444A941714214A04B8159419920@ITS-HCWNEM105.ds.vanderbilt.edu>
 <4F631481-F89E-4A1D-B934-64CE1BB398E1@stanford.edu>
 <18FE2944-380A-4473-B1CF-FD0E0EDA154D@vumc.org>
Message-ID: <B364F717-7054-44F9-AC83-A3E55B56BB77@stanford.edu>

Hi Sina,

I'm replying to give you a heads-up on this, namely that we will not be able to get to this problem very quickly I'm afraid.

At the moment, we have a number of pretty critical and time-consuming tasks we are trying to complete. UMLS is high on our list, but not high enough to happen in the next few weeks at least. And it is not clear how long it may take for us to succeed in tracking down that problem.

That said, here's a point. I notice that the first thing in your log says
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
Invalid byte sequence in UTF-8 strongly suggests that there is a mis-coded character or an unsupported character, or that binary data contaminated the file. I don't know the best way to check this, but I use BBEdit for text files and it gives pretty good warnings for bad characters. I expect there are web services that can test a file as well, though maybe not for really big files.

Perhaps if anyone else on the list has successfully parsed the latest(?) SNOMED using umls2rdf they can let us know.

Sorry we can't be more help sooner.

John



On Feb 2, 2018, at 5:25 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Thank you, John for the response.
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.

Thanks again for looking into this

Sina

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Friday, February 2, 2018 at 2:28 AM
To: "Madani, Sina" <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal

Hi Sina,

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.

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!)

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!).

I think we'll be able to come back to you with more thoughts soon, hopefully by the weekend.

John


On Feb 1, 2018, at 11:51 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi John,

Thank you for getting back to me. Yes, I meant similar functionality like the sparql end point at the Stanford instance.
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.
We are evaluating your appliance for search/browse and visualization purposes for our order sets catalogue, with mappings to standard terminologies, at this point.

Thanks!
Sina

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Wednesday, January 31, 2018 6:50 PM
To: Michael Dorf
Cc: support at bioontology.org<mailto:support at bioontology.org>; Madani, Sina
Subject: Re: [bioontology-support] search by id in a subtree -> sparql service in VA similar to BioPortal

Sina,

(Changing the topic line to focus on the SPARQL question that I'm addressing here.)

The exact answer to your last question may depend on what you mean by "similar to the BioPortal web site".

On BioPortal we have the 'front-end beta SPARQL query UI' set up at http://sparql.bioontology.org<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>. 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.

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.)

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.

I know the technical folks are thinking about your other questions, I'm not going to try to guess at those answers!

John




On Jan 31, 2018, at 3:05 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=UOXjV5Z7bctq%2Bh4r%2BhcKOS%2FIOZUDBJzynLRSFYUM7OU%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%7C3434890b2cca46bf04eb08d5690dbdf8%7Cef57503014244ed8b83c12c533d879ab%7C0%7C1%7C636530430119439315&sdata=C7B0qSamo%2BQz%2F1zW3G41kA3FzLCGJlKPYhMdXu7G8NU%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'"]


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https://mailman.stanford.edu/mailman/listinfo/bioontology-support<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>

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

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

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


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From jonquet at lirmm.fr  Fri Feb 16 09:30:33 2018
From: jonquet at lirmm.fr (Clement Jonquet)
Date: Fri, 16 Feb 2018 09:30:33 -0800
Subject: [bioontology-support] RDA VSSIG Ontology Metadata Task Group Survey
Message-ID: <1F9F352C-FAEC-4F21-BB88-7E123C738CD2@lirmm.fr>

Dear BioPortal, OBO and GACS communities, 

Your feedback will be more than welcome on this survey. 

------------

[Apologies for multiple receptions - this announcement has been sent to multiple mailing lists of the ontology/semantic Web/linked data/standardization communities.]

If you are somehow familiar with the use of ontologies, please consider answering this survey. 

In the context of the recent reconfiguration of the RDA Vocabulary Semantic Services Interest Group [1], we are leading a task group focused on ontology metadata. 

The goal of this task group is to review the current state related to metadata description of semantic resources in general (ontologies, vocabularies, thesauri and terminologies); and discuss recommendations and best practices in terms of metadata standards for ontologies.

To give insights to the group and drive our work, we have setup a survey on the topic and would really appreciate your participation. 
https://goo.gl/tXaaMf <https://goo.gl/tXaaMf> 
 
The survey is anonymous and uses GForm. It should take about 10-15 minutes. 
Please take a moment to send your feedback.

Thank you for your help
Clement Jonquet, Biswanath Dutta, Anne Toulet and Barbara Magana 

[1] https://www.rd-alliance.org/groups/vocabulary-services-interest-group.html <https://www.rd-alliance.org/groups/vocabulary-services-interest-group.html>
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From lynn.schriml at gmail.com  Fri Feb 16 07:43:33 2018
From: lynn.schriml at gmail.com (Lynn Schriml)
Date: Fri, 16 Feb 2018 10:43:33 -0500
Subject: [bioontology-support] updating the Pathogen Transmission Ontology
	page
Message-ID: <CAFN6i6ZEraWZQRkR+4GOkx4TuqACReMwcFkM5E24c94uYP+MwQ@mail.gmail.com>

Hello,
 I logged into the account, but am not seeing the Edit submission
information.

For comparison, I check the Disease Ontology, and on this Summary page I do
see the Edit links.

Can you add this ontology to my list of 'Submitted Ontologies' so that I
can update the information.


Cheers,
Lynn

-- 
Lynn M. Schriml, Ph.D.
Associate Professor

Institute for Genome Sciences
University of Maryland School of Medicine
Department of Epidemiology and Public Health
801 W. Baltimore St., Room 659
Baltimore, MD 21201
P: 410-706-6776 |  F: 410-706-6756
lschriml at som.umaryland.edu
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From vendetti at stanford.edu  Fri Feb 16 10:49:15 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 16 Feb 2018 18:49:15 +0000
Subject: [bioontology-support] updating the Pathogen Transmission
	Ontology	page
In-Reply-To: <CAFN6i6ZEraWZQRkR+4GOkx4TuqACReMwcFkM5E24c94uYP+MwQ@mail.gmail.com>
References: <CAFN6i6ZEraWZQRkR+4GOkx4TuqACReMwcFkM5E24c94uYP+MwQ@mail.gmail.com>
Message-ID: <1C40686A-C3EA-49A4-88A2-1938A04DFDED@stanford.edu>

Hi Lynn,

I added your account as an administrator for this ontology. If you log into BioPortal and refresh the browser window when you?re viewing the Pathogen Transmission Ontology summary page, you should see the edit link now.

Kind regards,
Jennifer



On Feb 16, 2018, at 7:43 AM, Lynn Schriml <lynn.schriml at gmail.com<mailto:lynn.schriml at gmail.com>> wrote:

Hello,
 I logged into the account, but am not seeing the Edit submission information.

For comparison, I check the Disease Ontology, and on this Summary page I do see the Edit links.

Can you add this ontology to my list of 'Submitted Ontologies' so that I can update the information.


