From babuken at gmail.com  Sun Jul  1 05:31:08 2018
From: babuken at gmail.com (Kenneth Babu)
Date: Sun, 1 Jul 2018 14:31:08 +0200
Subject: [bioontology-support] NCBO Mappings
In-Reply-To: <CAHDDsc+hKirKFvnwKaqNbLqpXqWD15-7N-+WD2Vg3DHWWZ7Ytw@mail.gmail.com>
References: <CAHDDscJaB4mP2W=+hZrd6BejECWNVo4hDhfNp7x6QM64Dua=YA@mail.gmail.com>
 <ADC72433-DA7B-44C9-93EE-1CB00C1AB46D@stanford.edu>
 <CAHDDscLzXUzByamgeQt4ni22OS0YYXkdaxypQ=k=xWnXeXJShw@mail.gmail.com>
 <CAHDDscJZsH7ozT5-3KzSPSk+Bprua_=zD-vASMC7UoM4Q0ph=w@mail.gmail.com>
 <E36C2D72-CC35-411F-8DCE-894D3B511353@stanford.edu>
 <CAHDDsc+d-TMU4S7T5+c9bO7fD7B2Vi3sYhyj2r776f4v9Ys6UQ@mail.gmail.com>
 <CAHDDscJr2eQsrLC628SoN909KpH=zGdMzi065zh4-RvGo7LAOw@mail.gmail.com>
 <04C5C450-3A78-4FA4-8027-9300F20074BF@stanford.edu>
 <CAHDDsc+hKirKFvnwKaqNbLqpXqWD15-7N-+WD2Vg3DHWWZ7Ytw@mail.gmail.com>
Message-ID: <CAHDDsc+QaNQQOgSPvGirVdr=yBKJddSRD2cUEU3w7ho+AB7asg@mail.gmail.com>

Hi Michael,
Is it possible to perform a mapping of an  ontology in a local disk
against NCBO ontologies. Say if I have a local ontology in OWL/OBO format
is possible to find matching terms in other ontologies that are available
on the NCBO Rest API?


On Sun, Jul 1, 2018 at 12:23 PM, Kenneth Babu <babuken at gmail.com> wrote:

> Thanks Michael. I'll have a look.
>
> On Fri, Jun 29, 2018 at 8:32 PM, Michael Dorf <mdorf at stanford.edu> wrote:
>
>> Hi Kenneth,
>>
>> Here is a paper that describes the LOOM mapping algorithm in depth. It?s
>> a bit dated, but the LOOM algorithm hasn?t really changed since then:
>>
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815474/
>>
>> And here is our basic Wiki page that has a concise description:
>>
>> https://www.bioontology.org/wiki/BioPortal_Mappings
>>
>> Hope these work for you.
>>
>> Thanks!
>>
>> Michael
>>
>>
>> On Jun 29, 2018, at 8:58 AM, Kenneth Babu <babuken at gmail.com> wrote:
>>
>> Hi Michael,
>> Is there an article that describes the mapping algorithm? I see the
>> source as 'LOOM'. I'd very much like to have a look at the algorithm.
>>
>>
>>
>
>
> --
> Kenneth Babu Opap
> CBIO Division
> Integrated Biomedical Sciences Dept.
> Health Sciences Campus
> University of Cape Town
> Werner Beit North
> N1.04.1
> Observatory
> Cape Town,
> South Africa
>
>
>


-- 
Kenneth Babu Opap
CBIO Division
Integrated Biomedical Sciences Dept.
Health Sciences Campus
University of Cape Town
Werner Beit North
N1.04.1
Observatory
Cape Town,
South Africa
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From mdorf at stanford.edu  Mon Jul  2 08:46:00 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Mon, 2 Jul 2018 15:46:00 +0000
Subject: [bioontology-support] NCBO Mappings
In-Reply-To: <CAHDDsc+QaNQQOgSPvGirVdr=yBKJddSRD2cUEU3w7ho+AB7asg@mail.gmail.com>
References: <CAHDDscJaB4mP2W=+hZrd6BejECWNVo4hDhfNp7x6QM64Dua=YA@mail.gmail.com>
 <ADC72433-DA7B-44C9-93EE-1CB00C1AB46D@stanford.edu>
 <CAHDDscLzXUzByamgeQt4ni22OS0YYXkdaxypQ=k=xWnXeXJShw@mail.gmail.com>
 <CAHDDscJZsH7ozT5-3KzSPSk+Bprua_=zD-vASMC7UoM4Q0ph=w@mail.gmail.com>
 <E36C2D72-CC35-411F-8DCE-894D3B511353@stanford.edu>
 <CAHDDsc+d-TMU4S7T5+c9bO7fD7B2Vi3sYhyj2r776f4v9Ys6UQ@mail.gmail.com>
 <CAHDDscJr2eQsrLC628SoN909KpH=zGdMzi065zh4-RvGo7LAOw@mail.gmail.com>
 <04C5C450-3A78-4FA4-8027-9300F20074BF@stanford.edu>
 <CAHDDsc+hKirKFvnwKaqNbLqpXqWD15-7N-+WD2Vg3DHWWZ7Ytw@mail.gmail.com>
 <CAHDDsc+QaNQQOgSPvGirVdr=yBKJddSRD2cUEU3w7ho+AB7asg@mail.gmail.com>
Message-ID: <73B8D67A-0AA1-4938-BE95-9B93C252876A@stanford.edu>

Hi Kenneth,

The best thing to do in this case would be for you to submit your ontology to BioPortal. If you don?t want it visible to the outside world, just mark it as ?private?.  Once the ontology is processed on our end, you should be able to use the aforementioned mappings service, with your ontology as one of the sources.

Michael


On Jul 1, 2018, at 5:31 AM, Kenneth Babu <babuken at gmail.com<mailto:babuken at gmail.com>> wrote:

Hi Michael,
Is it possible to perform a mapping of an  ontology in a local disk  against NCBO ontologies. Say if I have a local ontology in OWL/OBO format is possible to find matching terms in other ontologies that are available on the NCBO Rest API?


On Sun, Jul 1, 2018 at 12:23 PM, Kenneth Babu <babuken at gmail.com<mailto:babuken at gmail.com>> wrote:
Thanks Michael. I'll have a look.

On Fri, Jun 29, 2018 at 8:32 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Kenneth,

Here is a paper that describes the LOOM mapping algorithm in depth. It?s a bit dated, but the LOOM algorithm hasn?t really changed since then:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815474/

And here is our basic Wiki page that has a concise description:

https://www.bioontology.org/wiki/BioPortal_Mappings

Hope these work for you.

Thanks!

Michael


On Jun 29, 2018, at 8:58 AM, Kenneth Babu <babuken at gmail.com<mailto:babuken at gmail.com>> wrote:

Hi Michael,
Is there an article that describes the mapping algorithm? I see the source as 'LOOM'. I'd very much like to have a look at the algorithm.





--
Kenneth Babu Opap
CBIO Division
Integrated Biomedical Sciences Dept.
Health Sciences Campus
University of Cape Town
Werner Beit North
N1.04.1
Observatory
Cape Town,
South Africa





--
Kenneth Babu Opap
CBIO Division
Integrated Biomedical Sciences Dept.
Health Sciences Campus
University of Cape Town
Werner Beit North
N1.04.1
Observatory
Cape Town,
South Africa



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From support at bioontology.org  Tue Jul  3 20:14:33 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 03 Jul 2018 20:14:33 -0700
Subject: [bioontology-support] [BioPortal] Feedback from vmluan
Message-ID: <5b3c3b99123f9_39a23f9e284d81806145f@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Thu Jul  5 07:51:48 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 05 Jul 2018 07:51:48 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Dominick Leone
Message-ID: <5b3e30842e98c_61b33febf5de0f64819d8@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Jul  5 11:09:04 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 18:09:04 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Dominick Leone
In-Reply-To: <5b3e30842e98c_61b33febf5de0f64819d8@ncbo-prd-app-08.stanford.edu.mail>
References: <5b3e30842e98c_61b33febf5de0f64819d8@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <F030C52C-2764-4EC9-A755-40B8EDE2A33D@stanford.edu>

Hello Dominick,

Yes, we had an outage with our PURL server. It?s back online now. The URL you list below is accessible for me. Let us know if you?re continuing to have difficulties.

Kind regards,
Jennifer



On Jul 5, 2018, at 7:51 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Dominick Leone

Email: Dominick.Leone at Channing.harvard.edu<mailto:Dominick.Leone at Channing.harvard.edu>

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

Feedback:

Greetings,

Are you currently experiencing difficulties with the following domain: http://purl.bioontology.org/ontology

I was attempting to access http://purl.bioontology.org/ontology/SURGICAL and received the following error messages:
Proxy Error

The proxy server received an invalid response from an upstream server.
"The proxy server could not handle the request GET /ontology/SURGICAL.

Reason: Error reading from remote server"

I was accessing these resources from https://bioportal.bioontology.org/ontologies/SURGICAL.

Thank you!

Regards,
Dominick Leone

_______________________________________________
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  Thu Jul  5 11:12:18 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 18:12:18 +0000
Subject: [bioontology-support] [BioPortal] Feedback from vmluan
In-Reply-To: <5b3c3b99123f9_39a23f9e284d81806145f@ncbo-prd-app-09.stanford.edu.mail>
References: <5b3c3b99123f9_39a23f9e284d81806145f@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <12033794-6627-4B2D-ADDF-31BA966279FD@stanford.edu>

Hello,

We had an outage with one of our servers, but it?s back online. I?m able to see MEDDRA without issue now:

https://bioportal.bioontology.org/ontologies/MEDDRA?p=classes

Are you still experiencing difficulties?

Jennifer



On Jul 3, 2018, at 8:14 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: vmluan

Email: vominhluan88 at gmail.com<mailto:vominhluan88 at gmail.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500%3Fp%3Dclasses%26conceptid%3D10047700

Feedback:

I cannot access to MEDDRA ontology as before. Could you please explain what happened?

_______________________________________________
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 hoppesyd at umich.edu  Thu Jul  5 11:48:38 2018
From: hoppesyd at umich.edu (Sydney Hoppe)
Date: Thu, 5 Jul 2018 13:48:38 -0500
Subject: [bioontology-support] Help Deleting Troublesome Ontologies
Message-ID: <CACcE1G_adb7y9hbF2WwiSDzqkcinv6MyFQrfgZmQQUt6_Z84Xg@mail.gmail.com>

Hello,

I have ran into a rather large issue: I attempted to delete an ontology but
at some point the delete failed, but was halfway complete. Let me give a
bit of further background.

Currently my submissions API page returns a 500 Internal Server Error.
Through further investigation I have determined that the error stems from
an uncaught exception produced in the
/srv/ncbo/ontologies_api/current/helpers/application_helper.rb file in the
retrieve_latest_submissions function on line 350. Within this function
there is a loop "submission.each do |sub|". After a few iterations of the
loop an error is thrown. The error is as follows :

class: Goo::Base::AttributeNotLoaded

message: Persistent object with `acronym` not loaded

For a while I was unable to determine which ontology this statement was
referring to because, as it states, there is no acronym loaded for that
particular ontology. But, I was able to print out the Description
associated with the ontology and I have determined which ontology I am
struggling with. (Which one it is does not necessarily matter, lets call it
Ontology XYZ). I Continued to search my local bioportal instance for
Ontology XYZ but it is nowhere to be found, not even in the API. I tried to
re-delete Ontology XYZ but, an ontology with that acronym can not be found.

To summarize, while attempting to delete Ontology XYZ the delete failed,
and I am now left with an ontology in my system that has no acronym
associated with it.

Now to my question, Is there any other way to delete an ontology without
using their acronym? (Perhaps with some other piece of data about the
ontology?)

Thank you for your help!
-- 
*Sydney Hoppe*
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu | 614.282.1314
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From vendetti at stanford.edu  Thu Jul  5 11:52:27 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 18:52:27 +0000
Subject: [bioontology-support] Help Deleting Troublesome Ontologies
In-Reply-To: <CACcE1G_adb7y9hbF2WwiSDzqkcinv6MyFQrfgZmQQUt6_Z84Xg@mail.gmail.com>
References: <CACcE1G_adb7y9hbF2WwiSDzqkcinv6MyFQrfgZmQQUt6_Z84Xg@mail.gmail.com>
Message-ID: <C64277AE-BFAF-4FED-847B-7FFEF4191195@stanford.edu>

Hello Sydney,

Could you please clarify for us if you?re working on the main BioPortal, or a virtual appliance instance?

Jennifer



On Jul 5, 2018, at 11:48 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hello,

I have ran into a rather large issue: I attempted to delete an ontology but at some point the delete failed, but was halfway complete. Let me give a bit of further background.

Currently my submissions API page returns a 500 Internal Server Error. Through further investigation I have determined that the error stems from an uncaught exception produced in the /srv/ncbo/ontologies_api/current/helpers/application_helper.rb file in the retrieve_latest_submissions function on line 350. Within this function there is a loop "submission.each do |sub|". After a few iterations of the loop an error is thrown. The error is as follows :

class: Goo::Base::AttributeNotLoaded
message: Persistent object with `acronym` not loaded

For a while I was unable to determine which ontology this statement was referring to because, as it states, there is no acronym loaded for that particular ontology. But, I was able to print out the Description associated with the ontology and I have determined which ontology I am struggling with. (Which one it is does not necessarily matter, lets call it Ontology XYZ). I Continued to search my local bioportal instance for Ontology XYZ but it is nowhere to be found, not even in the API. I tried to re-delete Ontology XYZ but, an ontology with that acronym can not be found.

To summarize, while attempting to delete Ontology XYZ the delete failed, and I am now left with an ontology in my system that has no acronym associated with it.

Now to my question, Is there any other way to delete an ontology without using their acronym? (Perhaps with some other piece of data about the ontology?)

Thank you for your help!
--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314
_______________________________________________
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  Thu Jul  5 11:57:32 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 18:57:32 +0000
Subject: [bioontology-support] Help Deleting Troublesome Ontologies
In-Reply-To: <C64277AE-BFAF-4FED-847B-7FFEF4191195@stanford.edu>
References: <CACcE1G_adb7y9hbF2WwiSDzqkcinv6MyFQrfgZmQQUt6_Z84Xg@mail.gmail.com>
 <C64277AE-BFAF-4FED-847B-7FFEF4191195@stanford.edu>
Message-ID: <70033CA2-33F7-457E-81CA-B41AB2A21E8A@stanford.edu>

Apologies - you already included that information and I missed it upon first reading.

Are you issuing a REST API call to delete the ontology? Or, are you doing it via a console session, as described here:

https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_delete_an_ontology.3F

Jennifer



On Jul 5, 2018, at 11:52 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Sydney,

Could you please clarify for us if you?re working on the main BioPortal, or a virtual appliance instance?

Jennifer



On Jul 5, 2018, at 11:48 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hello,

I have ran into a rather large issue: I attempted to delete an ontology but at some point the delete failed, but was halfway complete. Let me give a bit of further background.

Currently my submissions API page returns a 500 Internal Server Error. Through further investigation I have determined that the error stems from an uncaught exception produced in the /srv/ncbo/ontologies_api/current/helpers/application_helper.rb file in the retrieve_latest_submissions function on line 350. Within this function there is a loop "submission.each do |sub|". After a few iterations of the loop an error is thrown. The error is as follows :

class: Goo::Base::AttributeNotLoaded
message: Persistent object with `acronym` not loaded

For a while I was unable to determine which ontology this statement was referring to because, as it states, there is no acronym loaded for that particular ontology. But, I was able to print out the Description associated with the ontology and I have determined which ontology I am struggling with. (Which one it is does not necessarily matter, lets call it Ontology XYZ). I Continued to search my local bioportal instance for Ontology XYZ but it is nowhere to be found, not even in the API. I tried to re-delete Ontology XYZ but, an ontology with that acronym can not be found.

To summarize, while attempting to delete Ontology XYZ the delete failed, and I am now left with an ontology in my system that has no acronym associated with it.

Now to my question, Is there any other way to delete an ontology without using their acronym? (Perhaps with some other piece of data about the ontology?)

Thank you for your help!
--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314
_______________________________________________
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  Thu Jul  5 12:08:27 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 19:08:27 +0000
Subject: [bioontology-support] Help Deleting Troublesome Ontologies
In-Reply-To: <CACcE1G8+B=ShWGPrU-E1X0zWBnKBmvVgKdzJuiaYv6EUmi6tVA@mail.gmail.com>
References: <CACcE1G_adb7y9hbF2WwiSDzqkcinv6MyFQrfgZmQQUt6_Z84Xg@mail.gmail.com>
 <C64277AE-BFAF-4FED-847B-7FFEF4191195@stanford.edu>
 <70033CA2-33F7-457E-81CA-B41AB2A21E8A@stanford.edu>
 <CACcE1G8+B=ShWGPrU-E1X0zWBnKBmvVgKdzJuiaYv6EUmi6tVA@mail.gmail.com>
Message-ID: <60FA0665-FFD1-4BCE-86BD-11392CFC0F52@stanford.edu>

Are you able to access the ontology object from a console session using the following syntax:

ont = LinkedData::Models::Ontology.find(RDF::URI.new("http://data.bioontology.org/ontologies/IEV")).first

You would need to replace the URL passed to the new() method with your domain name and your problematic ontology acronym. If you get an object back, you should then be able to call delete on it.

Jennifer



On Jul 5, 2018, at 11:59 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Originally I was issuing a REST API call in order to delete the ontology. When that failed I have since tried both methods

On Thu, Jul 5, 2018 at 1:57 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Apologies - you already included that information and I missed it upon first reading.

Are you issuing a REST API call to delete the ontology? Or, are you doing it via a console session, as described here:

https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_delete_an_ontology.3F

Jennifer



On Jul 5, 2018, at 11:52 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Sydney,

Could you please clarify for us if you?re working on the main BioPortal, or a virtual appliance instance?

Jennifer



On Jul 5, 2018, at 11:48 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hello,

I have ran into a rather large issue: I attempted to delete an ontology but at some point the delete failed, but was halfway complete. Let me give a bit of further background.

Currently my submissions API page returns a 500 Internal Server Error. Through further investigation I have determined that the error stems from an uncaught exception produced in the /srv/ncbo/ontologies_api/current/helpers/application_helper.rb file in the retrieve_latest_submissions function on line 350. Within this function there is a loop "submission.each do |sub|". After a few iterations of the loop an error is thrown. The error is as follows :

class: Goo::Base::AttributeNotLoaded
message: Persistent object with `acronym` not loaded

For a while I was unable to determine which ontology this statement was referring to because, as it states, there is no acronym loaded for that particular ontology. But, I was able to print out the Description associated with the ontology and I have determined which ontology I am struggling with. (Which one it is does not necessarily matter, lets call it Ontology XYZ). I Continued to search my local bioportal instance for Ontology XYZ but it is nowhere to be found, not even in the API. I tried to re-delete Ontology XYZ but, an ontology with that acronym can not be found.

To summarize, while attempting to delete Ontology XYZ the delete failed, and I am now left with an ontology in my system that has no acronym associated with it.

Now to my question, Is there any other way to delete an ontology without using their acronym? (Perhaps with some other piece of data about the ontology?)

Thank you for your help!
--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314
_______________________________________________
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




--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314

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From support at bioontology.org  Thu Jul  5 12:06:29 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 05 Jul 2018 12:06:29 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Risa Sayre
Message-ID: <5b3e6c358d9dd_6e803fe64c52aba86665f@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Jul  5 15:06:58 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 22:06:58 +0000
Subject: [bioontology-support] Help Deleting Troublesome Ontologies
In-Reply-To: <CACcE1G8O6uXpM-MKrcZU-=P3MFiEHq7iQZx42X=sD2LYeCSzBw@mail.gmail.com>
References: <CACcE1G_adb7y9hbF2WwiSDzqkcinv6MyFQrfgZmQQUt6_Z84Xg@mail.gmail.com>
 <C64277AE-BFAF-4FED-847B-7FFEF4191195@stanford.edu>
 <70033CA2-33F7-457E-81CA-B41AB2A21E8A@stanford.edu>
 <CACcE1G8+B=ShWGPrU-E1X0zWBnKBmvVgKdzJuiaYv6EUmi6tVA@mail.gmail.com>
 <60FA0665-FFD1-4BCE-86BD-11392CFC0F52@stanford.edu>
 <CACcE1G_D+6XB3fbkxrfvj2gM21srxHnU4+j7Mhsb=aTm2kbNCw@mail.gmail.com>
 <CACcE1G8O6uXpM-MKrcZU-=P3MFiEHq7iQZx42X=sD2LYeCSzBw@mail.gmail.com>
Message-ID: <53754A5E-B46E-4AAF-AECD-E4AE6AAE29BC@stanford.edu>

Hi Sydney,

I?m glad it?s working for you now.

If you run into anything similar in the future, another issue could be a corrupt entry in the cache. You can clear the application caches via the ?Admin" page in the user interface:


[cid:2F751492-B7CE-49BF-AACB-C1008A4CFCB7 at stanford.edu]
For Goo::Base::AttributeNotLoaded errors, you?d want to try flushing the Goo cache.

Another item of potential interest is turning on more extensive logging in order to debug issues like the one you saw. You would need to uncomment a couple of lines in your unicorn.rb file, i.e.:

https://github.com/ncbo/virtual_appliance/blob/master/appliance_config/ontologies_api/config/unicorn.rb#L11

? and restart your system.

Kind regards,
Jennifer



On Jul 5, 2018, at 1:48 PM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hello!

I just wanted to send an update with a very simple fix. (So simple that it just went right over my head). Because my local instance did not recognize that Ontology XYZ existed, it did not object to me submitting a 'new' ontology with the same name and data. This solved the issue!

Thanks for taking the time to help me out.

Best,

Sydney

On Thu, Jul 5, 2018 at 2:15 PM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:
unfortunately that returns 'nil'

On Thu, Jul 5, 2018 at 2:08 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Are you able to access the ontology object from a console session using the following syntax:

ont = LinkedData::Models::Ontology.find(RDF::URI.new("http://data.bioontology.org/ontologies/IEV")).first

You would need to replace the URL passed to the new() method with your domain name and your problematic ontology acronym. If you get an object back, you should then be able to call delete on it.

Jennifer



On Jul 5, 2018, at 11:59 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Originally I was issuing a REST API call in order to delete the ontology. When that failed I have since tried both methods

On Thu, Jul 5, 2018 at 1:57 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Apologies - you already included that information and I missed it upon first reading.

Are you issuing a REST API call to delete the ontology? Or, are you doing it via a console session, as described here:

https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#How_do_I_delete_an_ontology.3F

Jennifer



On Jul 5, 2018, at 11:52 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Sydney,

Could you please clarify for us if you?re working on the main BioPortal, or a virtual appliance instance?

Jennifer



On Jul 5, 2018, at 11:48 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hello,

I have ran into a rather large issue: I attempted to delete an ontology but at some point the delete failed, but was halfway complete. Let me give a bit of further background.

Currently my submissions API page returns a 500 Internal Server Error. Through further investigation I have determined that the error stems from an uncaught exception produced in the /srv/ncbo/ontologies_api/current/helpers/application_helper.rb file in the retrieve_latest_submissions function on line 350. Within this function there is a loop "submission.each do |sub|". After a few iterations of the loop an error is thrown. The error is as follows :

class: Goo::Base::AttributeNotLoaded
message: Persistent object with `acronym` not loaded

For a while I was unable to determine which ontology this statement was referring to because, as it states, there is no acronym loaded for that particular ontology. But, I was able to print out the Description associated with the ontology and I have determined which ontology I am struggling with. (Which one it is does not necessarily matter, lets call it Ontology XYZ). I Continued to search my local bioportal instance for Ontology XYZ but it is nowhere to be found, not even in the API. I tried to re-delete Ontology XYZ but, an ontology with that acronym can not be found.

To summarize, while attempting to delete Ontology XYZ the delete failed, and I am now left with an ontology in my system that has no acronym associated with it.

Now to my question, Is there any other way to delete an ontology without using their acronym? (Perhaps with some other piece of data about the ontology?)

Thank you for your help!
--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314
_______________________________________________
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




--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314




--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314



--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314

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From hoppesyd at umich.edu  Thu Jul  5 14:57:46 2018
From: hoppesyd at umich.edu (Sydney Hoppe)
Date: Thu, 5 Jul 2018 16:57:46 -0500
Subject: [bioontology-support] Swagger Documentation
Message-ID: <CACcE1G9s38f91ssBQeUXYcZ8siOkKi1SmxQDEX_vm6VSR0vd6A@mail.gmail.com>

Hello!

I am looking to create a Python Client so that other services I am using
can more easily use the REST API. (I am currently working on a Virtual
Appliance).  I was wondering if you had any type of either Python Clients
already written or Swagger documentation already ready to go.

Thanks,

-- 
*Sydney Hoppe*
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu | 614.282.1314
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From hoppesyd at umich.edu  Thu Jul  5 14:53:13 2018
From: hoppesyd at umich.edu (Sydney Hoppe)
Date: Thu, 5 Jul 2018 16:53:13 -0500
Subject: [bioontology-support] Upgrading AWS VS from 2.4 to 2.5
Message-ID: <CACcE1G_T6f=nam0_x9jSqbKH=h=MuDkn_7rq5KOUpuvuBYeNnQ@mail.gmail.com>

Hello,

I am hoping to upgrade the AWS virtual appliance I have from version 2.4 to
2.5. Do you have any tips/tricks, or experience doing this? I am hoping to
do it with as much ease as possible.

Thanks,

-- 
*Sydney Hoppe*
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu | 614.282.1314
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From vendetti at stanford.edu  Thu Jul  5 15:25:40 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 22:25:40 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Risa Sayre
In-Reply-To: <5b3e6c358d9dd_6e803fe64c52aba86665f@ncbo-prd-app-08.stanford.edu.mail>
References: <5b3e6c358d9dd_6e803fe64c52aba86665f@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <2AFAD84A-C5E3-4487-A19F-31C1A3677B06@stanford.edu>

Hello Risa,

Thanks for pointing that out. The link has been repaired.

Kind regards,
Jennifer



On Jul 5, 2018, at 12:06 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Risa Sayre

Email: sayre.risa at epa.gov<mailto:sayre.risa at epa.gov>

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

Feedback:

The page http://bioportal.bioontology.org/ontologies/EXO links to http://purl.bioontology.org/ontology/EXO, which is a dead link.

_______________________________________________
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  Thu Jul  5 15:37:04 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 22:37:04 +0000
Subject: [bioontology-support] Upgrading AWS VS from 2.4 to 2.5
In-Reply-To: <CACcE1G_T6f=nam0_x9jSqbKH=h=MuDkn_7rq5KOUpuvuBYeNnQ@mail.gmail.com>
References: <CACcE1G_T6f=nam0_x9jSqbKH=h=MuDkn_7rq5KOUpuvuBYeNnQ@mail.gmail.com>
Message-ID: <D6BF92D8-BD9B-4545-A638-D28150F51044@stanford.edu>

Hi Sydney,


> On Jul 5, 2018, at 2:53 PM, Sydney Hoppe <hoppesyd at umich.edu> wrote:
> 
> Hello,
> 
> I am hoping to upgrade the AWS virtual appliance I have from version 2.4 to 2.5. Do you have any tips/tricks, or experience doing this? I am hoping to do it with as much ease as possible.


Here is the scenario that has worked best for appliance users to date:

1. Leave your 2.4 version running.

2. Separately install and run 2.5 so that both versions are running simultaneously.

3. Run a script that imports ontologies from your older 2.4 version to 2.5. The script is ?bioportal_ontologies_import.rb? and you?ll need to fill in values for a few variables:

SOURCE_API
SOURCE_APIKEY
TARGET_API
ONTOLOGIES_TO_IMPORT (array of ontology acronyms for ontologies you want to import to your 2.5 version)

Note that this script will only import ontology data to your new 2.5 version. It won?t import user objects, etc. Unfortunately we haven?t had the resources to write comprehensive data migration scripts.

Kind regards,
Jennifer


From vendetti at stanford.edu  Thu Jul  5 15:42:54 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 22:42:54 +0000
Subject: [bioontology-support] Swagger Documentation
In-Reply-To: <CACcE1G9s38f91ssBQeUXYcZ8siOkKi1SmxQDEX_vm6VSR0vd6A@mail.gmail.com>
References: <CACcE1G9s38f91ssBQeUXYcZ8siOkKi1SmxQDEX_vm6VSR0vd6A@mail.gmail.com>
Message-ID: <B988DFE8-1052-46B2-B56A-85A95207C96C@stanford.edu>

Hi Sydney,


On Jul 5, 2018, at 2:57 PM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hello!

I am looking to create a Python Client so that other services I am using can more easily use the REST API. (I am currently working on a Virtual Appliance).  I was wondering if you had any type of either Python Clients already written or Swagger documentation already ready to go.


I don?t think we have what you?re asking for. The autogenerated documentation we have for the REST API was a homegrown solution, not Swagger:

http://data.bioontology.org/documentation

There?s some example code for interacting with our REST API in Python 2 and 3 in our GitHub repository:

https://github.com/ncbo/ncbo_rest_sample_code/tree/master/python

Not sure if that would be useful to you.

Kind regards,
Jennifer

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From vendetti at stanford.edu  Thu Jul  5 16:49:30 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 5 Jul 2018 23:49:30 +0000
Subject: [bioontology-support] Upgrading AWS VS from 2.4 to 2.5
In-Reply-To: <CACcE1G-ou7YcBE9BEY6=TT6KhhMG=ojzz9CgZCGLDubO2a4pqA@mail.gmail.com>
References: <CACcE1G_T6f=nam0_x9jSqbKH=h=MuDkn_7rq5KOUpuvuBYeNnQ@mail.gmail.com>
 <D6BF92D8-BD9B-4545-A638-D28150F51044@stanford.edu>
 <CACcE1G-ou7YcBE9BEY6=TT6KhhMG=ojzz9CgZCGLDubO2a4pqA@mail.gmail.com>
Message-ID: <99EF50A0-F713-4B7E-972D-7744E8EA3DDF@stanford.edu>

Hi Sydney,


On Jul 5, 2018, at 3:42 PM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hi Jennifer,

Unfortunately Bioportal 2.5 is not yet available on the AWS marketplace. How/where else can I run Bioportal 2.5?


Currently we have 2.5 available for download in OVF format. If you provide your BioPortal user account name and some other basic information detailed here:

https://www.bioontology.org/wiki/Category:NCBO_Virtual_Appliance#Getting_Started

? we give you access to the download page. You would need some kind of virtualization software installed like VMWare, Virtual Box, etc. in order to import the OVF file and run.

Is this a possibility for you?

Jennifer

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From kushida at biosciencedbc.jp  Sun Jul  8 16:40:30 2018
From: kushida at biosciencedbc.jp (Tatsuya Kushida)
Date: Mon, 9 Jul 2018 08:40:30 +0900
Subject: [bioontology-support] Ontology mapping
Message-ID: <CAJuGyWnmbDzOboNw+3TdyYE5JUYYVk3vP6wBF3vd=+9UY28Q+Q@mail.gmail.com>

Dear BioPortal staffs,

I'm a developer of IOBC (http://purl.bioontology.org/ontology/IOBC).
Can I ask you a question? How can I do mapping my ontology terms to
other ontology ones? I worry that my ontology mapping fully has not
been done yet (https://bioportal.bioontology.org/ontologies/IOBC/?p=mappings).


Best regards,
Tatsuya

--
Tatsuya Kushida, Ph.D.
National Bioscience Database Center (NBDC),
Japan SCIENCE AND TECHNOLOGY AGENCY (JST)
5-3, Yonbancho, Chiyoda-ku, Tokyo 102-0081, JAPAN
Phone: +81 3 5214 8491 FAX: 81 3 5214 8470
http://www.jst.go.jp/EN/index.html
http://biosciencedbc.jp/en/
t2kushida at jst.go.jp
kushida at biosciencedbc.jp

From support at bioontology.org  Sun Jul  8 17:45:07 2018
From: support at bioontology.org (support at bioontology.org)
Date: Sun, 08 Jul 2018 17:45:07 -0700
Subject: [bioontology-support] [BioPortal] Feedback from mconlon
Message-ID: <5b42b01317873_4fd53fdc10605af0935ee@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Mon Jul  9 06:44:47 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 09 Jul 2018 06:44:47 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Jeffrey Borrebach
Message-ID: <5b4366cfd2e8e_4823fcb1d710c00927f1@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Mon Jul  9 09:38:57 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 9 Jul 2018 16:38:57 +0000
Subject: [bioontology-support] Ontology mapping
In-Reply-To: <CAJuGyWnmbDzOboNw+3TdyYE5JUYYVk3vP6wBF3vd=+9UY28Q+Q@mail.gmail.com>
References: <CAJuGyWnmbDzOboNw+3TdyYE5JUYYVk3vP6wBF3vd=+9UY28Q+Q@mail.gmail.com>
Message-ID: <54BBD023-519D-4D54-81C9-316856CCF33D@stanford.edu>

Hello Tatsuya,


On Jul 8, 2018, at 4:40 PM, Tatsuya Kushida <kushida at biosciencedbc.jp<mailto:kushida at biosciencedbc.jp>> wrote:

Dear BioPortal staffs,

I'm a developer of IOBC (http://purl.bioontology.org/ontology/IOBC).
Can I ask you a question? How can I do mapping my ontology terms to
other ontology ones?


Mappings are automatically generated when you submit an ontology to BioPortal. You can also manually create mappings using our REST API:

http://data.bioontology.org/documentation#Mapping

We have example code for programmatically creating mappings in our GitHub sample code repository:

https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/CreateMapping.java



I worry that my ontology mapping fully has not
been done yet (https://bioportal.bioontology.org/ontologies/IOBC/?p=mappings).