Cheers,
Lynn

--
Lynn M. Schriml, Ph.D.
Associate Professor

Institute for Genome Sciences
University of Maryland School of Medicine
Department of Epidemiology and Public Health
801 W. Baltimore St., Room 659
Baltimore, MD 21201
P: 410-706-6776 |  F: 410-706-6756
lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From lynn.schriml at gmail.com  Fri Feb 16 12:35:11 2018
From: lynn.schriml at gmail.com (Lynn Schriml)
Date: Fri, 16 Feb 2018 15:35:11 -0500
Subject: [bioontology-support] updating the Pathogen Transmission
 Ontology page
In-Reply-To: <1C40686A-C3EA-49A4-88A2-1938A04DFDED@stanford.edu>
References: <CAFN6i6ZEraWZQRkR+4GOkx4TuqACReMwcFkM5E24c94uYP+MwQ@mail.gmail.com>
 <1C40686A-C3EA-49A4-88A2-1938A04DFDED@stanford.edu>
Message-ID: <442DFAE4-E413-4657-AD89-BB204E964CE5@gmail.com>

Thank you Jennifer, 
  Can you change the BioPortal Purl to use TRANS as the acronym ? 

I have updated the ontology.

Cheers,
Lynn

> On Feb 16, 2018, at 1:49 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:
> 
> Hi Lynn,
> 
> I added your account as an administrator for this ontology. If you log into BioPortal and refresh the browser window when you?re viewing the Pathogen Transmission Ontology summary page, you should see the edit link now.
> 
> Kind regards,
> Jennifer
> 
> 
> 
>> On Feb 16, 2018, at 7:43 AM, Lynn Schriml <lynn.schriml at gmail.com <mailto:lynn.schriml at gmail.com>> wrote:
>> 
>> Hello,
>>  I logged into the account, but am not seeing the Edit submission information. 
>> 
>> For comparison, I check the Disease Ontology, and on this Summary page I do see the Edit links. 
>> 
>> Can you add this ontology to my list of 'Submitted Ontologies' so that I can update the information.
>> 
>> 
>> Cheers,
>> Lynn
>> 
>> -- 
>> Lynn M. Schriml, Ph.D.
>> Associate Professor
>> 
>> Institute for Genome Sciences
>> University of Maryland School of Medicine
>> Department of Epidemiology and Public Health
>> 801 W. Baltimore St., Room 659  
>> Baltimore, MD 21201
>> P: 410-706-6776 |  F: 410-706-6756  
>> lschriml at som.umaryland.edu <mailto:lschriml at som.umaryland.edu>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 

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From vendetti at stanford.edu  Fri Feb 16 13:27:27 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 16 Feb 2018 21:27:27 +0000
Subject: [bioontology-support] updating the Pathogen Transmission
 Ontology page
In-Reply-To: <442DFAE4-E413-4657-AD89-BB204E964CE5@gmail.com>
References: <CAFN6i6ZEraWZQRkR+4GOkx4TuqACReMwcFkM5E24c94uYP+MwQ@mail.gmail.com>
 <1C40686A-C3EA-49A4-88A2-1938A04DFDED@stanford.edu>
 <442DFAE4-E413-4657-AD89-BB204E964CE5@gmail.com>
Message-ID: <128ED45A-D4A6-4F08-A672-2936B5E1E284@stanford.edu>

Hi Lynn,

Once created, ontology acronyms are unique / unmodifiable objects in BioPortal. The best we can do in these cases is to create a new ontology entry, move existing data under the new entry, and delete the old one.

Normally I?d ask if that?s a path you?d like us to proceed with, but I noticed that the TRANS acronym has already been claimed in BioPortal by the Nurse Transitional ontology.

Kind regards,
Jennifer



On Feb 16, 2018, at 12:35 PM, Lynn Schriml <lynn.schriml at gmail.com<mailto:lynn.schriml at gmail.com>> wrote:

Thank you Jennifer,
  Can you change the BioPortal Purl to use TRANS as the acronym ?

I have updated the ontology.

Cheers,
Lynn

On Feb 16, 2018, at 1:49 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Lynn,

I added your account as an administrator for this ontology. If you log into BioPortal and refresh the browser window when you?re viewing the Pathogen Transmission Ontology summary page, you should see the edit link now.

Kind regards,
Jennifer



On Feb 16, 2018, at 7:43 AM, Lynn Schriml <lynn.schriml at gmail.com<mailto:lynn.schriml at gmail.com>> wrote:

Hello,
 I logged into the account, but am not seeing the Edit submission information.

For comparison, I check the Disease Ontology, and on this Summary page I do see the Edit links.

Can you add this ontology to my list of 'Submitted Ontologies' so that I can update the information.


Cheers,
Lynn

--
Lynn M. Schriml, Ph.D.
Associate Professor

Institute for Genome Sciences
University of Maryland School of Medicine
Department of Epidemiology and Public Health
801 W. Baltimore St., Room 659
Baltimore, MD 21201
P: 410-706-6776 |  F: 410-706-6756
lschriml at som.umaryland.edu<mailto:lschriml at som.umaryland.edu>
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support



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From support at bioontology.org  Mon Feb 19 08:05:13 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 19 Feb 2018 08:05:13 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Mathias Brochhausen
Message-ID: <5a8af5b9e1a37_5f553feb7dbd22f430732@ncbo-prd-app-09.stanford.edu.mail>

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From jgraybeal at stanford.edu  Mon Feb 19 12:00:42 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 19 Feb 2018 20:00:42 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Mathias
 Brochhausen
In-Reply-To: <5a8af5b9e1a37_5f553feb7dbd22f430732@ncbo-prd-app-09.stanford.edu.mail>
References: <5a8af5b9e1a37_5f553feb7dbd22f430732@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <MWHPR0201MB351648E5677D73089AC9FB01DAC80@MWHPR0201MB3516.namprd02.prod.outlook.com>

Hello Mathias,


I was unable to find any account in BioPortal associated with your email at uams.edu. If there is a specific place you see this email in the tool, please let us know.