If you let us know what you think is missing, we could perhaps better comment on this point.

Kind regards,
Jennifer


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From vendetti at stanford.edu  Mon Jul  9 09:42:38 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 9 Jul 2018 16:42:38 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mconlon
In-Reply-To: <5b42b01317873_4fd53fdc10605af0935ee@ncbo-prd-app-09.stanford.edu.mail>
References: <5b42b01317873_4fd53fdc10605af0935ee@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <21D2FE05-E728-435B-97CA-E1307AD12D7A@stanford.edu>

Hi Mike,

On Jul 8, 2018, at 5:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

I'd like to update the information for the VIVO ontology, listed in bioportal here: https://bioportal.bioontology.org/ontologies/VIVO

Stella worked on the project some time back and submitted the entry. I've been the project director since 2015 and lead the ontology development effort. Would be helpful if I could upload the current version and upload the metadata.



Sure, no problem - we can make you an administrator for this ontology. Please let us know your BioPortal account name that you?d like us to use for the administrative privileges. If you haven?t created an account yet, you can do so at this page:

https://bioportal.bioontology.org/accounts/new

Kind regards,
Jennifer


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From vendetti at stanford.edu  Mon Jul  9 09:47:37 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 9 Jul 2018 16:47:37 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jeffrey
	Borrebach
In-Reply-To: <5b4366cfd2e8e_4823fcb1d710c00927f1@ncbo-prd-app-08.stanford.edu.mail>
References: <5b4366cfd2e8e_4823fcb1d710c00927f1@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <8757C3ED-CD7E-477D-9887-7EF5B9B43C13@stanford.edu>

Hello Jeffrey,

We?re currently in the process of importing releases 2017AB and 2018AA. We hope to have these newer versions available sometime in the next month. In the mean time, 2017AA is the most recent we?re serving. You can follow our progress in the relevant GitHub issues:

https://github.com/ncbo/bioportal-project/issues/60
https://github.com/ncbo/bioportal-project/issues/73

Kind regards,
Jennifer



On Jul 9, 2018, at 6:44 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jeffrey Borrebach

Email: borrebachjd2 at upmc.edu<mailto:borrebachjd2 at upmc.edu>

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

Feedback:

For the CPT ontology, it seems I can only access "2017AA". Is there a way for me to access other years (assuming that's even possible)? Thank you for your help!

_______________________________________________
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 mconlon at ufl.edu  Mon Jul  9 09:52:47 2018
From: mconlon at ufl.edu (Conlon, Mike)
Date: Mon, 9 Jul 2018 16:52:47 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mconlon
In-Reply-To: <21D2FE05-E728-435B-97CA-E1307AD12D7A@stanford.edu>
References: <5b42b01317873_4fd53fdc10605af0935ee@ncbo-prd-app-09.stanford.edu.mail>
 <21D2FE05-E728-435B-97CA-E1307AD12D7A@stanford.edu>
Message-ID: <37FAD35D-C321-46F9-A61D-4D6FB8EE4376@ufl.edu>

Jennifer,

My bioportal account name is mconlon at ufl.edu

Thanks!

Mike

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Monday, July 9, 2018 at 12:42 PM
To: "support at bioontology.org" <support at bioontology.org>
Cc: "Conlon, Mike" <mconlon at ufl.edu>
Subject: Re: [bioontology-support] [BioPortal] Feedback from mconlon

Hi Mike,


On Jul 8, 2018, at 5:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:
I'd like to update the information for the VIVO ontology, listed in bioportal here: https://bioportal.bioontology.org/ontologies/VIVO<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_VIVO&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VS4ultS9qpvz6EXJZ2Kmi5uqojirZ0dGQXsulpgq_OM&s=H6pt__X0Pw1-LpNku1RNxLadAAf1uD6yeB27ZOZ2B5U&e=>
Stella worked on the project some time back and submitted the entry. I've been the project director since 2015 and lead the ontology development effort. Would be helpful if I could upload the current version and upload the metadata.



Sure, no problem - we can make you an administrator for this ontology. Please let us know your BioPortal account name that you?d like us to use for the administrative privileges. If you haven?t created an account yet, you can do so at this page:

https://bioportal.bioontology.org/accounts/new<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_accounts_new&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VS4ultS9qpvz6EXJZ2Kmi5uqojirZ0dGQXsulpgq_OM&s=nCAesjmEuqZlp9GEa9Hmqr-mdzWxSqEVOWJVu1yOfb8&e=>

Kind regards,
Jennifer


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From vendetti at stanford.edu  Mon Jul  9 10:02:24 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 9 Jul 2018 17:02:24 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mconlon
In-Reply-To: <37FAD35D-C321-46F9-A61D-4D6FB8EE4376@ufl.edu>
References: <5b42b01317873_4fd53fdc10605af0935ee@ncbo-prd-app-09.stanford.edu.mail>
 <21D2FE05-E728-435B-97CA-E1307AD12D7A@stanford.edu>
 <37FAD35D-C321-46F9-A61D-4D6FB8EE4376@ufl.edu>
Message-ID: <88361D0E-C027-4C52-83FF-FE149742D9E3@stanford.edu>

Hi Mike,

I?ve added your account as an administrator to VIVO. If you refresh your browser at the summary page (https://bioportal.bioontology.org/ontologies/VIVO), you should now see links like ?Edit ontology information?, ?Add submission?, etc.

Kind regards,
Jennifer


On Jul 9, 2018, at 9:52 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Jennifer,

My bioportal account name is mconlon at ufl.edu<mailto:mconlon at ufl.edu>

Thanks!

Mike

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Date: Monday, July 9, 2018 at 12:42 PM
To: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Cc: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from mconlon

Hi Mike,


On Jul 8, 2018, at 5:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:
I'd like to update the information for the VIVO ontology, listed in bioportal here: https://bioportal.bioontology.org/ontologies/VIVO<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_VIVO&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VS4ultS9qpvz6EXJZ2Kmi5uqojirZ0dGQXsulpgq_OM&s=H6pt__X0Pw1-LpNku1RNxLadAAf1uD6yeB27ZOZ2B5U&e=>
Stella worked on the project some time back and submitted the entry. I've been the project director since 2015 and lead the ontology development effort. Would be helpful if I could upload the current version and upload the metadata.



Sure, no problem - we can make you an administrator for this ontology. Please let us know your BioPortal account name that you?d like us to use for the administrative privileges. If you haven?t created an account yet, you can do so at this page:

https://bioportal.bioontology.org/accounts/new<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_accounts_new&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VS4ultS9qpvz6EXJZ2Kmi5uqojirZ0dGQXsulpgq_OM&s=nCAesjmEuqZlp9GEa9Hmqr-mdzWxSqEVOWJVu1yOfb8&e=>

Kind regards,
Jennifer

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From mconlon at ufl.edu  Mon Jul  9 10:04:34 2018
From: mconlon at ufl.edu (Conlon, Mike)
Date: Mon, 9 Jul 2018 17:04:34 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mconlon
In-Reply-To: <88361D0E-C027-4C52-83FF-FE149742D9E3@stanford.edu>
References: <5b42b01317873_4fd53fdc10605af0935ee@ncbo-prd-app-09.stanford.edu.mail>
 <21D2FE05-E728-435B-97CA-E1307AD12D7A@stanford.edu>
 <37FAD35D-C321-46F9-A61D-4D6FB8EE4376@ufl.edu>
 <88361D0E-C027-4C52-83FF-FE149742D9E3@stanford.edu>
Message-ID: <2F5B134F-90AD-48DD-9F57-0FD63E2D2C62@ufl.edu>

Got it!

Thanks,

Mike

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Monday, July 9, 2018 at 1:02 PM
To: "Conlon, Mike" <mconlon at ufl.edu>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from mconlon

Hi Mike,

I?ve added your account as an administrator to VIVO. If you refresh your browser at the summary page (https://bioportal.bioontology.org/ontologies/VIVO<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_VIVO&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=HpKq2GWpm5jhO0zyB7wxmMmNe2Eqv41xOuywTKklfNo&s=xzuE0kZ7KW5jG7b30iOpqrrd5JXBy_hYnZaebCTAgIM&e=>), you should now see links like ?Edit ontology information?, ?Add submission?, etc.

Kind regards,
Jennifer



On Jul 9, 2018, at 9:52 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Jennifer,

My bioportal account name is mconlon at ufl.edu<mailto:mconlon at ufl.edu>

Thanks!

Mike

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Date: Monday, July 9, 2018 at 12:42 PM
To: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Cc: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from mconlon

Hi Mike,



On Jul 8, 2018, at 5:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:
I'd like to update the information for the VIVO ontology, listed in bioportal here: https://bioportal.bioontology.org/ontologies/VIVO<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_VIVO&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VS4ultS9qpvz6EXJZ2Kmi5uqojirZ0dGQXsulpgq_OM&s=H6pt__X0Pw1-LpNku1RNxLadAAf1uD6yeB27ZOZ2B5U&e=>
Stella worked on the project some time back and submitted the entry. I've been the project director since 2015 and lead the ontology development effort. Would be helpful if I could upload the current version and upload the metadata.



Sure, no problem - we can make you an administrator for this ontology. Please let us know your BioPortal account name that you?d like us to use for the administrative privileges. If you haven?t created an account yet, you can do so at this page:

https://bioportal.bioontology.org/accounts/new<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_accounts_new&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VS4ultS9qpvz6EXJZ2Kmi5uqojirZ0dGQXsulpgq_OM&s=nCAesjmEuqZlp9GEa9Hmqr-mdzWxSqEVOWJVu1yOfb8&e=>

Kind regards,
Jennifer

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From vendetti at stanford.edu  Mon Jul  9 10:14:21 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 9 Jul 2018 17:14:21 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jeffrey
	Borrebach
In-Reply-To: <BYAPR08MB4024DEA58DD982EE064AA385F7440@BYAPR08MB4024.namprd08.prod.outlook.com>
References: <5b4366cfd2e8e_4823fcb1d710c00927f1@ncbo-prd-app-08.stanford.edu.mail>
 <8757C3ED-CD7E-477D-9887-7EF5B9B43C13@stanford.edu>
 <BYAPR08MB4024DEA58DD982EE064AA385F7440@BYAPR08MB4024.namprd08.prod.outlook.com>
Message-ID: <21B56830-6F4F-4ABB-B938-678FFF8A66B3@stanford.edu>

Hi Jeffrey,


On Jul 9, 2018, at 10:01 AM, Borrebach, Jeffrey <borrebachjd2 at upmc.edu<mailto:borrebachjd2 at upmc.edu>> wrote:

Jennifer,

I appreciate your assistance on the matter. Is it possible to access past years such as 2015/16, or are old submissions gone forever once new submissions are imported?


We only serve data from the latest release uploaded into our system (currently 2017AA).


If possible, I would like to look up certain codes that were used prior to 2017 but have since been obsoleted. Thank you again for your help!


If you?re a current UMLS license holder, we may be able to provide you with a download link for ontology source files from earlier releases (they would be in TTL format).

Licenses are free and you can sign up here:

https://www.nlm.nih.gov/databases/umls.html#license_request

If you think this would be of use to you, please contact our Technical Program Manager John Graybeal (jgraybeal at stanford.edu<http://stanford.edu>).

Kind regards,
Jennifer

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From Simon.Vanderschaeghe at uzgent.be  Tue Jul 10 06:04:36 2018
From: Simon.Vanderschaeghe at uzgent.be (Vanderschaeghe Simon)
Date: Tue, 10 Jul 2018 13:04:36 +0000
Subject: [bioontology-support] BioPortal: Questions
Message-ID: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?


*         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using "Jump To" in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?



*         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org reacts differently depending on whether the user is logged in or not. For instance, when searching for the term "Event"<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:

o   Not logged in: expected behavior

o   Logged in: error message "We're sorry but something has gone wrong. We have been notified of this error."



*         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


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From jgraybeal at stanford.edu  Tue Jul 10 11:25:51 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 10 Jul 2018 18:25:51 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
Message-ID: <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term ?Event? and Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

?         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using ?Jump To? in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

?         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term ?Event?<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

?         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be/> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


_______________________________________________
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  Tue Jul 10 17:15:23 2018
From: swt at stanford.edu (Samson Tu)
Date: Wed, 11 Jul 2018 00:15:23 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
Message-ID: <4DAE8CC1-14DB-4BF7-9103-78B9B83FC5AD@stanford.edu>

Hi,

On Jul 10, 2018, at 11:25 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:


some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,


Bioportal got its ICD-10 resource from UMLS. This is probably a problem with UMLS rather with WHO?s ICD-10. If you search WHO?s online ICD-10 browser [1], 'Primary thrombophilia' and 'Other thrombophilia' are subcategories of ?Other coagulation defects?.  ICD-10CM, as published by the National Center for Health Statistics, also contains these two concepts. However, UMLS 2018AA doesn?t seem to have these two terms as part of ICD-10 (according to the Metathesaurus Browser hosted at NLM). I find this discrepancy rather surprising. It?s up to whoever maintains UMLS to explain or correct these missing concepts.

With best regards,
Samson

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From jgraybeal at stanford.edu  Wed Jul 11 09:11:14 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 11 Jul 2018 16:11:14 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>,
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
Message-ID: <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>

Yes, Samson?s suggestion is a good one.

I understand your frustration about what is and isn?t included. This is an inherent ambiguity in semantic artifacts, which is deliberately exploited?but with opposing intentions?by different ontology builders, many of which intentionally gather terms from multiple sources in an ontology.

Thinking further about what you want to achieve, you could create a View in a BioPortal ontology of just the STY terms you want to be accessed. I may reply to the list with more details, just so people know of this option.

John

________________________________
From: Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be> on behalf of redcap <redcap at uzgent.be>
Sent: Wednesday, July 11, 2018 12:09:27 AM
To: John Graybeal
Cc: Samson Tu; support at bioontology.org; redcap
Subject: RE: [bioontology-support] BioPortal: Questions

Hi John,


?         I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I look for ?Event? in the ATC index<https://www.whocc.no/atc_ddd_index/>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.
For example, the first result of the request https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102 is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}



?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true



o   Not logged in
[cid:image001.png at 01D418F5.E61BE930]


o   Logged in
[cid:image004.png at 01D418F6.DE19C800]


?         Regarding the missing classes in ICD10, I don?t think contacting info at who.int<mailto:info at who.int> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact ?whoever maintains UMLS to explain or correct these missing concepts?.

Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: dinsdag 10 juli 2018 20:26
Aan: Vanderschaeghe Simon <Simon.Vanderschaeghe at UZGENT.be>
CC: support at bioontology.org; redcap <redcap at UZGENT.be>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term ?Event? and Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

?         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using ?Jump To? in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

?         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term ?Event?<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

?         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be/> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


_______________________________________________
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  Wed Jul 11 10:16:30 2018
From: swt at stanford.edu (Samson Tu)
Date: Wed, 11 Jul 2018 17:16:30 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
Message-ID: <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>

Hi,

When I searched NLM?s Metathesaurus browser for ?Antibiotic? with ATC as the source terminology, I didn't get STY?s Antibiotic in the results. In that respect Bioportal?s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal?s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?

With best regards,
Samson


On Jul 11, 2018, at 9:11 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Yes, Samson?s suggestion is a good one.

I understand your frustration about what is and isn?t included. This is an inherent ambiguity in semantic artifacts, which is deliberately exploited?but with opposing intentions?by different ontology builders, many of which intentionally gather terms from multiple sources in an ontology.

Thinking further about what you want to achieve, you could create a View in a BioPortal ontology of just the STY terms you want to be accessed. I may reply to the list with more details, just so people know of this option.

John

________________________________
From: Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> on behalf of redcap <redcap at uzgent.be<mailto:redcap at uzgent.be>>
Sent: Wednesday, July 11, 2018 12:09:27 AM
To: John Graybeal
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; redcap
Subject: RE: [bioontology-support] BioPortal: Questions

Hi John,

?         I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I look for ?Event? in the ATC index<https://www.whocc.no/atc_ddd_index/>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.
For example, the first result of the request https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102 is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}



?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true



o   Not logged in
<image001.png>

o   Logged in
<image004.png>

?         Regarding the missing classes in ICD10, I don?t think contacting info at who.int<mailto:info at who.int> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact ?whoever maintains UMLS to explain or correct these missing concepts?.

Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: dinsdag 10 juli 2018 20:26
Aan: Vanderschaeghe Simon <Simon.Vanderschaeghe at UZGENT.be<mailto:erschaeghe at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term ?Event? and Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

?         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using ?Jump To? in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

?         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term ?Event?<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

?         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be/> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


_______________________________________________
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 redcap at uzgent.be  Wed Jul 11 00:09:27 2018
From: redcap at uzgent.be (redcap)
Date: Wed, 11 Jul 2018 07:09:27 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
Message-ID: <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>

Hi John,


?         I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I look for ?Event? in the ATC index<https://www.whocc.no/atc_ddd_index/>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.
For example, the first result of the request https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102 is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}



?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true



o   Not logged in
[cid:image001.png at 01D418F5.E61BE930]


o   Logged in
[cid:image004.png at 01D418F6.DE19C800]


?         Regarding the missing classes in ICD10, I don?t think contacting info at who.int<mailto:info at who.int> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact ?whoever maintains UMLS to explain or correct these missing concepts?.

Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: dinsdag 10 juli 2018 20:26
Aan: Vanderschaeghe Simon <Simon.Vanderschaeghe at UZGENT.be>
CC: support at bioontology.org; redcap <redcap at UZGENT.be>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term ?Event? and Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

?         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using ?Jump To? in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

?         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term ?Event?<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

?         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be/> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


_______________________________________________
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 jgraybeal at stanford.edu  Wed Jul 11 14:00:45 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 11 Jul 2018 21:00:45 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
 <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
Message-ID: <A0C10FAA-E2C4-4429-9605-E80529C48036@stanford.edu>

Thanks very much for this followup Samson. The only 'documentation' of which I am aware is the repository itself for the conversion software (https://github.com/ncbo/umls2rdf). I'm not seeing any documentation there; https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py is the relevant code I believe.

Your research suggests we need to take a closer look at this (while recognizing it was written by others, who have since left the team), though to be honest we will be constrained by resources for at least a while. We will welcome any further input you or Simon care to offer to improve our understanding.

John


On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

Hi,

When I searched NLM?s Metathesaurus browser for ?Antibiotic? with ATC as the source terminology, I didn't get STY?s Antibiotic in the results. In that respect Bioportal?s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal?s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?

With best regards,
Samson


On Jul 11, 2018, at 9:11 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Yes, Samson?s suggestion is a good one.

I understand your frustration about what is and isn?t included. This is an inherent ambiguity in semantic artifacts, which is deliberately exploited?but with opposing intentions?by different ontology builders, many of which intentionally gather terms from multiple sources in an ontology.

Thinking further about what you want to achieve, you could create a View in a BioPortal ontology of just the STY terms you want to be accessed. I may reply to the list with more details, just so people know of this option.

John

________________________________
From: Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> on behalf of redcap <redcap at uzgent.be<mailto:redcap at uzgent.be>>
Sent: Wednesday, July 11, 2018 12:09:27 AM
To: John Graybeal
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; redcap
Subject: RE: [bioontology-support] BioPortal: Questions

Hi John,

?         I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I look for ?Event? in the ATC index<https://www.whocc.no/atc_ddd_index/>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.
For example, the first result of the request https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102 is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}



?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true



o   Not logged in
<image001.png>

o   Logged in
<image004.png>

?         Regarding the missing classes in ICD10, I don?t think contacting info at who.int<mailto:info at who.int> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact ?whoever maintains UMLS to explain or correct these missing concepts?.

Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: dinsdag 10 juli 2018 20:26
Aan: Vanderschaeghe Simon <Simon.Vanderschaeghe at UZGENT.be<mailto:erschaeghe at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term ?Event? and Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

?         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using ?Jump To? in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

?         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term ?Event?<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

?         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be/> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


_______________________________________________
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 swt at stanford.edu  Wed Jul 11 16:57:15 2018
From: swt at stanford.edu (Samson Tu)
Date: Wed, 11 Jul 2018 23:57:15 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <A0C10FAA-E2C4-4429-9605-E80529C48036@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
 <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
 <A0C10FAA-E2C4-4429-9605-E80529C48036@stanford.edu>
Message-ID: <AE60FA8A-474E-4503-8BB5-13CD09F55B0A@stanford.edu>

Hi John,

I downloaded ATC from Bioportal and also took a very cursory look at umls2rdf.py ( < 1 minute). What I saw was that NCBO, for whatever reason, models ATC concepts with ?hasSTY? object property. So, for example, (Potassium hasSTY ?Pharmacoloic Substance?) and (Potassium hasSTY ?Inorganic Chemical?) and umls2rdf.py contains flags like ?HAS_STY? and codes for dealing with STY. I think  Bioportal?s ATC contains STY because of the ?hasSTY? relation it introduces.

My expectation is that the original ATC doesn?t contain the hasSTY relation. My guess is that, in trying to make an UMLS-sourced terminology into more of an ?ontology? that includes the UMLS-derived semantic types, the Bioportal version of the terminology is ?augmented" with STY concepts that are showing up in search results. I wonder whether this is true of all UMLS-derived terminologies in Bioportal. Maybe someone can check.

I know that NCBO has limited resource. Someone with more urgent need for the ?original? versions of UMLS-derived terminologies such as ATC may want to examine the umls2rdf.py code to see how inclusion of STY can be turned off in the extraction process.

With best regards,
Samson


On Jul 11, 2018, at 2:00 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Thanks very much for this followup Samson. The only 'documentation' of which I am aware is the repository itself for the conversion software (https://github.com/ncbo/umls2rdf). I'm not seeing any documentation there; https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py is the relevant code I believe.

Your research suggests we need to take a closer look at this (while recognizing it was written by others, who have since left the team), though to be honest we will be constrained by resources for at least a while. We will welcome any further input you or Simon care to offer to improve our understanding.

John


On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

Hi,

When I searched NLM?s Metathesaurus browser for ?Antibiotic? with ATC as the source terminology, I didn't get STY?s Antibiotic in the results. In that respect Bioportal?s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal?s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?

With best regards,
Samson


On Jul 11, 2018, at 9:11 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Yes, Samson?s suggestion is a good one.

I understand your frustration about what is and isn?t included. This is an inherent ambiguity in semantic artifacts, which is deliberately exploited?but with opposing intentions?by different ontology builders, many of which intentionally gather terms from multiple sources in an ontology.

Thinking further about what you want to achieve, you could create a View in a BioPortal ontology of just the STY terms you want to be accessed. I may reply to the list with more details, just so people know of this option.

John

________________________________
From: Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> on behalf of redcap <redcap at uzgent.be<mailto:redcap at uzgent.be>>
Sent: Wednesday, July 11, 2018 12:09:27 AM
To: John Graybeal
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; redcap
Subject: RE: [bioontology-support] BioPortal: Questions

Hi John,

?         I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I look for ?Event? in the ATC index<https://www.whocc.no/atc_ddd_index/>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.
For example, the first result of the request https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102 is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}



?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true



o   Not logged in
<image001.png>

o   Logged in
<image004.png>

?         Regarding the missing classes in ICD10, I don?t think contacting info at who.int<mailto:info at who.int> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact ?whoever maintains UMLS to explain or correct these missing concepts?.

Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: dinsdag 10 juli 2018 20:26
Aan: Vanderschaeghe Simon <Simon.Vanderschaeghe at UZGENT.be<mailto:erschaeghe at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term ?Event? and Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

?         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using ?Jump To? in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

?         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term ?Event?<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

?         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be/> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


_______________________________________________
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 vendetti at stanford.edu  Wed Jul 11 17:25:58 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 12 Jul 2018 00:25:58 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
 <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
Message-ID: <329F8ABC-B087-4D9D-9EF2-DB7F4A163795@stanford.edu>

Hi Samson,


On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

When I searched NLM?s Metathesaurus browser for ?Antibiotic? with ATC as the source terminology, I didn't get STY?s Antibiotic in the results. In that respect Bioportal?s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal?s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?


Each time the UMLS releases a new version (e.g., 2018AA), we use their MetamorphoSys installation wizard [1] to install a local copy of the relational database that contains source vocabulary data.

We then execute a Python program [2] that reads data out of that relational database and generates ontology files for each of the source vocabularies. These ontologies are written in RDF (Turtle syntax) and are in turn consumable by the BioPortal application. The developer that wrote the Python program is no longer here, so I can?t speak with complete authority on this topic. I?ll try to add some information to this thread after doing some initial research today. The UMLS relational database has an ?MRSTY? table with an ?STY? column that provides semantic type information for terms. For example, I can execute a search in the MRSTY table for CUI C0282686 (class from ATC with label ?RESPIRATORY SYSTEM DRUGS?), and see that they provide semantic type data in the result:


[cid:81C939D2-C7A6-4343-BA99-4353C0ECB641 at stanford.edu]


It appears that our Python program includes semantic type data in the ontology files. I looked at the TTL file for the ATC ontology and can see the class declaration for Event:

<http://purl.bioontology.org/ontology/STY/T051> a owl:Class ;
skos:notation "T051"^^xsd:string ;
skos:prefLabel "Event"@en .

This sort of semantic type information is displayed by the UMLS Metathesaurus Browser on the right-hand side:


[cid:BD4651B4-E667-4D31-80D5-73ED6572B169 at stanford.edu]



Best,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html
[2] https://github.com/ncbo/umls2rdf




With best regards,
Samson


On Jul 11, 2018, at 9:11 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Yes, Samson?s suggestion is a good one.

I understand your frustration about what is and isn?t included. This is an inherent ambiguity in semantic artifacts, which is deliberately exploited?but with opposing intentions?by different ontology builders, many of which intentionally gather terms from multiple sources in an ontology.

Thinking further about what you want to achieve, you could create a View in a BioPortal ontology of just the STY terms you want to be accessed. I may reply to the list with more details, just so people know of this option.

John

________________________________
From: Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> on behalf of redcap <redcap at uzgent.be<mailto:redcap at uzgent.be>>
Sent: Wednesday, July 11, 2018 12:09:27 AM
To: John Graybeal
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; redcap
Subject: RE: [bioontology-support] BioPortal: Questions

Hi John,

?         I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I look for ?Event? in the ATC index<https://www.whocc.no/atc_ddd_index/>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.
For example, the first result of the request https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102 is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}



?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true



o   Not logged in
<image001.png>

o   Logged in
<image004.png>

?         Regarding the missing classes in ICD10, I don?t think contacting info at who.int<mailto:info at who.int> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact ?whoever maintains UMLS to explain or correct these missing concepts?.

Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: dinsdag 10 juli 2018 20:26
Aan: Vanderschaeghe Simon <Simon.Vanderschaeghe at UZGENT.be<mailto:erschaeghe at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term ?Event? and Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

?         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using ?Jump To? in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

?         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term ?Event?<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

?         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be/> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


_______________________________________________
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  Wed Jul 11 23:53:54 2018
From: swt at stanford.edu (Samson Tu)
Date: Thu, 12 Jul 2018 06:53:54 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <329F8ABC-B087-4D9D-9EF2-DB7F4A163795@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
 <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
 <329F8ABC-B087-4D9D-9EF2-DB7F4A163795@stanford.edu>
Message-ID: <70A67CC6-3A35-4963-94AC-FC08E589C71E@stanford.edu>

Hi Jennifer,

For me, the question is not whether the Metathesaurus browser display semantic type information of an UMLS concept derived from a terminology. The question is why Bioportal should model semantic type information as part of a terminology?s representation as an ontology, and therefore include STY as part of the ontology. First, when NCBO makes a UMLS-derived terminology available on Bioportal, is the expectation that it has UMLS-augmented relations or that it has only relations that are in the original terminology? Until today I didn?t realize that UMSL-derived terminologies I download from Bioportal have extra concepts that are not in the original terminology. Second, why isn?t it sufficient to encode the semantic types as string annotations (as it does already)? Doing so would avoid the problem of unexpected concepts turning up in search results.

I suspect that there are good reasons for the design choices made in the UMLS-terminology-extraction code. In any case, we probably have to live with the constraints imposed by these choices. It is better that we clarify that UMLS-derived terminologies on Bioportal, by design, have STY included so that semantic type information is explicitly modeled. Those who need a ?clean? version probably can adapt the UMLS-terminology-extraction code to get different versions of the terminologies. (Or they need to filter out STY concepts in search results obtained from Bioportal. Or Bioportal search API can do the filtering.)

With best regards,
Samson


On Jul 11, 2018, at 5:25 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Samson,


On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

When I searched NLM?s Metathesaurus browser for ?Antibiotic? with ATC as the source terminology, I didn't get STY?s Antibiotic in the results. In that respect Bioportal?s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal?s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?


Each time the UMLS releases a new version (e.g., 2018AA), we use their MetamorphoSys installation wizard [1] to install a local copy of the relational database that contains source vocabulary data.

We then execute a Python program [2] that reads data out of that relational database and generates ontology files for each of the source vocabularies. These ontologies are written in RDF (Turtle syntax) and are in turn consumable by the BioPortal application. The developer that wrote the Python program is no longer here, so I can?t speak with complete authority on this topic. I?ll try to add some information to this thread after doing some initial research today. The UMLS relational database has an ?MRSTY? table with an ?STY? column that provides semantic type information for terms. For example, I can execute a search in the MRSTY table for CUI C0282686 (class from ATC with label ?RESPIRATORY SYSTEM DRUGS?), and see that they provide semantic type data in the result:


<Screenshot 2018-07-11 16.58.22.png>


It appears that our Python program includes semantic type data in the ontology files. I looked at the TTL file for the ATC ontology and can see the class declaration for Event:

<http://purl.bioontology.org/ontology/STY/T051> a owl:Class ;
skos:notation "T051"^^xsd:string ;
skos:prefLabel "Event"@en .

This sort of semantic type information is displayed by the UMLS Metathesaurus Browser on the right-hand side:


<Screenshot 2018-07-11 17.21.29.png>



Best,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html
[2] https://github.com/ncbo/umls2rdf


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From mdorf at stanford.edu  Thu Jul 12 04:58:39 2018
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 12 Jul 2018 11:58:39 +0000
Subject: [bioontology-support] Reg: sending of query about the annotator
In-Reply-To: <CACqU87FWiiO2W55t+o7C6idwG4s98UAqHDcyw_rVWA6aHQoBgw@mail.gmail.com>
References: <CACqU87FWiiO2W55t+o7C6idwG4s98UAqHDcyw_rVWA6aHQoBgw@mail.gmail.com>
Message-ID: <D18C3A4C-4140-432E-A1F0-ADECC5C70891@stanford.edu>

Hi Spelmen,

Thank you for contacting us again.  I am currently away from the office.  In general, please direct all your BioPortal related questions to support at bioontology.org<mailto:support at bioontology.org> instead of my personal mailbox. Someone on our staff should be able to help.

Thanks!

Michael


On Jul 12, 2018, at 1:48 AM, spellz . <spelmen at gmail.com<mailto:spelmen at gmail.com>> wrote:

Dear sir,
                  I have done all the works programticaly but it took more time to write as xml file.

for ex: for writing 600 kb of xml file it took more than 4 hours.
Kindly do the needful.



Thanks & Regards,
SPELMEN VIMALRAJ S
Ph.D Research Scholar
Department Of Computer Science
Bharathiar University
coimbatore-46
Ph: 8807650056


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From andon.tchechmedjiev at lirmm.fr  Thu Jul 12 05:25:30 2018
From: andon.tchechmedjiev at lirmm.fr (Andon Tchechmedjiev)
Date: Thu, 12 Jul 2018 14:25:30 +0200
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <70A67CC6-3A35-4963-94AC-FC08E589C71E@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
 <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
 <329F8ABC-B087-4D9D-9EF2-DB7F4A163795@stanford.edu>
 <70A67CC6-3A35-4963-94AC-FC08E589C71E@stanford.edu>
Message-ID: <23F91C03-6651-44EB-B2A2-609CBE3A3A37@lirmm.fr>

Dear Samson, 

Generally speaking, the ontologies and terminologies integrated into UMLS become distinct entities compared to the source ontologies and terminologies and should never be considered as canonical (there are numerous differences that aren?t always obvious at first) when used in applications. As Jennifer stated, semantic types and CUIs are pieces of information intrinsic to UMLS and relevant for the resources in BioPortal that were extracted from UMLS. The reason for including the umls:hasSty and umls:cui properties is to enable the BioPortal Annotator to use this information to filter annotations based on semantic types, which is an extremely common use-case and an important feature. You will notice that the aforementioned properties live in their own namespace: "@prefix umls: <http://bioportal.bioontology.org/ontologies/umls/> .?, while everything else lives in "http://purl.bioontology.org/ontology/ACRONYM?. This is actually the right way of of doing things as far as ontology engineering standards and practices go, as opposed to an ad-hoc string encoding of the information (a bad practice that makes querying with SPARQL much less practical). 

The proper (semantically enabled) way of dealing with this for applications that rely on the ?purity? of the terminological information is to discard anything that lives outside of the namespace of the terminology or ontology of interest (i.e. only keeping entities that are in "http://purl.bioontology.org/ontology/ACRONYM? in the case of BioPortal ontologies extracted from UMLS). The fact that STY concepts appear in the search results and the concept hierarchy and the fact that this is problematic or inconvenient for some specific applications are different issues altogether, however. Changing the behaviour of BioPortal because of an issue with one specific use-case among many (others may be reliant on this specific behaviour) wouldn?t necessarily be the most logical solution. In this instance, if the behaviour is problematic for redcap users, fixing the issue directly in redcap?s BioPortal adapter by filtering all concepts in the umls prefix namespace would very likely be the simplest solution.

Best Regards, 
Andon


?
Andon Tchechmedjiev, PhD. Postdoctoral researcher in Natural Language Processing in the Biomedical Domain at LIRMM, Office 3/164, B?t. 5 - 860 rue de St Priest 34095 Montpellier cedex 5,  FRANCE | andon.tchechmedjiev.eu

> On 12 Jul 2018, at 08:53, Samson Tu <swt at stanford.edu> wrote:
> 
> Hi Jennifer,
> 
> For me, the question is not whether the Metathesaurus browser display semantic type information of an UMLS concept derived from a terminology. The question is why Bioportal should model semantic type information as part of a terminology?s representation as an ontology, and therefore include STY as part of the ontology. First, when NCBO makes a UMLS-derived terminology available on Bioportal, is the expectation that it has UMLS-augmented relations or that it has only relations that are in the original terminology? Until today I didn?t realize that UMSL-derived terminologies I download from Bioportal have extra concepts that are not in the original terminology. Second, why isn?t it sufficient to encode the semantic types as string annotations (as it does already)? Doing so would avoid the problem of unexpected concepts turning up in search results.
> 
> I suspect that there are good reasons for the design choices made in the UMLS-terminology-extraction code. In any case, we probably have to live with the constraints imposed by these choices. It is better that we clarify that UMLS-derived terminologies on Bioportal, by design, have STY included so that semantic type information is explicitly modeled. Those who need a ?clean? version probably can adapt the UMLS-terminology-extraction code to get different versions of the terminologies. (Or they need to filter out STY concepts in search results obtained from Bioportal. Or Bioportal search API can do the filtering.)
> 
> With best regards,
> Samson
> 
> 
>> On Jul 11, 2018, at 5:25 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu <mailto:vendetti at stanford.edu>> wrote:
>> 
>> Hi Samson,
>> 
>> 
>>> On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at stanford.edu <mailto:swt at stanford.edu>> wrote:
>>> 
>>> When I searched NLM?s Metathesaurus browser for ?Antibiotic? with ATC as the source terminology, I didn't get STY?s Antibiotic in the results. In that respect Bioportal?s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal?s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?
>> 
>> 
>> Each time the UMLS releases a new version (e.g., 2018AA), we use their MetamorphoSys installation wizard [1] to install a local copy of the relational database that contains source vocabulary data. 
>> 
>> We then execute a Python program [2] that reads data out of that relational database and generates ontology files for each of the source vocabularies. These ontologies are written in RDF (Turtle syntax) and are in turn consumable by the BioPortal application. The developer that wrote the Python program is no longer here, so I can?t speak with complete authority on this topic. I?ll try to add some information to this thread after doing some initial research today. The UMLS relational database has an ?MRSTY? table with an ?STY? column that provides semantic type information for terms. For example, I can execute a search in the MRSTY table for CUI C0282686 (class from ATC with label ?RESPIRATORY SYSTEM DRUGS?), and see that they provide semantic type data in the result:
>> 
>> 
>> <Screenshot 2018-07-11 16.58.22.png>
>> 
>> 
>> It appears that our Python program includes semantic type data in the ontology files. I looked at the TTL file for the ATC ontology and can see the class declaration for Event:
>> 
>> <http://purl.bioontology.org/ontology/STY/T051 <http://purl.bioontology.org/ontology/STY/T051>> a owl:Class ;
>> skos:notation "T051"^^xsd:string ;
>> skos:prefLabel "Event"@en .
>> 
>> This sort of semantic type information is displayed by the UMLS Metathesaurus Browser on the right-hand side:
>> 
>> 
>> <Screenshot 2018-07-11 17.21.29.png>
>> 
>> 
>> 
>> Best,
>> Jennifer
>> 
>> [1] https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html <https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html>
>> [2] https://github.com/ncbo/umls2rdf <https://github.com/ncbo/umls2rdf>
>> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From support at bioontology.org  Thu Jul 12 07:18:09 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 12 Jul 2018 07:18:09 -0700
Subject: [bioontology-support] [BioPortal] Feedback from dawn
Message-ID: <5b47632125cc3_777c3f8ee1bdd198103d6@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Thu Jul 12 06:25:25 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 12 Jul 2018 06:25:25 -0700
Subject: [bioontology-support] [BioPortal] Feedback from ORDO_Orphanet
Message-ID: <5b4756c5a7895_5c8d3f8be27201349999a@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Thu Jul 12 09:29:01 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 12 Jul 2018 16:29:01 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <329F8ABC-B087-4D9D-9EF2-DB7F4A163795@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
 <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
 <329F8ABC-B087-4D9D-9EF2-DB7F4A163795@stanford.edu>
Message-ID: <4E4BD822-4912-494F-A56D-D3D6541925ED@stanford.edu>

So I see two central decisions in question, which I would like to share with the list for reference (and discussion as appropriate). At the end I suggest a longer-term approach that would enable tools like RedCAP (i think the tool presenting these choices) can choose whether or not to use the complete list of terms in an ontology.

First, there is the process that converts the database to the semantic artifact, and the decision to include annotational information like the descriptive type. It is consistent in my experience for an ontological representation to include this type of annotation, and it seems to me making it a class in a type relation is also consistent with general practice. The fact the STY is described as a semantic type in the UI screenshot Jennifer provided, and is clearly using a class for the concept, confirms the type relation is the appropriate one. Perhaps the original decision to explicitly declare the term as a class is a convenience for viewing the relations (e.g., all the classes of a given type) without requiring inferencing, but it is before my time also. In any case, it has been done that way for a long time now, and does not seem wrong to me.

Second, there is how BioPortal chooses to display classes that are declared in the ontology, but that have a different path than the ontology does. (The following pattern is true for all BioPortal ontologies, not just those in UMLS.) My understanding is that the tree view generally does not display these classes, nor some of the classifier classes used in ontologies like those in the OBO Library, because they are not of interest to most viewers. But they can be found in a search, and I understood were added to the displayed tree (once found) so their context was clear and they could be accessed again. For completeness they are presented in the API results; if I am not mistaken, many studies have relied on their inclusion as a means of indicating ontology reuse patterns.

It is worth noting that BioPortal has never been a strict "ontology presentation" system; it is a system for presenting and working with a wide variety of ontologies using many different formats and best practices. This often involves decisions in modeling and presentation in order to normalize all the content in a reasonably consistent way. Some systems, like RedCAP and CEDAR, may find that normalization helpful, but choices are made in the ingest process which will not be perfect in all circumstances.

While there is a workaround for the problem that inspired this sub-thread (namely, creating an ontology view that includes the necessary 'native' terms and excluding the undesirable 'foreign' terms), it makes sense to me that there should also be API support for the content seen in the tree view that is provided in the summary page. Then the decision of whether to use that view universally, or an on ontology-by-ontology basis could be controlled by the developers of the application endpoints like RedCAP or CEDAR, or maybe even up to their users.

John

On Jul 11, 2018, at 5:25 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Samson,


On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

When I searched NLM?s Metathesaurus browser for ?Antibiotic? with ATC as the source terminology, I didn't get STY?s Antibiotic in the results. In that respect Bioportal?s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal?s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?


Each time the UMLS releases a new version (e.g., 2018AA), we use their MetamorphoSys installation wizard [1] to install a local copy of the relational database that contains source vocabulary data.

We then execute a Python program [2] that reads data out of that relational database and generates ontology files for each of the source vocabularies. These ontologies are written in RDF (Turtle syntax) and are in turn consumable by the BioPortal application. The developer that wrote the Python program is no longer here, so I can?t speak with complete authority on this topic. I?ll try to add some information to this thread after doing some initial research today. The UMLS relational database has an ?MRSTY? table with an ?STY? column that provides semantic type information for terms. For example, I can execute a search in the MRSTY table for CUI C0282686 (class from ATC with label ?RESPIRATORY SYSTEM DRUGS?), and see that they provide semantic type data in the result:


<Screenshot 2018-07-11 16.58.22.png>


It appears that our Python program includes semantic type data in the ontology files. I looked at the TTL file for the ATC ontology and can see the class declaration for Event:

<http://purl.bioontology.org/ontology/STY/T051> a owl:Class ;
skos:notation "T051"^^xsd:string ;
skos:prefLabel "Event"@en .

This sort of semantic type information is displayed by the UMLS Metathesaurus Browser on the right-hand side:


<Screenshot 2018-07-11 17.21.29.png>



Best,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html
[2] https://github.com/ncbo/umls2rdf




With best regards,
Samson


On Jul 11, 2018, at 9:11 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Yes, Samson?s suggestion is a good one.

I understand your frustration about what is and isn?t included. This is an inherent ambiguity in semantic artifacts, which is deliberately exploited?but with opposing intentions?by different ontology builders, many of which intentionally gather terms from multiple sources in an ontology.

Thinking further about what you want to achieve, you could create a View in a BioPortal ontology of just the STY terms you want to be accessed. I may reply to the list with more details, just so people know of this option.

John

________________________________
From: Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> on behalf of redcap <redcap at uzgent.be<mailto:redcap at uzgent.be>>
Sent: Wednesday, July 11, 2018 12:09:27 AM
To: John Graybeal
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; redcap
Subject: RE: [bioontology-support] BioPortal: Questions

Hi John,

?         I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I look for ?Event? in the ATC index<https://www.whocc.no/atc_ddd_index/>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.
For example, the first result of the request https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102 is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}



?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true



o   Not logged in
<image001.png>

o   Logged in
<image004.png>

?         Regarding the missing classes in ICD10, I don?t think contacting info at who.int<mailto:info at who.int> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact ?whoever maintains UMLS to explain or correct these missing concepts?.

Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: dinsdag 10 juli 2018 20:26
Aan: Vanderschaeghe Simon <Simon.Vanderschaeghe at UZGENT.be<mailto:erschaeghe at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term ?Event? and Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

?         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using ?Jump To? in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

?         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term ?Event?<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

?         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be/> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


_______________________________________________
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 vendetti at stanford.edu  Thu Jul 12 11:23:36 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 12 Jul 2018 18:23:36 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
Message-ID: <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>

Hi Simon,

With regard to the 500 error you?re seeing when logged in, I think there may be an issue with the cache. Could you please try clearing the browser cache for BioPortal? To selectively clear the cache for only our site, you could use the following steps in a Chrome browser:

1). Right click anywhere on the page and choose "Inspect?. This will open the Chrome developer console.
2). In the top left of the page, right click on the refresh icon and choose ?Empty Cache and Hard Reload?:


[cid:2F9F2649-7627-4603-9C51-E2D01ED32345 at stanford.edu]


If you?re using a different browser, let us know and I?ll try to provide similar instructions.

Kind regards,
Jennifer




On Jul 11, 2018, at 12:09 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true

o   Not logged in
<image001.png>

o   Logged in
<image004.png>


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From jgraybeal at stanford.edu  Thu Jul 12 12:58:29 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 12 Jul 2018 19:58:29 +0000
Subject: [bioontology-support] [BioPortal] Feedback from dawn
In-Reply-To: <5b47632125cc3_777c3f8ee1bdd198103d6@ncbo-prd-app-08.stanford.edu.mail>
References: <5b47632125cc3_777c3f8ee1bdd198103d6@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <33237FE9-298C-4D12-A91B-E1EECC854524@stanford.edu>

Dawn,

If you go to the BioPortal front page and enter NS5a into the "Search for a class" box, you will arrive at this page:
  http://bioportal.bioontology.org/search?utf8=%E2%9C%93&query=NS5a&button=<http://bioportal.bioontology.org/search?utf8=?&query=NS5a&button=>

None of us are domain experts, so I can't guess which of those is the one you want. But if you click on the links you can see each of these terms, including their ID, class, long and short names, and you can decide for yourself the best match. For example clicking on the LOINC entry takes you to http://bioportal.bioontology.org/ontologies/LOINC?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FLNC%2FLP220405-7<http://bioportal.bioontology.org/ontologies/LOINC?p=classes&conceptid=http://purl.bioontology.org/ontology/LNC/LP220405-7> which shows many of those attributes; other concepts in other ontologies might be a better fit, or might have more of the attributes you need.

John



On Jul 12, 2018, at 7:18 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: dawn

Email: dninness at nethealth.com<mailto:dninness at nethealth.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FLOINC%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FLNC%252FLP220405-7

Feedback:

Looking for the ID#, Class, Long and Short Name for :

Hepatitis C virus genotype 1 NS5a gene

_______________________________________________
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 jgraybeal at stanford.edu  Thu Jul 12 17:06:06 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 13 Jul 2018 00:06:06 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ORDO_Orphanet
In-Reply-To: <5b4756c5a7895_5c8d3f8be27201349999a@ncbo-prd-app-08.stanford.edu.mail>
References: <5b4756c5a7895_5c8d3f8be27201349999a@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <56BEBDE4-D26B-46EB-AE21-D3EE626398CF@stanford.edu>

Unfortunately, we are not able to duplicate your problem when we try it here.

We're seeing a number of complaints that suggest that people in different locations are getting different BioPortal experiences, and we haven't fully analyzed this situation yet. If you would like to help us directly troubleshoot this problem, please contact me off-list about coordinating a call. Otherwise we hope to learn more soon about the nature of this unusual problem.

Some questions for you, just to be sure we understand the problem correctly:

* Are you using the account of someone who has authority to edit the page?
* What exactly are you doing when you "try to edit our page"?editing the ontology information or submission information?
* What browser are you using? Can you try it from another browser and/or another machine?

You could try following instructions such as the following, to make sure your browser is not cacheing the error.
1) Open the Chrome developer tools as described at http://anti-code.com/devtools-cheatsheet/.
2) In the top left of the page, right click or control-click on the refresh icon and choose ?Empty Cache and Hard Reload?
3) Close the developer tools with the small X at upper right, or by entering the key sequence again.

Thanks for your contribution, and sorry for the trouble. We'll post as soon as we know more.

John


[cid:2F9F2649-7627-4603-9C51-E2D01ED32345 at stanford.edu]


On Jul 12, 2018, at 6:25 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: ORDO_Orphanet

Email: ordo.orphanet at inserm.fr<mailto:ordo.orphanet at inserm.fr>

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

Feedback:

Hi Bioportal team,

Once logged, when we try to edit our page :
https://bioportal.bioontology.org/ontologies/ORDO
we always get this error message:
We're sorry but something has gone wrong. We have been notified of this error.

We would like to add/change text and linked to other projects.

Best regards,

_______________________________________________
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 redcap at uzgent.be  Thu Jul 12 23:48:46 2018
From: redcap at uzgent.be (redcap)
Date: Fri, 13 Jul 2018 06:48:46 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
Message-ID: <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>

Hi Jennifer,

I tried clearing the browser cache, but unfortunately the error persists. I did however notice that there is a JavaScript error in the console. Could this be related to the error message I am getting when logged in?[cid:image001.png at 01D41A86.0F4F1D90]

Also, when I close and reopen the console, I am getting an additional error.
[cid:image003.png at 01D41A86.4F359B00]

Thanks in advance!
Kind regards,
Simon

Van: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Verzonden: donderdag 12 juli 2018 20:24
Aan: redcap <redcap at UZGENT.be>
CC: support at bioontology.org
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Hi Simon,

With regard to the 500 error you?re seeing when logged in, I think there may be an issue with the cache. Could you please try clearing the browser cache for BioPortal? To selectively clear the cache for only our site, you could use the following steps in a Chrome browser:

1). Right click anywhere on the page and choose "Inspect?. This will open the Chrome developer console.
2). In the top left of the page, right click on the refresh icon and choose ?Empty Cache and Hard Reload?:


[cid:image002.png at 01D41A86.0F4F1D90]


If you?re using a different browser, let us know and I?ll try to provide similar instructions.

Kind regards,
Jennifer





On Jul 11, 2018, at 12:09 AM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true

o   Not logged in
<image001.png>

o   Logged in
<image004.png>


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From redcap at uzgent.be  Thu Jul 12 23:42:02 2018
From: redcap at uzgent.be (redcap)
Date: Fri, 13 Jul 2018 06:42:02 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <4E4BD822-4912-494F-A56D-D3D6541925ED@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
 <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
 <329F8ABC-B087-4D9D-9EF2-DB7F4A163795@stanford.edu>
 <4E4BD822-4912-494F-A56D-D3D6541925ED@stanford.edu>
Message-ID: <ada65ab14fcf48d0b1ccbf234ea20f21@UZGENT.be>

Dear all,

Thank you for the enlightening discussion! I contacted the REDCap developers, and for now the terms that belong to STY will be filtered out when searching any ontology that is not STY.

The idea of the long-term approach that would enable choosing the complete list of terms in an ontology or not seems very appealing to me, as this would eliminate the need to hard-code the filtering into tools like REDCap.