John

________________________________
From: bioontology-support <bioontology-support-bounces at lists.stanford.edu> on behalf of support at bioontology.org <support at bioontology.org>
Sent: Monday, February 19, 2018 8:05:13 AM
To: support at bioontology.org; mbrochhausen at uams.edu
Subject: [bioontology-support] [BioPortal] Feedback from Mathias Brochhausen


Name: Mathias Brochhausen

Email: mbrochhausen at uams.edu

Location: https%3A%2F%2Fbioportal.bioontology.org%2Flost_pass

Feedback:

Hi,

It seems I have two accounts (one with the e-mail mbrochhausen at gmail.com, the other with mbrochhausen at uams.edu). For the second one, I am unable to reset my password because I do not remember my user name. Please help.
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From support at bioontology.org  Mon Feb 19 14:33:44 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 19 Feb 2018 14:33:44 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Ramona Walls
Message-ID: <5a8b50c836e9f_e3a3f947c3bca54624df@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Tue Feb 20 05:12:55 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 20 Feb 2018 05:12:55 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Alsayed Algergawy
Message-ID: <5a8c1ed71e6e5_27453ff148724c2c838a0@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Tue Feb 20 11:51:47 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 20 Feb 2018 19:51:47 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Ramona Walls
In-Reply-To: <CAJYF1k6t7q=ubY1D-ss30u0Di7vamEcY=qEUEtWPYc++5a6obQ@mail.gmail.com>
References: <5a8b50c836e9f_e3a3f947c3bca54624df@ncbo-prd-app-09.stanford.edu.mail>
 <MWHPR0201MB35168B23CF8A1C09F50EC425DAC80@MWHPR0201MB3516.namprd02.prod.outlook.com>
 <CAJYF1k6EOgBp_cr-+Vib7UneDumunXTmdEs2-uspGCtCodjihQ@mail.gmail.com>
 <CAJYF1k4vPDXxQDOueZjPfkF2KEPViJuH4-JgO19YtCMMobZ1aw@mail.gmail.com>
 <CAJYF1k5YLqXq=awB5g6Eky0kS_VTpB2NZWM5f+9c4fXnLaZtsg@mail.gmail.com>
 <MWHPR0201MB351664116C34A5B0915FD8C7DAC80@MWHPR0201MB3516.namprd02.prod.outlook.com>
 <CAJYF1k6t7q=ubY1D-ss30u0Di7vamEcY=qEUEtWPYc++5a6obQ@mail.gmail.com>
Message-ID: <1595EB3F-2119-49BF-8042-800932A094E5@stanford.edu>

Hi Ramona,

Usernames, once created, are unique identifiers in our system / unmodifiable resources. If you want the ?rwalls? username, please create a new account [1]. If you decided to go that route, let us know which ontologies you need administrative privileges for.

Kind regards,
Jennifer

[1] https://bioportal.bioontology.org/accounts/new


On Feb 19, 2018, at 3:20 PM, Ramona Walls <rlwalls2008 at gmail.com<mailto:rlwalls2008 at gmail.com>> wrote:

Thanks again, John. If Jennifer is not able to change it (or tell me how), I can live with rwallls. I now have lastpass, so I don't have to remember things!

Thank you for answering on a holiday! We have to work today in Arizona. :)

------------------------------------------------------
Ramona L. Walls, Ph.D.
Senior Scientific Analyst, CyVerse, University of Arizona
Research Associate, Bio5 Institute, University of Arizona

On Mon, Feb 19, 2018 at 4:04 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:
Hi Ramona,

I know that?s SO frustrating!  I?m pretty sure there?s a way, but haven?t had to do it so I will have to defer to my colleague (copied). You?re of course welcome to create another account until then. (Most of us are on holiday today.)

John

________________________________
From: Ramona Walls <rlwalls2008 at gmail.com<mailto:rlwalls2008 at gmail.com>>
Sent: Monday, February 19, 2018 2:56:26 PM
To: John Graybeal
Subject: Re: [bioontology-support] [BioPortal] Feedback from Ramona Walls

Looks like I can change the email and password, but not user name. Any chance you could change my user name to rwalls, or, if that is taken, rlwalls?

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Senior Scientific Analyst, CyVerse, University of Arizona
Research Associate, Bio5 Institute, University of Arizona

On Mon, Feb 19, 2018 at 3:54 PM, Ramona Walls <rlwalls2008 at gmail.com<mailto:rlwalls2008 at gmail.com>> wrote:
Oh never mind! I tried one more old password, and it worked. I guess I can now reset my account information. Thanks for you fast help.

Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Senior Scientific Analyst, CyVerse, University of Arizona
Research Associate, Bio5 Institute, University of Arizona

On Mon, Feb 19, 2018 at 3:52 PM, Ramona Walls <rlwalls2008 at gmail.com<mailto:rlwalls2008 at gmail.com>> wrote:
Thank you John! An extra l and a dead email - lucky me.

Even using rwallls, I'm having no luck with remembering the password,  I am not going to be able reset it, because rwalls at nybg.org<mailto:rwalls at nybg.org> no longer exists. Is it possible for you to change my account email to rlwalls2008 at gmail.com<mailto:rlwalls2008 at gmail.com>, so I can reset my password then fix the user name?

Thanks,
Ramona

------------------------------------------------------
Ramona L. Walls, Ph.D.
Senior Scientific Analyst, CyVerse, University of Arizona
Research Associate, Bio5 Institute, University of Arizona

On Mon, Feb 19, 2018 at 3:44 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:
Hi Ramona,

Your user name is rwallls (note the third 'l', which is probably why you couldn't find it), at rwalls at nybg.org<mailto:rwalls at nybg.org>.

John
________________________________
From: bioontology-support <bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>> on behalf of support at bioontology.org<mailto:support at bioontology.org> <support at bioontology.org<mailto:support at bioontology.org>>
Sent: Monday, February 19, 2018 2:33:44 PM
To: support at bioontology.org<mailto:support at bioontology.org>; rlwalls2008 at gmail.com<mailto:rlwalls2008 at gmail.com>
Subject: [bioontology-support] [BioPortal] Feedback from Ramona Walls


Name: Ramona Walls

Email: rlwalls2008 at gmail.com<mailto:rlwalls2008 at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Flost_pass

Feedback:

I am trying to reset my forgotten password, but I can't remember my associated email and user name either. None of my tries have worked. Could you please send me my user name and email associated with my account, so I can reset my password?

Thanks,
Ramona






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From vendetti at stanford.edu  Tue Feb 20 12:27:13 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 20 Feb 2018 20:27:13 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ulfschwarz
In-Reply-To: <CABfB3ijY2UvzJO9mPOSBmrLzKUCKW0BCF8yvQbb=A+y81GsqVg@mail.gmail.com>
References: <5a82a744cc60e_320e3f8150a3561863984@ncbo-prd-app-08.stanford.edu.mail>
 <D038F4F3-80B1-4116-AF9D-E496BD429A46@stanford.edu>
 <CABfB3ii7SgOaS8+eAZDOX94takJ7AJ0_7BvoLCz-PO7fs_1YBQ@mail.gmail.com>
 <B130BA6B-BE2B-49CB-8365-5CF8B6A73B1E@stanford.edu>
 <CABfB3iiEsEnaR9jzJ8EobfJ47g_=OgBL1yoQ=MJdmw_+=z2W=g@mail.gmail.com>
 <913C55D6-2C77-4D48-8C65-578F983A7DE1@stanford.edu>
 <CABfB3ijY2UvzJO9mPOSBmrLzKUCKW0BCF8yvQbb=A+y81GsqVg@mail.gmail.com>
Message-ID: <0486A1C2-3AC9-45DA-9F00-B5A120D7C050@stanford.edu>

Hi Ulf,


On Feb 20, 2018, at 12:30 AM, Ulf Schwarz <ulf.schwarz at ifomis.uni-saarland.de<mailto:ulf.schwarz at ifomis.uni-saarland.de>> wrote:

Yes, I would like to delete both VDOT_CORE and TES


OK - I?ve deleted both of those ontology entries from our system.


and I would like to keep Viral Disease Ontology Trunk. Additionally I would like to change its setting from private to public once I checked that everything is fine.

It looks like the upload for the Viral Disease Ontology Trunk Ontology was successful now. Am I right?


No, I didn?t see any submissions associated with VDOT. I manually created one using the pull URL that you sent in a previous email, which seemed to process without errors. You can examine the result and let us know if you see any issues:

http://bioportal.bioontology.org/ontologies/VDOT/?p=summary

Kind regards,
Jennifer


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From vendetti at stanford.edu  Tue Feb 20 16:02:37 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 21 Feb 2018 00:02:37 +0000
Subject: [bioontology-support] BioPortal DTO license CC BY-SA 4.0
In-Reply-To: <SN2PR0701MB7657F3D6BFE469EF50C7A4BB9F40@SN2PR0701MB765.namprd07.prod.outlook.com>
References: <SN2PR0701MB7654C72D249ABE12ED6D5F8B9F40@SN2PR0701MB765.namprd07.prod.outlook.com>
 <B3F2815E-FEB0-4EA8-829D-CEC6F547DC8F@stanford.edu>
 <SN2PR0701MB7657F3D6BFE469EF50C7A4BB9F40@SN2PR0701MB765.namprd07.prod.outlook.com>
Message-ID: <210200B6-0EDD-4DCA-810A-C9F851C5AFB9@stanford.edu>

Hi Caty,

The license information is live on the production site (http://bioportal.bioontology.org/ontologies/DTO). Have a look and let us know if it appears as desired.

Kind regards,
Jennifer



On Feb 15, 2018, at 12:28 PM, Chung, Caty Elizabeth <c.chung at med.miami.edu<mailto:c.chung at med.miami.edu>> wrote:


Thank you Jennifer, it would be great if you could add the license for us: https://github.com/DrugTargetOntology/DTO/blob/master/LICENSE.md
Caty

________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Thursday, February 15, 2018 2:51:01 PM
To: Chung, Caty Elizabeth
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] BioPortal DTO license CC BY-SA 4.0

Hello Caty,


On Feb 15, 2018, at 7:24 AM, Chung, Caty Elizabeth <c.chung at med.miami.edu<mailto:c.chung at med.miami.edu>> wrote:


Hello,

The ontology file (http://drugtargetontology.org/dto/dto_complete.owl<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdrugtargetontology.org%2Fdto%2Fdto_complete.owl&data=02%7C01%7Cc.chung%40med.miami.edu%7C5a069016dd2342b2945408d574ad7d13%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C1%7C636543210867782524&sdata=8aHKkRT2CTOsB2h09EuyJV9Z026zzN6WQ%2B3F05vA%2BeY%3D&reserved=0>) has the license CC BY-SA 4.0 (<dc:license rdf:resource="https://creativecommons.org/licenses/by-sa/4.0<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcreativecommons.org%2Flicenses%2Fby-sa%2F4.0&data=02%7C01%7Cc.chung%40med.miami.edu%7C5a069016dd2342b2945408d574ad7d13%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C1%7C636543210867782524&sdata=szf4sV9Fh7CBwIRbuKMyD3JB6IDTiCyR929NudiOOX0%3D&reserved=0>/"/>)

On BioPortal (https://bioportal.bioontology.org/ontologies/DTO<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDTO&data=02%7C01%7Cc.chung%40med.miami.edu%7C5a069016dd2342b2945408d574ad7d13%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C1%7C636543210867782524&sdata=kJHtMACGarJoR%2B%2BpVizzgzn3m4rDFTeCse1K4hJSdeA%3D&reserved=0>) I do not see the field (LICENSE INFORMATION) and value for the license.

Can you let me know why?


Allowing end users to enter ontology license information via the BioPortal user interface is functionality we haven?t implemented. I?m not aware of a particular reason for this, other than we?re a small team and providing this functionality hasn?t hit the top of our priority list. For ontologies that do display license information (e.g., ontologies from the UMLS with download restrictions like SNOMEDCT, CPT, etc.) that license text has been manually added to a configuration file that's read by the user interface when the ontology summary pages are displayed.

If it?s critical to display license information for a particular ontology, there is the option of having us add it manually to our configuration file.

Kind regards,
Jennifer

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From jgraybeal at stanford.edu  Tue Feb 20 17:35:28 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 21 Feb 2018 01:35:28 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Alsayed
	Algergawy
In-Reply-To: <5a8c1ed71e6e5_27453ff148724c2c838a0@ncbo-prd-app-08.stanford.edu.mail>
References: <5a8c1ed71e6e5_27453ff148724c2c838a0@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <18953BEA-0D99-4417-AEB7-3E8D688D318D@stanford.edu>

Hi Alsayed,

It's hard to say without more information.

If you are using the API to load ontology content one page at a time, it can be extremely time consuming and resource-intensive to do that for an ontology with several hundred thousand to a million terms in it. While I expect some people have been successful, they probably took great care to space out their requests far apart, making sure one page came back before the next page was requested, and so on. (You might find useful tips searching the mail list, as similar questions have been addressed before.)

So if there is a resource issue, I can't tell you who is more short of resources, BioPortal or your system. My guess would be your system just doesn't have enough resources allocated at some point, or there could be a memory leak in your code. But that's just a guess based on my understanding that others have successfully downloaded all the ontologies.

In any case, the problem may be with ontology 110, than it is with the fact you have already downloaded 110 ontologies. But we don't know what ontology 110 is, so we can't tell you much about the possible issues.

If you want more detailed answers, you might want to include examples of your source code, the last dozen or so API requests that your code made, and the last few transmissions from BioPortal before the downloads stopped. And if your application is actually crashing, the crash log would provide valuable insights too. (If your application is crashing, that's probably the first place you should look, is your application and system logs.)

John


On Feb 20, 2018, at 5:12 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Alsayed Algergawy

Email: alsayed.algergawy at uni-jena.de<mailto:alsayed.algergawy at uni-jena.de>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Faccounts%2Falsayed

Feedback:

dear all,
I am trying to download the available set of ontologies on the Bioportal side using the available API. It works fine till downloading 110 ontologies, and the process crashes. Do you have any explanation for this behavior?
thank you in advance!!
yours,
alsayed

_______________________________________________
bioontology-support mailing list
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


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From support at bioontology.org  Wed Feb 21 08:42:36 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 21 Feb 2018 08:42:36 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Michal Lijowski
Message-ID: <5a8da17c71211_27c63fbdd38309ac627d7@ncbo-prd-app-09.stanford.edu.mail>

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From alsayed.algergawy at uni-jena.de  Wed Feb 21 04:31:27 2018
From: alsayed.algergawy at uni-jena.de (Dr. Ing. Algergawy)
Date: Wed, 21 Feb 2018 13:31:27 +0100
Subject: [bioontology-support] [BioPortal] Feedback from Alsayed
	Algergawy
In-Reply-To: <18953BEA-0D99-4417-AEB7-3E8D688D318D@stanford.edu>
References: <5a8c1ed71e6e5_27453ff148724c2c838a0@ncbo-prd-app-08.stanford.edu.mail>
 <18953BEA-0D99-4417-AEB7-3E8D688D318D@stanford.edu>
Message-ID: <d0498e6a-8d85-3c75-efa6-0a697f286498@uni-jena.de>

Dear John,

many thanks for your reply. However, I expected the problem is not
related to available resources to your or our sides. Since I have
already one time to download the set of ontologies. Currently, the
process of downloading is not completed especially when the number of
downloaded ontologies reaches 110 with the following error message

" ERROR de.julielab.bioportal.ontologies.HttpHandler - Error when
posting a request to BioPortal Server: Internal server error"

actually I tried many times with different API keys (for me and my
colleagues), but the same problem remains.