Thanks again!
Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: donderdag 12 juli 2018 18:29
Aan: Jennifer Leigh Vendetti <vendetti at stanford.edu>
CC: Samson Tu <swt at stanford.edu>; support at bioontology.org; redcap <redcap at UZGENT.be>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

So I see two central decisions in question, which I would like to share with the list for reference (and discussion as appropriate). At the end I suggest a longer-term approach that would enable tools like RedCAP (i think the tool presenting these choices) can choose whether or not to use the complete list of terms in an ontology.

First, there is the process that converts the database to the semantic artifact, and the decision to include annotational information like the descriptive type. It is consistent in my experience for an ontological representation to include this type of annotation, and it seems to me making it a class in a type relation is also consistent with general practice. The fact the STY is described as a semantic type in the UI screenshot Jennifer provided, and is clearly using a class for the concept, confirms the type relation is the appropriate one. Perhaps the original decision to explicitly declare the term as a class is a convenience for viewing the relations (e.g., all the classes of a given type) without requiring inferencing, but it is before my time also. In any case, it has been done that way for a long time now, and does not seem wrong to me.

Second, there is how BioPortal chooses to display classes that are declared in the ontology, but that have a different path than the ontology does. (The following pattern is true for all BioPortal ontologies, not just those in UMLS.) My understanding is that the tree view generally does not display these classes, nor some of the classifier classes used in ontologies like those in the OBO Library, because they are not of interest to most viewers. But they can be found in a search, and I understood were added to the displayed tree (once found) so their context was clear and they could be accessed again. For completeness they are presented in the API results; if I am not mistaken, many studies have relied on their inclusion as a means of indicating ontology reuse patterns.

It is worth noting that BioPortal has never been a strict "ontology presentation" system; it is a system for presenting and working with a wide variety of ontologies using many different formats and best practices. This often involves decisions in modeling and presentation in order to normalize all the content in a reasonably consistent way. Some systems, like RedCAP and CEDAR, may find that normalization helpful, but choices are made in the ingest process which will not be perfect in all circumstances.

While there is a workaround for the problem that inspired this sub-thread (namely, creating an ontology view that includes the necessary 'native' terms and excluding the undesirable 'foreign' terms), it makes sense to me that there should also be API support for the content seen in the tree view that is provided in the summary page. Then the decision of whether to use that view universally, or an on ontology-by-ontology basis could be controlled by the developers of the application endpoints like RedCAP or CEDAR, or maybe even up to their users.

John

On Jul 11, 2018, at 5:25 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Samson,



On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

When I searched NLM?s Metathesaurus browser for ?Antibiotic? with ATC as the source terminology, I didn't get STY?s Antibiotic in the results. In that respect Bioportal?s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal?s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?


Each time the UMLS releases a new version (e.g., 2018AA), we use their MetamorphoSys installation wizard [1] to install a local copy of the relational database that contains source vocabulary data.

We then execute a Python program [2] that reads data out of that relational database and generates ontology files for each of the source vocabularies. These ontologies are written in RDF (Turtle syntax) and are in turn consumable by the BioPortal application. The developer that wrote the Python program is no longer here, so I can?t speak with complete authority on this topic. I?ll try to add some information to this thread after doing some initial research today. The UMLS relational database has an ?MRSTY? table with an ?STY? column that provides semantic type information for terms. For example, I can execute a search in the MRSTY table for CUI C0282686 (class from ATC with label ?RESPIRATORY SYSTEM DRUGS?), and see that they provide semantic type data in the result:


<Screenshot 2018-07-11 16.58.22.png>


It appears that our Python program includes semantic type data in the ontology files. I looked at the TTL file for the ATC ontology and can see the class declaration for Event:

<http://purl.bioontology.org/ontology/STY/T051> a owl:Class ;
skos:notation "T051"^^xsd:string ;
skos:prefLabel "Event"@en .

This sort of semantic type information is displayed by the UMLS Metathesaurus Browser on the right-hand side:


<Screenshot 2018-07-11 17.21.29.png>



Best,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html
[2] https://github.com/ncbo/umls2rdf





With best regards,
Samson



On Jul 11, 2018, at 9:11 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Yes, Samson?s suggestion is a good one.

I understand your frustration about what is and isn?t included. This is an inherent ambiguity in semantic artifacts, which is deliberately exploited?but with opposing intentions?by different ontology builders, many of which intentionally gather terms from multiple sources in an ontology.

Thinking further about what you want to achieve, you could create a View in a BioPortal ontology of just the STY terms you want to be accessed. I may reply to the list with more details, just so people know of this option.

John

________________________________
From: Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> on behalf of redcap <redcap at uzgent.be<mailto:redcap at uzgent.be>>
Sent: Wednesday, July 11, 2018 12:09:27 AM
To: John Graybeal
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; redcap
Subject: RE: [bioontology-support] BioPortal: Questions

Hi John,

?         I understand that there are links between ATC & STY. However, I do not think that STY terms should ever be suggested when searching ATC. If I look for ?Event? in the ATC index<https://www.whocc.no/atc_ddd_index/>, no matches are found, and I would expect the same behavior when searching ATC through BioPortal.
We are using the ontologies available at BioPortal through REDCap. When users are completing a field that is validated as ATC, they can currently also search & select STY terms, which are not an inherent part of the ontology.
For example, the first result of the request https://data.bioontology.org/search?q=antibiotic&ontologies=ATC&suggest=true&include=prefLabel,notation,cui&display_links=false&display_context=false&format=json&apikey=6c7cd4f4-830c-4af4-a06d-1454043f6102 is {"prefLabel":"Antibiotic","notation":"T195","@id":"http://purl.bioontology.org/ontology/STY/T195","@type":"http://www.w3.org/2002/07/owl#Class"}


?         I just finished testing again: https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true


o   Not logged in
<image001.png>

o   Logged in
<image004.png>

?         Regarding the missing classes in ICD10, I don?t think contacting info at who.int<mailto:info at who.int> will resolve the issue. I will follow the suggestion Samson Tu made to try and contact ?whoever maintains UMLS to explain or correct these missing concepts?.

Kind regards,
Simon

Van: John Graybeal [mailto:jgraybeal at stanford.edu]
Verzonden: dinsdag 10 juli 2018 20:26
Aan: Vanderschaeghe Simon <Simon.Vanderschaeghe at UZGENT.be<mailto:erschaeghe at UZGENT.be>>
CC: support at bioontology.org<mailto:support at bioontology.org>; redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>>
Onderwerp: Re: [bioontology-support] BioPortal: Questions

Simon,

Thank you for your questions.

As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

There appear to be STY terms declared and used in the ontology; I am not sure if you would argue they should be ignored. We only show the ATC terms (and not the STY terms) in the tree view because we filter the tree view to only include the terms that have the same root as the ontology, but the other terms are also present and can be found, as you observe. This BioPortal behavior is by design.

when searching for the term ?Event? and Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

While this can be an indication there is faulty information in our index, I am not able to duplicate it. As we just finished uploading the vocabularies in UMLS 2018AA, it is quite possible that you caught the system in a temporary state. Can you try this again, please?

some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10), because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

We provided the notes capabiity as a service to ontology authors, some of whom use it to inform changes to ontologies; and also to other users of the ontology. In many other cases, ontologies are considered fixed once released, and will not be changed. ICD10 is one of these, as it goes through a major revision cycle that takes many years, and the underlying model is often changed considerably as well. For the last several years the authoring community has been working on ICD11, which is likely to be a major overhaud of ICD10.

To answer your specific question, what I will do if I see a concern with an ontology is to see the contact email on the summary page for that ontology, and send an email to that address with my concern. If I get no information back or can't reach that address, I will look up the ontology in Google to see if I can determine where and how it is maintained; many are maintained on GitHub or have their own web sites, often with issue trackers or contact information. If those methods fail, the BioPortal support list is a reasonable last-ditch effort to find the current status and owners of an ontolog, and determine whether issue reports are likely to be addressed.

I hope these answers help,

John

On Jul 10, 2018, at 6:04 AM, Vanderschaeghe Simon <Simon.Vanderschaeghe at uzgent.be<mailto:Simon.Vanderschaeghe at uzgent.be>> wrote:

Dear Support,

I have some questions regarding the use of BioPortal. Would it be possible for you to provide me with some feedback?

?         It seems that somehow the Semantic Type Ontology (STY) got mixed up within the Anatomical Therapeutic Chemical Classification (ATC). Initially, when looking at the classes for ATC<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=root>, everything seems fine. However, when using ?Jump To? in combination with any of the classes for STY<https://bioportal.bioontology.org/ontologies/STY/?p=classes&conceptid=root>, all classes from STY can be found within ATC (e.g. Jump To: Event<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>). As a result, when searching for ATC terms using the API, STY terms are also returned. Could this be fixed please?

?         By looking at the aforementioned issue, I noticed that https://bioportal.bioontology.org<https://bioportal.bioontology.org/> reacts differently depending on whether the user is logged in or not. For instance, when searching for the term ?Event?<https://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051&jump_to_nav=true>:
o   Not logged in: expected behavior
o   Logged in: error message ?We're sorry but something has gone wrong. We have been notified of this error.?

?         Finally, some time ago (2018-04-24) I added some notes to International Classification of Diseases, Version 10 (ICD10)<https://bioportal.bioontology.org/ontologies/ICD10/?p=notes>, because I found out that some classes are missing. As I noticed that these classes are not yet added, could you please enlighten me on the correct procedure to correct an  ontology?

If you need any other information (e.g. screenshots), please do not hesitate to contact me.

Thanks in advance!
Kind regards,
Simon

SIMON VANDERSCHAEGHE
Clinical Data Manager
Bimetra, Clinical Research Center Gent | www.bimetra.be<http://www.bimetra.be/>

[UZ Gent]<https://www.uzgent.be/>

Universitair Ziekenhuis Gent | C. Heymanslaan 10 | 9000 Gent
T +32 9 332 09 23 | T +32 9 332 05 30 (secr.)
simon.vanderschaeghe at uzgent.be<mailto:simon.vanderschaeghe at uzgent.be>
Ingang 81 | Route 812 | uzgent.be<http://www.uzgent.be/> | [Facebook UZ Gent] <https://www.facebook.com/uzgent> | [Twitter UZ Gent] <https://twitter.com/UZGent>



[Banner UZ Gent]


_______________________________________________
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
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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 vendetti at stanford.edu  Fri Jul 13 12:03:41 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 13 Jul 2018 19:03:41 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
 <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
Message-ID: <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>

Hi Simon,


On Jul 12, 2018, at 11:48 PM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

I tried clearing the browser cache, but unfortunately the error persists. I did however notice that there is a JavaScript error in the console. Could this be related to the error message I am getting when logged in?<image001.png>


This JS error is reproducible on our end, but is unrelated and can be ignored.


Also, when I close and reopen the console, I am getting an additional error.
<image003.png>



Ok. I?m wondering if you could try something else for me? For the page that you see the 500 error:

1). Open the developer console.
2). Navigate to the Network tab.
3). Click the Clear icon in the top left of the developer console to clear any contents that might already be visible in the Network tab.
4). Tick the ?Disable cache? checkbox.
5). Refresh the page.

I?m interested to see what you get for results in the Network tab. For example, mine looks as such with a 200 response at the top for the API call to retrieve the Event concept:

[cid:71AEC965-C2A5-4B20-B266-B58880B0DDC7 at stanford.edu]

Another thing that would be helpful, is for you to let me know roughly the date and time that you perform the page refresh, as well as your BioPortal user account name that you are logged in with. I would like to try to grep the various production logs for this 500 error you?re seeing.

Apologies that you?re continuing to have difficulties.

Kind regards,
Jennifer



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From swt at stanford.edu  Fri Jul 13 15:17:31 2018
From: swt at stanford.edu (Samson Tu)
Date: Fri, 13 Jul 2018 22:17:31 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <23F91C03-6651-44EB-B2A2-609CBE3A3A37@lirmm.fr>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <SN6PR02MB4639D68DCB4E190C641EBC58DA5A0@SN6PR02MB4639.namprd02.prod.outlook.com>
 <28C897F3-A2C0-4F69-A3E1-A58E8B307AE8@stanford.edu>
 <329F8ABC-B087-4D9D-9EF2-DB7F4A163795@stanford.edu>
 <70A67CC6-3A35-4963-94AC-FC08E589C71E@stanford.edu>
 <23F91C03-6651-44EB-B2A2-609CBE3A3A37@lirmm.fr>
Message-ID: <09DF3FCB-9EFC-4084-92F1-0DDC18056605@stanford.edu>

Dear Andon,

No doubt the semantic type information is useful in many applications.

I don?t think it?s appropriate to "discard anything that lives outside of the namespace of the terminology or ontology of interest.? A terminology or ontology, as it is constructed, may re-use entities from other ontologies. These re-used entities are very much part of the source ontology as intended by the developers of the ontology.

The issue is how to represent UMLS semantic type information that UMLS/NCBO adds to a source like ATC. My preferred design would involve an ATC-UMLS ontology that imports the ATC ontology, where the ATC ontology includes only information in the original source terminology and ATC-UMLS contains the UMLS extensions that are deemed useful. With this design, a user or an application can easily determine how to access the information they need.

With best regards,
Samson


On Jul 12, 2018, at 5:25 AM, Andon Tchechmedjiev <andon.tchechmedjiev at lirmm.fr<mailto:andon.tchechmedjiev at lirmm.fr>> wrote:

Dear Samson,

Generally speaking, the ontologies and terminologies integrated into UMLS become distinct entities compared to the source ontologies and terminologies and should never be considered as canonical (there are numerous differences that aren?t always obvious at first) when used in applications. As Jennifer stated, semantic types and CUIs are pieces of information intrinsic to UMLS and relevant for the resources in BioPortal that were extracted from UMLS. The reason for including the umls:hasSty and umls:cui properties is to enable the BioPortal Annotator to use this information to filter annotations based on semantic types, which is an extremely common use-case and an important feature. You will notice that the aforementioned properties live in their own namespace: "@prefix umls: <http://bioportal.bioontology.org/ontologies/umls/> .?, while everything else lives in "http://purl.bioontology.org/ontology/ACRONYM?<http://purl.bioontology.org/ontology/ACRONYM%E2%80%9C>. This is actually the right way of of doing things as far as ontology engineering standards and practices go, as opposed to an ad-hoc string encoding of the information (a bad practice that makes querying with SPARQL much less practical).

The proper (semantically enabled) way of dealing with this for applications that rely on the ?purity? of the terminological information is to discard anything that lives outside of the namespace of the terminology or ontology of interest (i.e. only keeping entities that are in "http://purl.bioontology.org/ontology/ACRONYM? in the case of BioPortal ontologies extracted from UMLS). The fact that STY concepts appear in the search results and the concept hierarchy and the fact that this is problematic or inconvenient for some specific applications are different issues altogether, however. Changing the behaviour of BioPortal because of an issue with one specific use-case among many (others may be reliant on this specific behaviour) wouldn?t necessarily be the most logical solution. In this instance, if the behaviour is problematic for redcap users, fixing the issue directly in redcap?s BioPortal adapter by filtering all concepts in the umls prefix namespace would very likely be the simplest solution.

Best Regards,
Andon


?
Andon Tchechmedjiev, PhD. Postdoctoral researcher in Natural Language Processing in the Biomedical Domain at LIRMM, Office 3/164, B?t. 5 - 860 rue de St Priest 34095 Montpellier cedex 5,  FRANCE | andon.tchechmedjiev.eu<http://andon.tchechmedjiev.eu/>

On 12 Jul 2018, at 08:53, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

Hi Jennifer,

For me, the question is not whether the Metathesaurus browser display semantic type information of an UMLS concept derived from a terminology. The question is why Bioportal should model semantic type information as part of a terminology?s representation as an ontology, and therefore include STY as part of the ontology. First, when NCBO makes a UMLS-derived terminology available on Bioportal, is the expectation that it has UMLS-augmented relations or that it has only relations that are in the original terminology? Until today I didn?t realize that UMSL-derived terminologies I download from Bioportal have extra concepts that are not in the original terminology. Second, why isn?t it sufficient to encode the semantic types as string annotations (as it does already)? Doing so would avoid the problem of unexpected concepts turning up in search results.

I suspect that there are good reasons for the design choices made in the UMLS-terminology-extraction code. In any case, we probably have to live with the constraints imposed by these choices. It is better that we clarify that UMLS-derived terminologies on Bioportal, by design, have STY included so that semantic type information is explicitly modeled. Those who need a ?clean? version probably can adapt the UMLS-terminology-extraction code to get different versions of the terminologies. (Or they need to filter out STY concepts in search results obtained from Bioportal. Or Bioportal search API can do the filtering.)

With best regards,
Samson


On Jul 11, 2018, at 5:25 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Samson,


On Jul 11, 2018, at 10:16 AM, Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>> wrote:

When I searched NLM?s Metathesaurus browser for ?Antibiotic? with ATC as the source terminology, I didn't get STY?s Antibiotic in the results. In that respect Bioportal?s behavior is different from that of UMLS Metathesaurus, from which NCBO gets ATC. I find it surprising that Bioportal?s ATC should contain STY. Is there some documentation on how Bioportal extract terminologies from UMLS?