I hope you can help me to discover what is the problem

yours,

alsayed


On 2/21/2018 2:35 AM, John Graybeal wrote:
> Hi Alsayed,
>
> It's hard to say without more information.
>
> If you are using the API to load ontology content one page at a time, it can be extremely time consuming and resource-intensive to do that for an ontology with several hundred thousand to a million terms in it. While I expect some people have been successful, they probably took great care to space out their requests far apart, making sure one page came back before the next page was requested, and so on. (You might find useful tips searching the mail list, as similar questions have been addressed before.)
>
> So if there is a resource issue, I can't tell you who is more short of resources, BioPortal or your system. My guess would be your system just doesn't have enough resources allocated at some point, or there could be a memory leak in your code. But that's just a guess based on my understanding that others have successfully downloaded all the ontologies.
>
> In any case, the problem may be with ontology 110, than it is with the fact you have already downloaded 110 ontologies. But we don't know what ontology 110 is, so we can't tell you much about the possible issues.
>
> If you want more detailed answers, you might want to include examples of your source code, the last dozen or so API requests that your code made, and the last few transmissions from BioPortal before the downloads stopped. And if your application is actually crashing, the crash log would provide valuable insights too. (If your application is crashing, that's probably the first place you should look, is your application and system logs.)
>
> John
>
>
> On Feb 20, 2018, at 5:12 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:
>
>
> Name: Alsayed Algergawy
>
> Email: alsayed.algergawy at uni-jena.de<mailto:alsayed.algergawy at uni-jena.de>
>
> Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Faccounts%2Falsayed
>
> Feedback:
>
> dear all,
> I am trying to download the available set of ontologies on the Bioportal side using the available API. It works fine till downloading 110 ontologies, and the process crashes. Do you have any explanation for this behavior?
> thank you in advance!!
> yours,
> alsayed
>
> _______________________________________________
> bioontology-support mailing list
> 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
>
>
>

-- 
Dr. Ing. Alsayed Algergawy

Institut f?r Informatik
Friedrich-Schiller-Universit?t Jena
http://fusion.cs.uni-jena.de
alsayed.algergawy at uni-jena.de 
T: +49(0)3641-946438

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From vendetti at stanford.edu  Wed Feb 21 11:31:15 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 21 Feb 2018 19:31:15 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Michal Lijowski
In-Reply-To: <5a8da17c71211_27c63fbdd38309ac627d7@ncbo-prd-app-09.stanford.edu.mail>
References: <5a8da17c71211_27c63fbdd38309ac627d7@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <85D7AF92-7CA5-4100-8004-2674DC1EB7E6@stanford.edu>

Hello Michal,


On Feb 21, 2018, at 8:42 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Michal Lijowski

Email: michal.lijowski at gmail.com<mailto:michal.lijowski at gmail.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:

For over a week, I have been trying to do the following.

We read and do our best to respond to questions on our support list daily. Feel free to post immediately if you?re having an issue with BioPortal.


1. Enter Bioportal page.
2. In a field below Find an ontology enter
Syst
3. Select System Biology Ontology (OBO)
4. Click Search
5. The result is
We're sorry but something has gone wrong. We have been notified of this error.

We?ve tracked down and fixed the issue that was preventing the ontology summary page from displaying properly for SBO. You should have full access now. Let us know if you?re still having issues.

Kind regards,
Jennifer


[cid:3FD0537A-5560-4EC9-8D3F-6D7AF14C45B1 at stanford.edu]
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From vendetti at stanford.edu  Wed Feb 21 17:51:32 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 22 Feb 2018 01:51:32 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Andrey Fedorov
In-Reply-To: <010001618f47e349-c4b0592f-f92a-4f0c-bc8c-0652dc43bf9c-000000@email.amazonses.com>
References: <5a7f2f529c525_7c683f89f27fdef4796fb@ncbo-prd-app-08.stanford.edu.mail>
 <D9F38B5C-4BCF-42DF-AC3E-2C930169ACCC@stanford.edu>
 <CAMw6MkcAxMwnRoTKxrMSHYq20xaT+kognvC-zjwnQ4OBx-5uqA@mail.gmail.com>
 <37CFB969-7A9A-486F-85EB-3B67A2809D09@stanford.edu>
 <961733e8-70f6-641b-deb8-9ee7eebb5fce@dclunie.com>
 <010001618f47e349-c4b0592f-f92a-4f0c-bc8c-0652dc43bf9c-000000@email.amazonses.com>
Message-ID: <37629F43-4AA3-4E7A-8D0B-7669DB275274@stanford.edu>

Hi David,

On Feb 13, 2018, at 5:08 AM, David Clunie <dclunie at dclunie.com<mailto:dclunie at dclunie.com>> wrote:

Thanks for explaining why the DCM "ontology" loads more
slowly initially. In this day and age, loading a flat
list of just under 4,000 entries shouldn't take noticeable
time, IMHO, but I understand that your implementation may not
be optimized for this pattern, and 7 seconds is not that
bad for the first response if it is cached afterwards.

However, through the web browser, if I "jump to" a term
after having loaded the top level, say "Segmentation", it
takes quite a few seconds to actually load the class and
quite a few seconds more to "jump to" it in the list.
Again I understand that this may be lack of optimization
for the "large flat list" case (choice of data structure,
size of nodes, indexing/insertion mechanism, re-sending the
list for the user interface frame rather than moving around
in what was already sent if content unchanged, etc.).


I wasn?t on the team when BioPortal was architected, so I can?t speak with complete authority regarding original design decisions. I think it?s fair to say that the ?Classes? tab in the BioPortal user interface wasn?t optimized for things on the far left of the ontology spectrum (catalogs, glossaries). It performs better with things a little farther along the spectrum (taxonomies, thesauri, etc.).

In terms of our REST API though, I?m not aware of any performance issues for ontologies like DCM with little or no hierarchy. The REST API is what applications like radlex.org<http://radlex.org> use to access BioPortal?s data.

If you?d like to verify that statement, I?ve listed example calls below that you can enter into a browser window, all of which are quite performant. Use of our REST API requires an API key, and there are instructions for getting one on our wiki:

https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key

Example REST calls for DCM

1). Get all classes:

http://data.bioontology.org/ontologies/DCM/classes

2). Get a particular class ("Segmentation"):

http://data.bioontology.org/ontologies/DCM/classes/http%3A%2F%2Fdicom.nema.org%2Fresources%2Fontology%2FDCM%2FSEG<http://data.bioontology.org/ontologies/DCM/classes/http://dicom.nema.org/resources/ontology/DCM/SEG>

3). Search for a particular class (?Linear spiculation?):

http://data.bioontology.org/search?q=Linear%20spiculation&ontologies=DCM



On the other hand, if I search for a term across all ontologies,
e.g., "Segmentation" it is pretty fast and finds the DCM class(es).
I assume this is because it a different index is used.


BioPortal only has one index, where each entry corresponds to an ontology class. The search page in the UI is fast because it?s a straight term search across ontologies. The classes page is slower because we?re issuing a different set of queries in order to place the class in the surrounding hierarchical structure, as well as retrieve associated data for display, e.g. notes, mappings, and properties.



One of these days we may make the DCM ontology into
a proper ontology, but mostly it is used as a grab bag
of independent concepts that are used when we can't find
concepts in a "real" ontology like SNOMED, LOINC, FMA or
NCIt, so it doesn't have a meaningful class "hierarchy" (yet),
and building one hasn't been a priority for us (in DICOM). I
have considered various mechanical ways to do this (e.g., using
the context group (value set) labels as pseudo-classes to
produce at least a two level hierarchy), but I haven't got
very far with that yet.

I haven't used the REST API myself.

The only other data point for speed is the RSNA's RadLex
term browser (http://www.radlex.org/) which is sometimes glacial,
and they attribute that to poor performance of Bioportal,
but I have no direct evidence of that myself, and the alleged
slowness does not manifest when using the Bioportal web
browser directly.

E.g., search for "spiculation" from the top level in the RadLex
ontology in Bioportal and compare that with doing the same at
www.radlex.org<http://www.radlex.org> ... I just tried it again and the latter just
says "Loading" forever, which is not uncommon.

I spent some time looking at the RadLex term browser in Chrome with the developer console open. When you start typing in the search box for the Radlex Tree Browser on the home page, they?re issuing calls to our REST API search endpoint to facilitate the autocomplete functionality. For example, I typed the characters ?drain?, and I can see in the Network tab of the developer console a REST call like the following:

http://data.bioontology.org/search?also_search_properties=true&ontologies=RADLEX&q=drain

? (API key parameter removed for privacy). I tested a number of these calls, entering different characters in the search box, and they're all returning in roughly 180 to 300ms. I don?t see any performance issue there.

The only way I was able to reproduce the behavior you describe was to enter a term in the search box, then click the search icon. After clicking the icon, the ?Loading?? dialog came up, and stayed up overnight until I finally killed the page. The Network tab showed no further traffic after clicking the Search icon, so it doesn?t appear that anything on the BioPortal side is causing the loading failure.

In order to investigate further, our technical program manager John Graybeal arranged a conference call with one of the main developers of radlex.org<http://radlex.org>. We spoke with him this morning, and via screen sharing were able to show the issue you describe. He acknowledged that it looked to be an issue on their side and is looking into it.

If there are any further issues in radlex.org<http://radlex.org> that anyone thinks are attributable to BioPortal, please don?t hesitate to post on this list.

Kind regards,
Jennifer



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From vendetti at stanford.edu  Wed Feb 21 18:07:23 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 22 Feb 2018 02:07:23 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
	Alsayed	Algergawy
In-Reply-To: <d0498e6a-8d85-3c75-efa6-0a697f286498@uni-jena.de>
References: <5a8c1ed71e6e5_27453ff148724c2c838a0@ncbo-prd-app-08.stanford.edu.mail>
 <18953BEA-0D99-4417-AEB7-3E8D688D318D@stanford.edu>
 <d0498e6a-8d85-3c75-efa6-0a697f286498@uni-jena.de>
Message-ID: <30AB4E54-D342-46DF-A116-B43203ACA038@stanford.edu>

Hello Dr. Algergawy,

We don?t have enough information from you yet to offer help.

When you say ?downloading ontologies?, what does this mean? Are you downloading ontology source files to disk? Or, are you retrieving class data from each ontology in Bioportal using the /classes endpoint?

Also, you say that your code fails reliably on the 110th ontology. Please add some log statements to your code that outputs which ontology you?re processing. We can?t do much if we don?t know which ontology is causing issues. In addition, please indicate the REST call that returns a 500 error. Also helpful would be some sort of a code snippet from you for the portion of the code that?s failing.

Kind regards,
Jennifer


On Feb 21, 2018, at 4:31 AM, Dr. Ing. Algergawy <alsayed.algergawy at uni-jena.de<mailto:alsayed.algergawy at uni-jena.de>> wrote:


Dear John,

many thanks for your reply. However, I expected the problem is not related to available resources to your or our sides. Since I have already one time to download the set of ontologies. Currently, the process of downloading is not completed especially when the number of downloaded ontologies reaches 110 with the following error message

" ERROR de.julielab.bioportal.ontologies.HttpHandler - Error when posting a request to BioPortal Server: Internal server error"

actually I tried many times with different API keys (for me and my colleagues), but the same problem remains.

I hope you can help me to discover what is the problem

yours,

alsayed

On 2/21/2018 2:35 AM, John Graybeal wrote:

Hi Alsayed,

It's hard to say without more information.

If you are using the API to load ontology content one page at a time, it can be extremely time consuming and resource-intensive to do that for an ontology with several hundred thousand to a million terms in it. While I expect some people have been successful, they probably took great care to space out their requests far apart, making sure one page came back before the next page was requested, and so on. (You might find useful tips searching the mail list, as similar questions have been addressed before.)

So if there is a resource issue, I can't tell you who is more short of resources, BioPortal or your system. My guess would be your system just doesn't have enough resources allocated at some point, or there could be a memory leak in your code. But that's just a guess based on my understanding that others have successfully downloaded all the ontologies.

In any case, the problem may be with ontology 110, than it is with the fact you have already downloaded 110 ontologies. But we don't know what ontology 110 is, so we can't tell you much about the possible issues.

If you want more detailed answers, you might want to include examples of your source code, the last dozen or so API requests that your code made, and the last few transmissions from BioPortal before the downloads stopped. And if your application is actually crashing, the crash log would provide valuable insights too. (If your application is crashing, that's probably the first place you should look, is your application and system logs.)