Each time the UMLS releases a new version (e.g., 2018AA), we use their MetamorphoSys installation wizard [1] to install a local copy of the relational database that contains source vocabulary data.

We then execute a Python program [2] that reads data out of that relational database and generates ontology files for each of the source vocabularies. These ontologies are written in RDF (Turtle syntax) and are in turn consumable by the BioPortal application. The developer that wrote the Python program is no longer here, so I can?t speak with complete authority on this topic. I?ll try to add some information to this thread after doing some initial research today. The UMLS relational database has an ?MRSTY? table with an ?STY? column that provides semantic type information for terms. For example, I can execute a search in the MRSTY table for CUI C0282686 (class from ATC with label ?RESPIRATORY SYSTEM DRUGS?), and see that they provide semantic type data in the result:


<Screenshot 2018-07-11 16.58.22.png>


It appears that our Python program includes semantic type data in the ontology files. I looked at the TTL file for the ATC ontology and can see the class declaration for Event:

<http://purl.bioontology.org/ontology/STY/T051> a owl:Class ;
skos:notation "T051"^^xsd:string ;
skos:prefLabel "Event"@en .

This sort of semantic type information is displayed by the UMLS Metathesaurus Browser on the right-hand side:


<Screenshot 2018-07-11 17.21.29.png>



Best,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html
[2] https://github.com/ncbo/umls2rdf


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From vendetti at stanford.edu  Fri Jul 13 15:19:37 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 13 Jul 2018 22:19:37 +0000
Subject: [bioontology-support] BioPortal: Questions
In-Reply-To: <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>
References: <1bf7210449274a259dbf5e7f05159ec6@UZGENT.be>
 <1DA0299E-C17F-4A51-A886-A4EDEBF07EEE@stanford.edu>
 <5f193880a2e0424ca1d264afa4ca3e86@UZGENT.be>
 <8852AD92-460A-4F30-BD6F-0D3CCC523DCA@stanford.edu>
 <2da2ee1bbf814b0c8ac490c3640d3b57@UZGENT.be>
 <A2633758-2123-459B-9C98-0238E384B868@stanford.edu>
Message-ID: <EB703FDD-1F87-4438-9283-F087F4B2A4C7@stanford.edu>

Hi again Simon,

There?s one other thing I?m wondering about. Are you able to issue a REST call in your browser for this term with our REST API? You would enter this URL in the browser:

http://data.bioontology.org/ontologies/ATC/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSTY%2FT051?apikey=your_api_key_here<http://data.bioontology.org/ontologies/ATC/classes/http://purl.bioontology.org/ontology/STY/T051?apikey=your_api_key_here>

You need to enter your API key at the end of the URL, which you can access in the Account Settings section of the BioPortal UI. (After logging in, click on your account name to open the drop down menu and choose Account Settings). If the call is successful, you would see this in the way of a return result:



[cid:366A6131-2B51-4615-8D36-5BD85730D373 at stanford.edu]

Kind regards,
Jennifer



On Jul 13, 2018, at 12:03 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Simon,


On Jul 12, 2018, at 11:48 PM, redcap <redcap at UZGENT.be<mailto:redcap at UZGENT.be>> wrote:

I tried clearing the browser cache, but unfortunately the error persists. I did however notice that there is a JavaScript error in the console. Could this be related to the error message I am getting when logged in?<image001.png>


This JS error is reproducible on our end, but is unrelated and can be ignored.


Also, when I close and reopen the console, I am getting an additional error.
<image003.png>



Ok. I?m wondering if you could try something else for me? For the page that you see the 500 error:

1). Open the developer console.
2). Navigate to the Network tab.
3). Click the Clear icon in the top left of the developer console to clear any contents that might already be visible in the Network tab.
4). Tick the ?Disable cache? checkbox.
5). Refresh the page.

I?m interested to see what you get for results in the Network tab. For example, mine looks as such with a 200 response at the top for the API call to retrieve the Event concept:

<Screenshot 2018-07-13 11.46.07.png>

Another thing that would be helpful, is for you to let me know roughly the date and time that you perform the page refresh, as well as your BioPortal user account name that you are logged in with. I would like to try to grep the various production logs for this 500 error you?re seeing.

Apologies that you?re continuing to have difficulties.

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

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From mconlon at ufl.edu  Sat Jul 14 08:24:52 2018
From: mconlon at ufl.edu (Conlon, Mike)
Date: Sat, 14 Jul 2018 15:24:52 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mconlon
In-Reply-To: <2F5B134F-90AD-48DD-9F57-0FD63E2D2C62@ufl.edu>
References: <5b42b01317873_4fd53fdc10605af0935ee@ncbo-prd-app-09.stanford.edu.mail>
 <21D2FE05-E728-435B-97CA-E1307AD12D7A@stanford.edu>
 <37FAD35D-C321-46F9-A61D-4D6FB8EE4376@ufl.edu>
 <88361D0E-C027-4C52-83FF-FE149742D9E3@stanford.edu>
 <2F5B134F-90AD-48DD-9F57-0FD63E2D2C62@ufl.edu>
Message-ID: <etPan.5b4a15c0.34cf0e35.a844@ufl.edu>

Hi,

I tried to login to bioportal with the credentails I had created ? account name mconlon, email mconlon at ufl.edu<mailto:mconlon at ufl.edu> and a password I had stored. No luck.  I tried to reset the password and it said there was no such account.

I had made changes to the VIVO record in bioportal and updated the record and the ontology file.  The changes had been saved.  But when I went back the next day, the changes were gone and there was no sign of my being an editor for the VIVO ontology.

So I need to start again.  I don?t know if I have an account, and the VIVO record does not show me as an editor.

What should I do next?

Mike

Michael Conlon
Emeritus Faculty Member
University of Florida


On July 9, 2018 at 1:04:34 PM, Conlon, Mike (mconlon at ufl.edu<mailto:mconlon at ufl.edu>) wrote:
Got it!

Thanks,

Mike

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Monday, July 9, 2018 at 1:02 PM
To: "Conlon, Mike" <mconlon at ufl.edu>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from mconlon

Hi Mike,

I?ve added your account as an administrator to VIVO. If you refresh your browser at the summary page (https://bioportal.bioontology.org/ontologies/VIVO<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_VIVO&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=HpKq2GWpm5jhO0zyB7wxmMmNe2Eqv41xOuywTKklfNo&s=xzuE0kZ7KW5jG7b30iOpqrrd5JXBy_hYnZaebCTAgIM&e=>), you should now see links like ?Edit ontology information?, ?Add submission?, etc.

Kind regards,
Jennifer



On Jul 9, 2018, at 9:52 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Jennifer,

My bioportal account name is mconlon at ufl.edu<mailto:mconlon at ufl.edu>

Thanks!

Mike

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Date: Monday, July 9, 2018 at 12:42 PM
To: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Cc: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from mconlon

Hi Mike,



On Jul 8, 2018, at 5:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:
I'd like to update the information for the VIVO ontology, listed in bioportal here: https://bioportal.bioontology.org/ontologies/VIVO<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_VIVO&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VS4ultS9qpvz6EXJZ2Kmi5uqojirZ0dGQXsulpgq_OM&s=H6pt__X0Pw1-LpNku1RNxLadAAf1uD6yeB27ZOZ2B5U&e=>
Stella worked on the project some time back and submitted the entry. I've been the project director since 2015 and lead the ontology development effort. Would be helpful if I could upload the current version and upload the metadata.



Sure, no problem - we can make you an administrator for this ontology. Please let us know your BioPortal account name that you?d like us to use for the administrative privileges. If you haven?t created an account yet, you can do so at this page:

https://bioportal.bioontology.org/accounts/new<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_accounts_new&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VS4ultS9qpvz6EXJZ2Kmi5uqojirZ0dGQXsulpgq_OM&s=nCAesjmEuqZlp9GEa9Hmqr-mdzWxSqEVOWJVu1yOfb8&e=>

Kind regards,
Jennifer

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From support at bioontology.org  Mon Jul 16 06:49:55 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 16 Jul 2018 06:49:55 -0700
Subject: [bioontology-support] [BioPortal] Feedback from cvnbioportal
Message-ID: <5b4ca28326183_17af3fa301504f2c57661@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Mon Jul 16 07:11:09 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 16 Jul 2018 14:11:09 +0000
Subject: [bioontology-support] [BioPortal] Feedback from cvnbioportal
In-Reply-To: <5b4ca28326183_17af3fa301504f2c57661@ncbo-prd-app-09.stanford.edu.mail>
References: <5b4ca28326183_17af3fa301504f2c57661@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <F0413509-CF2B-4DBD-8800-2AB9B74E2AAD@stanford.edu>


On Jul 16, 2018, at 6:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Connections are not secure.

You provide a really nice resource, but it is really important to offer it in a secure way. I personally use random passwords, so doesn't affect me to much, but for other users it might be exposing their passwords..



We use HTTPS but the security certificate for out site expired over the weekend. Apologies for the inconvenience. We?re working to rectify the situation.

Jennifer


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From marc.hanauer at inserm.fr  Mon Jul 16 07:11:58 2018
From: marc.hanauer at inserm.fr (Marc Hanauer)
Date: Mon, 16 Jul 2018 16:11:58 +0200
Subject: [bioontology-support] [BioPortal] Feedback from ORDO_Orphanet
In-Reply-To: <56BEBDE4-D26B-46EB-AE21-D3EE626398CF@stanford.edu>
References: <5b4756c5a7895_5c8d3f8be27201349999a@ncbo-prd-app-08.stanford.edu.mail>
 <56BEBDE4-D26B-46EB-AE21-D3EE626398CF@stanford.edu>
Message-ID: <6075b2c2-ca67-7b2e-34d9-8ae0ae66dcaa@inserm.fr>

Dear John,

Thanks for your reply.

Well the sequence is quiet simple :

Going to bioportal, login/password entered then error message.

I still have access to the account information but can't reach ORDO page 
(and yes, we would like to edit the ontology information).

I've tried with both Firefox and Chrome. At home as well with a 
different computer and network.

By the way, we've updated our ontology on our own server this friday (as 
usual, twice a year). The file was correctly processed by EBI OLS tool 
but not correctly by bioportal: "RDF error". We've already experienced 
parser issues with bioportal on some previous version. Seems to be a 
similar situation again.

Thanks for your help.

Best regards,

www.orpha.net <https://www.orpha.net> | Twitter @Orphanet 
<https://twitter.com/Orphanet>
*Marc HANAUER*
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Strat?gie et Innovation
marc.hanauer at inserm.fr

ORPHANET - INSERM US14
Plateforme Maladies Rares / Rare Disease Platform
96 rue Didot
75014 PARIS
FRANCE
Le 13/07/2018 ? 02:06, John Graybeal a ?crit?:
> Unfortunately, we are not able to duplicate your problem when we try 
> it here.
>
> We're seeing a number of complaints that suggest that people in 
> different locations are getting different BioPortal experiences, and 
> we haven't fully analyzed this situation yet. If you would like to 
> help us directly troubleshoot this problem, please contact me off-list 
> about coordinating a call. Otherwise we hope to learn more soon about 
> the nature of this unusual problem.
>
> Some questions for you, just to be sure we understand the problem 
> correctly:
>
> * Are you using the account of someone who has authority to edit the page?
> * What exactly are you doing when you "try to edit our page"?editing 
> the ontology information or submission information?
> * What browser are you using? Can you try it from another browser 
> and/or another machine?
>
> You could try following instructions such as the following, to make 
> sure your browser is not cacheing the error.
> 1) Open the Chrome developer tools as described at 
> http://anti-code.com/devtools-cheatsheet/.
> 2) In the top left of the page, right click or control-click on the 
> refresh icon and choose ?Empty Cache and Hard Reload?
> 3) Close the developer tools with the small X at upper right, or by 
> entering the key sequence again.
>
> Thanks for your contribution, and sorry for the trouble. We'll post as 
> soon as we know more.
>
> John
>
>
>
>
>> On Jul 12, 2018, at 6:25 AM, support at bioontology.org 
>> <mailto:support at bioontology.org> wrote:
>>
>> Name: ORDO_Orphanet
>>
>> Email: ordo.orphanet at inserm.fr <mailto:ordo.orphanet at inserm.fr>
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org 
>> <http://2Fbioportal.bioontology.org>%2Faccount
>>
>>
>> *Feedback:*
>>
>> Hi Bioportal team,
>>
>> Once logged, when we try to edit our page :
>> https://bioportal.bioontology.org/ontologies/ORDO
>> we always get this error message:
>> We're sorry but something has gone wrong. We have been notified of 
>> this error.
>>
>> We would like to add/change text and linked to other projects.
>>
>> Best regards,
>>
>>
>> _______________________________________________
>> 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 hoppesyd at umich.edu  Mon Jul 16 07:44:51 2018
From: hoppesyd at umich.edu (Sydney Hoppe)
Date: Mon, 16 Jul 2018 09:44:51 -0500
Subject: [bioontology-support] Expired Certificate
Message-ID: <CACcE1G9WR76CsiuNKxJmh+p4dK4W4=NBCw-_sFKmUG2561mNVg@mail.gmail.com>

Good morning,

I was trying to access Bioportal this morning and when I attempted to login
I was presented with an "expired certificate" message. Your certificate
expired yesterday. I just wanted to let you know in case you were not yet
aware.

Thanks!

-- 
*Sydney Hoppe*
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu | 614.282.1314
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From vendetti at stanford.edu  Mon Jul 16 08:23:28 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 16 Jul 2018 15:23:28 +0000
Subject: [bioontology-support] Expired Certificate
In-Reply-To: <CACcE1G9WR76CsiuNKxJmh+p4dK4W4=NBCw-_sFKmUG2561mNVg@mail.gmail.com>
References: <CACcE1G9WR76CsiuNKxJmh+p4dK4W4=NBCw-_sFKmUG2561mNVg@mail.gmail.com>
Message-ID: <CD230C13-8E69-4F44-9CD5-D69A964701FF@stanford.edu>

Hi Sydney,

Thank you for contacting us. We?re aware and working to rectify the issue. Apologies for the inconvenience.

Kind regards,
Jennifer



On Jul 16, 2018, at 7:44 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Good morning,

I was trying to access Bioportal this morning and when I attempted to login I was presented with an "expired certificate" message. Your certificate expired yesterday. I just wanted to let you know in case you were not yet aware.

Thanks!

--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314
_______________________________________________
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 Jul 16 12:53:23 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 16 Jul 2018 19:53:23 +0000
Subject: [bioontology-support] Expired Certificate
In-Reply-To: <CD230C13-8E69-4F44-9CD5-D69A964701FF@stanford.edu>
References: <CACcE1G9WR76CsiuNKxJmh+p4dK4W4=NBCw-_sFKmUG2561mNVg@mail.gmail.com>
 <CD230C13-8E69-4F44-9CD5-D69A964701FF@stanford.edu>
Message-ID: <11456DF8-2781-4FCE-9A6E-EDF27DA4EAD4@stanford.edu>

Hi again Sydney,

The security certificate is renewed / fixed for BioPortal now.

Kind regards,
Jennifer



On Jul 16, 2018, at 8:23 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Sydney,

Thank you for contacting us. We?re aware and working to rectify the issue. Apologies for the inconvenience.

Kind regards,
Jennifer



On Jul 16, 2018, at 7:44 AM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Good morning,

I was trying to access Bioportal this morning and when I attempted to login I was presented with an "expired certificate" message. Your certificate expired yesterday. I just wanted to let you know in case you were not yet aware.

Thanks!

--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314
_______________________________________________
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  Mon Jul 16 12:54:59 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 16 Jul 2018 19:54:59 +0000
Subject: [bioontology-support] [BioPortal] Feedback from cvnbioportal
In-Reply-To: <F0413509-CF2B-4DBD-8800-2AB9B74E2AAD@stanford.edu>
References: <5b4ca28326183_17af3fa301504f2c57661@ncbo-prd-app-09.stanford.edu.mail>
 <F0413509-CF2B-4DBD-8800-2AB9B74E2AAD@stanford.edu>
Message-ID: <CC558D60-87EE-4123-872D-455E9FAEAAB1@stanford.edu>

Hello Cristophe,

The BioPortal security certificates are renewed / fixed now.

Jennifer



On Jul 16, 2018, at 7:11 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:


On Jul 16, 2018, at 6:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Connections are not secure.

You provide a really nice resource, but it is really important to offer it in a secure way. I personally use random passwords, so doesn't affect me to much, but for other users it might be exposing their passwords..



We use HTTPS but the security certificate for out site expired over the weekend. Apologies for the inconvenience. We?re working to rectify the situation.