John


On Feb 20, 2018, at 5:12 AM, support at bioontology.org<mailto:support at bioontology.org><mailto:support at bioontology.org><mailto:support at bioontology.org> wrote:


Name: Alsayed Algergawy

Email: alsayed.algergawy at uni-jena.de<mailto:alsayed.algergawy at uni-jena.de><mailto:alsayed.algergawy at uni-jena.de><mailto:alsayed.algergawy at uni-jena.de>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org><http://2Fbioportal.bioontology.org><http://2fbioportal.bioontology.org/>%2Faccounts%2Falsayed

Feedback:

dear all,
I am trying to download the available set of ontologies on the Bioportal side using the available API. It works fine till downloading 110 ontologies, and the process crashes. Do you have any explanation for this behavior?
thank you in advance!!
yours,
alsayed

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu><mailto: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






--
Dr. Ing. Alsayed Algergawy

Institut f?r Informatik
Friedrich-Schiller-Universit?t Jena
http://fusion.cs.uni-jena.de<http://fusion.cs.uni-jena.de/>
alsayed.algergawy at uni-jena.de<mailto:alsayed.algergawy at uni-jena.de>
T: +49(0)3641-946438

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From vendetti at stanford.edu  Wed Feb 21 18:25:35 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 22 Feb 2018 02:25:35 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ulfschwarz
In-Reply-To: <CABfB3ijWOHH4L3EHWX5i=fFFuSe9BF=fjS8MDetUZJw-y3+Fwg@mail.gmail.com>
References: <5a82a744cc60e_320e3f8150a3561863984@ncbo-prd-app-08.stanford.edu.mail>
 <D038F4F3-80B1-4116-AF9D-E496BD429A46@stanford.edu>
 <CABfB3ii7SgOaS8+eAZDOX94takJ7AJ0_7BvoLCz-PO7fs_1YBQ@mail.gmail.com>
 <B130BA6B-BE2B-49CB-8365-5CF8B6A73B1E@stanford.edu>
 <CABfB3iiEsEnaR9jzJ8EobfJ47g_=OgBL1yoQ=MJdmw_+=z2W=g@mail.gmail.com>
 <913C55D6-2C77-4D48-8C65-578F983A7DE1@stanford.edu>
 <CABfB3ijY2UvzJO9mPOSBmrLzKUCKW0BCF8yvQbb=A+y81GsqVg@mail.gmail.com>
 <0486A1C2-3AC9-45DA-9F00-B5A120D7C050@stanford.edu>
 <CABfB3ijWOHH4L3EHWX5i=fFFuSe9BF=fjS8MDetUZJw-y3+Fwg@mail.gmail.com>
Message-ID: <258B94D7-0372-4367-B4D1-4BF541AFA49B@stanford.edu>

Hello Ulf,

Unfortunately, changing acronyms isn?t allowed. They are used as unique and unchangeable identifiers in the system. The only way to do this would be to create a new ontology entry with your desired acronym. Acronyms in BioPortal are always uppercase. Using VDOT_CORE is an option, though that?s the one you just asked me to delete. Let us know what you?d like to do.

Kind regards,
Jennifer



On Feb 21, 2018, at 1:19 AM, Ulf Schwarz <ulf.schwarz at ifomis.uni-saarland.de<mailto:ulf.schwarz at ifomis.uni-saarland.de>> wrote:

Thanks a lot Jennifer,

It looks fine now. I would like to change the acronym from VDOT to VDOT_core. How can I do that?

Best regards,

Ulf


On Feb 20, 2018, at 12:30 AM, Ulf Schwarz <ulf.schwarz at ifomis.uni-saarland.de<mailto:ulf.schwarz at ifomis.uni-saarland.de>> wrote:

Yes, I would like to delete both VDOT_CORE and TES


OK - I?ve deleted both of those ontology entries from our system.


and I would like to keep Viral Disease Ontology Trunk. Additionally I would like to change its setting from private to public once I checked that everything is fine.

It looks like the upload for the Viral Disease Ontology Trunk Ontology was successful now. Am I right?


No, I didn?t see any submissions associated with VDOT. I manually created one using the pull URL that you sent in a previous email, which seemed to process without errors. You can examine the result and let us know if you see any issues:

http://bioportal.bioontology.org/ontologies/VDOT/?p=summary

Kind regards,
Jennifer




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From Sina.Madani at vumc.org  Thu Feb 22 06:13:46 2018
From: Sina.Madani at vumc.org (Madani, Sina)
Date: Thu, 22 Feb 2018 14:13:46 +0000
Subject: [bioontology-support] Archived previous submissions
Message-ID: <90A9AC60-6690-458F-AE9D-F3E7F2271A52@vumc.org>

Hi,

Is there a way to prevent Ontoportal from archiving (inactivating the link of) previous submissions, in our local instance, when a new submission is uploaded and parsed?

Thanks!
Sina


[cid:image001.png at 01D3ABB5.0F4840A0]

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From vendetti at stanford.edu  Thu Feb 22 11:40:44 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 22 Feb 2018 19:40:44 +0000
Subject: [bioontology-support] Archived previous submissions
In-Reply-To: <90A9AC60-6690-458F-AE9D-F3E7F2271A52@vumc.org>
References: <90A9AC60-6690-458F-AE9D-F3E7F2271A52@vumc.org>
Message-ID: <232DB379-A26C-4EA2-9FAF-B78FF1B08192@stanford.edu>

Hi Sina,

No, I?m not aware of a way to do this. BioPortal was specifically architected to only serve the content of the latest submission of an ontology. It was felt that serving content for all submissions of ontologies wouldn?t scale well, e.g., BioPortal has close to 1000 ontologies, some of which are updated frequently and have submissions numbering anywhere from several hundred to just under 2000.

Kind regards,
Jennifer



On Feb 22, 2018, at 6:13 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi,

Is there a way to prevent Ontoportal from archiving (inactivating the link of) previous submissions, in our local instance, when a new submission is uploaded and parsed?

Thanks!
Sina


<image001.png>

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From support at bioontology.org  Thu Feb 22 12:03:02 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 22 Feb 2018 12:03:02 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Kati Carson
Message-ID: <5a8f21f64caea_7fda3ff5f68193dc8283f@ncbo-prd-app-09.stanford.edu.mail>

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From jgraybeal at stanford.edu  Thu Feb 22 13:47:15 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 22 Feb 2018 21:47:15 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Kati Carson
In-Reply-To: <5a8f21f64caea_7fda3ff5f68193dc8283f@ncbo-prd-app-09.stanford.edu.mail>
References: <5a8f21f64caea_7fda3ff5f68193dc8283f@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <77032DCB-C606-47C6-AAB6-C4CAB2FD6E52@stanford.edu>

Kati,

I assume you are considering creating a new entry for this ADI in the existing BioPortal?  Because the answer has several parts (hoping I have all these details right at this point!).

First, there is a way to specify the license wording explicitly in the metadata for the ontology, this is entered as part of the ontology submission information. If that's all you want, you can stop reading all the 'enhancement' ideas below.

As you know, though, the license words do not provide any enforcement. I know of no reasonable way to enforce this within BioPortal. Here are the options:

* If there are very few users expected, then you could make the ontology private until the user registers with you, then give them access on BioPortal one at a time (by adding them to the accession list by their BioPortal ID, one at a time). But they would not see the metadata for the private ontology, so no one would not see the ontology advertised unless they have permission to see it.

* Conversely, you could enter a metadata-only ontology, but then no one would see the content at all, and BioPortal couldn't make its services available for that ontology's terms. And there is no mechanism in BioPortal to constrain access to a full ontology until  the person has registered.  (Though definitely a feature to be considered.)  If you referred users to a site outside BioPortal, you could get them to register at that site if you wanted to collect their information before giving them access.

* If not too many users would be involved, you could mix both approaches by creating one BioPortal entry for the metadata, and another for the private ontology. That just seems wrong somehow, but I don't think we could fix BioPortal any time soon.

* Finally, in an extended variation, you could create your own BioPortal virtual appliance just for this ontology, and implement whatever rules you want for people to get accounts on it.

I would note that the thing that makes ontologies most valuable?the ability for anyone to interoperate with them in lots of different ways?also makes them all but ungovernable. But if you/HIPxChange are really motivated to make this happen, you could consult with us about adding a feature to enable what they want. I'm imagining any actual cost might be out of their price range, but I wanted to put that option on the table.

John


On Feb 22, 2018, at 12:03 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Kati Carson

Email: Katherine.Carson at seattlechildrens.org<mailto:Katherine.Carson at seattlechildrens.org>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:

My team is considering creating a bioportal for the Area Deprivation Index (ADI) based on 9-digit zip codes. This data is owned by HIPxChange who are interested in tracking those who use the data. Is it possible to do specific terms & agreements for specific ontologies?

Thanks
Kati

_______________________________________________
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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


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From support at bioontology.org  Sat Feb 24 11:40:44 2018
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 24 Feb 2018 11:40:44 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Davide Cirillo
Message-ID: <5a91bfbc3c972_1f043fa699ee01cc513e0@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Mon Feb 26 11:00:52 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 26 Feb 2018 19:00:52 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Davide Cirillo
In-Reply-To: <5a91bfbc3c972_1f043fa699ee01cc513e0@ncbo-prd-app-09.stanford.edu.mail>
References: <5a91bfbc3c972_1f043fa699ee01cc513e0@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <85D05BB8-3705-43C2-84A4-F46BE5030D48@stanford.edu>

Hello Davide,


On Feb 24, 2018, at 11:40 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Davide Cirillo

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FGO

Feedback:

I cannot find GO release 2013-07-01 at https://bioportal.bioontology.org/ontologies/GO

That release is instead available at ftp://ftp.geneontology.org/pub/go/ontology-archive/



BioPortal is configured to check the following URL nightly for new versions of GO:

http://purl.obolibrary.org/obo/go.obo

I don?t know what the difference is between this URL and the FTP address you list above. You would need to contact the ontology authors/maintainers to find out (http://help.geneontology.org/).

Kind regards,
Jennifer




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From support at bioontology.org  Wed Feb 28 00:03:54 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 28 Feb 2018 00:03:54 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Christian Kamann
Message-ID: <5a96626acdf36_7b163f9b1a5a5038404e3@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Wed Feb 28 03:37:35 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 28 Feb 2018 03:37:35 -0800
Subject: [bioontology-support] [BioPortal] Feedback from Ward Weistra
Message-ID: <5a96947fb793e_56293fcea5bf560410035@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Wed Feb 28 10:16:32 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 28 Feb 2018 18:16:32 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Ward Weistra
In-Reply-To: <5a96947fb793e_56293fcea5bf560410035@ncbo-prd-app-09.stanford.edu.mail>
References: <5a96947fb793e_56293fcea5bf560410035@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <8467B26E-A40F-4129-BCF7-E36D2C66AD5D@stanford.edu>

Hello Ward,

Apologies for the outage. BioPortal is back up.

Kind regards,
Jennifer



On Feb 28, 2018, at 3:37 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Ward Weistra

Email: ward at thehyve.nl<mailto:ward at thehyve.nl>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500

Feedback:

Hi!

Bioportal seems down. Could you please bring it back up?

Thanks for your work,
Ward

_______________________________________________
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From vendetti at stanford.edu  Wed Feb 28 12:08:06 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 28 Feb 2018 20:08:06 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Christian Kamann
In-Reply-To: <5a96626acdf36_7b163f9b1a5a5038404e3@ncbo-prd-app-08.stanford.edu.mail>
References: <5a96626acdf36_7b163f9b1a5a5038404e3@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <CF23B168-8608-4225-AAEF-4C7A4C93DF69@stanford.edu>

Hello Christian,

Are you referring to the ?Has finding site? property?

Here?s an example of a REST call that uses the include=all parameter to include property value pairs when retrieving data for a particular class:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F472763005?include=all<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/472763005?include=all>

I used as an example the ?Disorder of left atrium? class from SNOMEDCT. If you enter the above URL in a browser window, you can take a look at the JSON results and notice that there?s an array of property value pairs under ?properties?. You would need to loop through those to extract the value for the ?Has finding site? property.

The classes endpoint is documented here:

http://data.bioontology.org/documentation#Class

? and the general usage section of the documentation elaborates on common parameters like include=all, etc.:

 http://data.bioontology.org/documentation#nav_usage

Kind regards,
Jennifer


On Feb 28, 2018, at 12:03 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Christian Kamann

Email: christian.kamann at student.uni-luebeck.de<mailto:christian.kamann at student.uni-luebeck.de>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500

Feedback:

Hi,

I would like to extract the "Finding site" for specific SNOMED CT disorders via the API. Unfortunately I could not manage to figure out how this is possible. I am currently working on my master thesis and this would really help me a lot.

Thanks,
Christian

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From ward at thehyve.nl  Wed Feb 28 13:43:44 2018
From: ward at thehyve.nl (Ward Weistra)
Date: Wed, 28 Feb 2018 21:43:44 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Ward Weistra
In-Reply-To: <8467B26E-A40F-4129-BCF7-E36D2C66AD5D@stanford.edu>
References: <5a96947fb793e_56293fcea5bf560410035@ncbo-prd-app-09.stanford.edu.mail>
 <8467B26E-A40F-4129-BCF7-E36D2C66AD5D@stanford.edu>
Message-ID: <CAGG5KPwN3var5TuMhW-3U5AHfrZ39-iNqVi2nRxCWcWfcGwNnw@mail.gmail.com>

Very much appreciated! Love the API.

All best,
Ward

On Wed, Feb 28, 2018 at 7:16 PM Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Ward,
>
> Apologies for the outage. BioPortal is back up.
>
> Kind regards,
> Jennifer
>
>
>
> On Feb 28, 2018, at 3:37 AM, support at bioontology.org wrote:
>
> Name: Ward Weistra
>
> Email: ward at thehyve.nl <ward at thehyve.nl>
>
> Location: https%3A%2F%2Fbioportal.bioontology.org%2F500
>
>
> *Feedback:*
>
> Hi!
>
> Bioportal seems down. Could you please bring it back up?
>
> Thanks for your work,
> Ward
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> --

Ward Weistra | Team Lead Data Warehousing
*Out of office on Friday*

E.   ward at thehyve.nl
T.   +31 30 700 9713
W.  www.thehyve.nl
Skype. wardweistra | M. +1 347 979 2731 |  Twitter
<https://twitter.com/WardWeistra>. |  LinkedIn
<https://www.linkedin.com/in/wardweistra/>.
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