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

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From vendetti at stanford.edu  Mon Jul 16 16:09:49 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 16 Jul 2018 23:09:49 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ORDO_Orphanet
In-Reply-To: <6075b2c2-ca67-7b2e-34d9-8ae0ae66dcaa@inserm.fr>
References: <5b4756c5a7895_5c8d3f8be27201349999a@ncbo-prd-app-08.stanford.edu.mail>
 <56BEBDE4-D26B-46EB-AE21-D3EE626398CF@stanford.edu>
 <6075b2c2-ca67-7b2e-34d9-8ae0ae66dcaa@inserm.fr>
Message-ID: <254F3430-5E5A-4E98-BC48-A5F9C4C4BB9D@stanford.edu>

Hello Marc,


On Jul 16, 2018, at 7:11 AM, Marc Hanauer <marc.hanauer at inserm.fr<mailto:marc.hanauer at inserm.fr>> wrote:


Dear John,

Thanks for your reply.

Well the sequence is quiet simple :

Going to bioportal, login/password entered then error message.

I still have access to the account information but can't reach ORDO page (and yes, we would like to edit the ontology information).

I noticed in a screen shot you provided that you?ve configured BioPortal to use a custom ontology set. I tested the steps you provided using a custom ontology set, and I?m now able to reproduce the 500 error.

This issue was reported by another user and recorded in our issue tracker (https://github.com/ncbo/bioportal_web_ui/issues/36). In short, there?s a bug in the BioPortal software that prevents the use of custom ontology sets for ontologies that have views. ORDO has a view attached called "Orphanet Rare Diseases Ontology in OBO?. I will add more information to the issue report, including where exactly the code is failing and associated error messages.

Apologies, but until this issue is fixed and released to our production system, you?ll need to remove your custom ontology set in order to see the ORDO page. You can do that by:

1). Navigating to your account settings page in BioPortal.
2). At the bottom of the account settings page in the ?Custom Ontology Set? section, click the ?select ontologies? link.
3). Under the ?Select Custom Ontologies? text box, click the ?clear selection? link.
4). Click the ?Save Custom Ontologies? button.

You should then see a message at the top of the page that reads ?Custom Ontologies were cleared?. You should also then be able to navigate to the ORDO summary page and make your desired edits.


I've tried with both Firefox and Chrome. At home as well with a different computer and network.

By the way, we've updated our ontology on our own server this friday (as usual, twice a year). The file was correctly processed by EBI OLS tool but not correctly by bioportal: "RDF error?.

I manually reprocessed your ontology in BioPortal. Version 2.6 is now fully parsed and available:

https://bioportal.bioontology.org/ontologies/ORDO?p=summary


[cid:86D2606C-4B3E-4FA7-AD83-AB0FE4624162 at stanford.edu]


I looked at the log files for the initial attempt to process 2.6. It appears that our system was under heavy load and there were issues writing the data to our backend triplestore. Apologies for that inconvenience.


We've already experienced parser issues with bioportal on some previous version. Seems to be a similar situation again.

There was an issue with version 2.4 where the 3rd party library we use for parsing ontologies (OWL API) was generating blank node identifiers with illegal characters. Details were recorded in our GitHub issue tracker:

https://github.com/ncbo/bioportal-project/issues/31

The OWL API developers fixed the issue with blank node identifiers, as detailed in their issue tracker:

https://github.com/owlcs/owlapi/issues/689

I haven?t seen a reoccurrence of this particular issue since those fixes were incorporated into our system.

Kind regards,
Jennifer



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From vendetti at stanford.edu  Mon Jul 16 17:02:05 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 17 Jul 2018 00:02:05 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mconlon
In-Reply-To: <etPan.5b4a15c0.34cf0e35.a844@ufl.edu>
References: <5b42b01317873_4fd53fdc10605af0935ee@ncbo-prd-app-09.stanford.edu.mail>
 <21D2FE05-E728-435B-97CA-E1307AD12D7A@stanford.edu>
 <37FAD35D-C321-46F9-A61D-4D6FB8EE4376@ufl.edu>
 <88361D0E-C027-4C52-83FF-FE149742D9E3@stanford.edu>
 <2F5B134F-90AD-48DD-9F57-0FD63E2D2C62@ufl.edu>
 <etPan.5b4a15c0.34cf0e35.a844@ufl.edu>
Message-ID: <CA8B46CA-F9F3-4F86-9269-625F3870A138@stanford.edu>

Hello Mike,


On Jul 14, 2018, at 8:24 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

I tried to login to bioportal with the credentails I had created ? account name mconlon, email mconlon at ufl.edu<mailto:mconlon at ufl.edu> and a password I had stored. No luck.  I tried to reset the password and it said there was no such account.

I had made changes to the VIVO record in bioportal and updated the record and the ontology file.  The changes had been saved.  But when I went back the next day, the changes were gone and there was no sign of my being an editor for the VIVO ontology.

So I need to start again.  I don?t know if I have an account, and the VIVO record does not show me as an editor.


I?ve been looking into this issue today. I confirmed the behavior you?re seeing that the system no longer has a user account with account name ?mconlon?. Apologies that I don?t have a complete answer for you at the moment. What I can say is that we did a bulk import of a large amount of ontology data from the National Library of Medicine?s UMLS resource on the same day that I made you an administrator for the VIVO ontology. It seems likely that the import process was responsible for the accidental purge of your user account, though we need to continue looking at this in more detail.

Unfortunately we have very limited IT support and are without a way to expediently restore your account from backups. Would you be willing to recreate your user account in BioPortal? Alternatively, if you don?t have time, I could create the account on your behalf and you could simply reset your password. Once your account is in place, I can re-add you as an administrator to VIVO.

Sincere apologies for the difficulties you?ve experienced thus far.

Kind regards,
Jennifer

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From marc.hanauer at inserm.fr  Tue Jul 17 04:02:42 2018
From: marc.hanauer at inserm.fr (marc.hanauer at inserm.fr)
Date: Tue, 17 Jul 2018 13:02:42 +0200
Subject: [bioontology-support] [BioPortal] Feedback from ORDO_Orphanet
In-Reply-To: <254F3430-5E5A-4E98-BC48-A5F9C4C4BB9D@stanford.edu>
References: <5b4756c5a7895_5c8d3f8be27201349999a@ncbo-prd-app-08.stanford.edu.mail>
 <56BEBDE4-D26B-46EB-AE21-D3EE626398CF@stanford.edu>
 <6075b2c2-ca67-7b2e-34d9-8ae0ae66dcaa@inserm.fr>
 <254F3430-5E5A-4E98-BC48-A5F9C4C4BB9D@stanford.edu>
Message-ID: <0319eb8166801cc7e5a7c43ce594ccb6@inserm.fr>

Hello Jennifer, 

Thanks for your reply. It seems ok now. I've now an access to the
ontology page and also to the edition functionalities. 

Great! 

Best regards,

---

Marc HANAUER
Directeur Adjoint / Deputy Director
Directeur technique / Chief technology officer
Strat?gie et Innovation
marc.hanauer at inserm.fr

ORPHANET - INSERM US14
Plateforme Maladies Rares / Rare Disease Platform
96 rue Didot
75014 PARIS
FRANCE 

Le 17-07-2018 01:09, Jennifer Leigh Vendetti a ?crit :

> Hello Marc, 
> 
>> On Jul 16, 2018, at 7:11 AM, Marc Hanauer <marc.hanauer at inserm.fr> wrote: 
>> 
>> Dear John, 
>> 
>> Thanks for your reply.
>> 
>> Well the sequence is quiet simple : 
>> 
>> Going to bioportal, login/password entered then error message. 
>> 
>> I still have access to the account information but can't reach ORDO page (and yes, we would like to edit the ontology information).
> 
> I noticed in a screen shot you provided that you've configured BioPortal to use a custom ontology set. I tested the steps you provided using a custom ontology set, and I'm now able to reproduce the 500 error. 
> 
> This issue was reported by another user and recorded in our issue tracker (https://github.com/ncbo/bioportal_web_ui/issues/36). In short, there's a bug in the BioPortal software that prevents the use of custom ontology sets for ontologies that have views. ORDO has a view attached called "Orphanet Rare Diseases Ontology in OBO". I will add more information to the issue report, including where exactly the code is failing and associated error messages. 
> 
> Apologies, but until this issue is fixed and released to our production system, you'll need to remove your custom ontology set in order to see the ORDO page. You can do that by: 
> 
> 1). Navigating to your account settings page in BioPortal. 
> 2). At the bottom of the account settings page in the "Custom Ontology Set" section, click the "select ontologies" link. 
> 3). Under the "Select Custom Ontologies" text box, click the "clear selection" link. 
> 4). Click the "Save Custom Ontologies" button.  
> 
> You should then see a message at the top of the page that reads "Custom Ontologies were cleared". You should also then be able to navigate to the ORDO summary page and make your desired edits. 
> 
>> I've tried with both Firefox and Chrome. At home as well with a different computer and network. 
>> 
>> By the way, we've updated our ontology on our own server this friday (as usual, twice a year). The file was correctly processed by EBI OLS tool but not correctly by bioportal: "RDF error".
> 
> I manually reprocessed your ontology in BioPortal. Version 2.6 is now fully parsed and available: 
> 
> https://bioportal.bioontology.org/ontologies/ORDO?p=summary 
> 
> I looked at the log files for the initial attempt to process 2.6. It appears that our system was under heavy load and there were issues writing the data to our backend triplestore. Apologies for that inconvenience.  
> 
>> We've already experienced parser issues with bioportal on some previous version. Seems to be a similar situation again.
> 
> There was an issue with version 2.4 where the 3rd party library we use for parsing ontologies (OWL API) was generating blank node identifiers with illegal characters. Details were recorded in our GitHub issue tracker: 
> 
> https://github.com/ncbo/bioportal-project/issues/31 
> 
> The OWL API developers fixed the issue with blank node identifiers, as detailed in their issue tracker: 
> 
> https://github.com/owlcs/owlapi/issues/689 
> 
> I haven't seen a reoccurrence of this particular issue since those fixes were incorporated into our system. 
> 
> Kind regards, 
> Jennifer
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From msgolec at yahoo.com  Tue Jul 17 01:19:17 2018
From: msgolec at yahoo.com (Marcin Golec)
Date: Tue, 17 Jul 2018 08:19:17 +0000 (UTC)
Subject: [bioontology-support] Hypersensitivity Pneumonitis Ontology (HP_O)
References: <1575438302.5560846.1531815557299.ref@mail.yahoo.com>
Message-ID: <1575438302.5560846.1531815557299@mail.yahoo.com>

Jennifer,
following our e-mail echange earlier this year, I have uploaded our Hypersensitivity Pneumonitis Ontology (HP_O) to the Bioportal, however, it seems that the ontology is not accessible (i.e. when I click on Bioportal purl there is a communicate saying "We are sorry but something has gone wrong").
I would be grateful for your help.
Best regards from Luxembourg,
Marcin

Marcin Golec MD, PhD, MScmsgolec at yahoo.commarcinkgolec@gmal.com??
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From mconlon at ufl.edu  Tue Jul 17 06:25:50 2018
From: mconlon at ufl.edu (Conlon, Mike)
Date: Tue, 17 Jul 2018 13:25:50 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mconlon
In-Reply-To: <CA8B46CA-F9F3-4F86-9269-625F3870A138@stanford.edu>
References: <5b42b01317873_4fd53fdc10605af0935ee@ncbo-prd-app-09.stanford.edu.mail>
 <21D2FE05-E728-435B-97CA-E1307AD12D7A@stanford.edu>
 <37FAD35D-C321-46F9-A61D-4D6FB8EE4376@ufl.edu>
 <88361D0E-C027-4C52-83FF-FE149742D9E3@stanford.edu>
 <2F5B134F-90AD-48DD-9F57-0FD63E2D2C62@ufl.edu>
 <etPan.5b4a15c0.34cf0e35.a844@ufl.edu>
 <CA8B46CA-F9F3-4F86-9269-625F3870A138@stanford.edu>
Message-ID: <87A08BD0-E7D1-4AF8-B466-3E04A981A51D@ufl.edu>

Dang.

I tried to create a new account on bioportal this morning using the same credentials I had used before account name mconlon, email mconlon at ufl.edu<mailto:mconlon at ufl.edu>

I got the error shown in the attached screenshot.
[cid:image001.png at 01D41DB0.264B0F90]

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Monday, July 16, 2018 at 8:02 PM
To: "Conlon, Mike" <mconlon at ufl.edu>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from mconlon

Hello Mike,



On Jul 14, 2018, at 8:24 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

I tried to login to bioportal with the credentails I had created ? account name mconlon, email mconlon at ufl.edu<mailto:mconlon at ufl.edu> and a password I had stored. No luck.  I tried to reset the password and it said there was no such account.

I had made changes to the VIVO record in bioportal and updated the record and the ontology file.  The changes had been saved.  But when I went back the next day, the changes were gone and there was no sign of my being an editor for the VIVO ontology.

So I need to start again.  I don?t know if I have an account, and the VIVO record does not show me as an editor.


I?ve been looking into this issue today. I confirmed the behavior you?re seeing that the system no longer has a user account with account name ?mconlon?. Apologies that I don?t have a complete answer for you at the moment. What I can say is that we did a bulk import of a large amount of ontology data from the National Library of Medicine?s UMLS resource on the same day that I made you an administrator for the VIVO ontology. It seems likely that the import process was responsible for the accidental purge of your user account, though we need to continue looking at this in more detail.

Unfortunately we have very limited IT support and are without a way to expediently restore your account from backups. Would you be willing to recreate your user account in BioPortal? Alternatively, if you don?t have time, I could create the account on your behalf and you could simply reset your password. Once your account is in place, I can re-add you as an administrator to VIVO.

Sincere apologies for the difficulties you?ve experienced thus far.

Kind regards,
Jennifer

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From vendetti at stanford.edu  Tue Jul 17 07:02:46 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 17 Jul 2018 14:02:46 +0000
Subject: [bioontology-support] Hypersensitivity Pneumonitis Ontology
	(HP_O)
In-Reply-To: <1575438302.5560846.1531815557299@mail.yahoo.com>
References: <1575438302.5560846.1531815557299.ref@mail.yahoo.com>
 <1575438302.5560846.1531815557299@mail.yahoo.com>
Message-ID: <B9539C6F-58D4-4522-A4CC-3AC986D0F296@stanford.edu>

Hello Marcin,


On Jul 17, 2018, at 1:19 AM, Marcin Golec <msgolec at yahoo.com<mailto:msgolec at yahoo.com>> wrote:

Jennifer,

following our e-mail echange earlier this year, I have uploaded our Hypersensitivity Pneumonitis Ontology (HP_O) to the Bioportal, however, it seems that the ontology is not accessible (i.e. when I click on Bioportal purl there is a communicate saying "We are sorry but something has gone wrong?).


I looked at our system log files and there appears to have been an error on the first attempt to process the ontology. I manually reprocessed your ontology and cleared our application caches. I?m able to access the ontology now without errors. Let me know if you?re seeing the same.

Apologies for the inconvenience.

Kind regards,
Jennifer



[cid:B148B4EF-0D2C-4448-BF72-B3A2F6EEC974 at stanford.edu]



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From jgraybeal at stanford.edu  Tue Jul 17 07:54:15 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 17 Jul 2018 14:54:15 +0000
Subject: [bioontology-support] your registration to BioPortal
Message-ID: <FD44957C-1E11-4FCD-966F-0FEF708128F1@stanford.edu>

Hello Mike,

I just tried to register and it seemed to go OK. There may have been an ongoing outage when you tried it, I'm not sure.

I've requested a password reset, you should have instructions in your email on how to reset your password.

John


On Jul 17, 2018, at 6:25 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

<image001.png>

========================
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  Tue Jul 17 09:18:50 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 17 Jul 2018 16:18:50 +0000
Subject: [bioontology-support] your registration to BioPortal
In-Reply-To: <A1487A98-2CC9-4888-BDAB-D3AAAFAC5517@ufl.edu>
References: <FD44957C-1E11-4FCD-966F-0FEF708128F1@stanford.edu>,
 <A1487A98-2CC9-4888-BDAB-D3AAAFAC5517@ufl.edu>
Message-ID: <SN6PR02MB4639EA2002598E9A4D39A5BBDA5C0@SN6PR02MB4639.namprd02.prod.outlook.com>

Ok, thank you for trying that and I?m very sorry for all this difficulty. I will have to ask Jennifer to take it from here, as I am on travel and these are some very unusual symptoms.

John

________________________________
From: Conlon, Mike <mconlon at ufl.edu>
Sent: Tuesday, July 17, 2018 8:47:21 AM
To: John Graybeal
Cc: NCBO User Support
Subject: Re: your registration to BioPortal

Hi John,

I tried to use the link in the password reset to reset my password.  Error message attached:

[cid:image001.png at 01D41DC3.EB559630]

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: John Graybeal <jgraybeal at stanford.edu>
Date: Tuesday, July 17, 2018 at 10:54 AM
To: "Conlon, Mike" <mconlon at ufl.edu>
Cc: NCBO User Support <support at bioontology.org>
Subject: your registration to BioPortal

Hello Mike,

I just tried to register and it seemed to go OK. There may have been an ongoing outage when you tried it, I'm not sure.

I've requested a password reset, you should have instructions in your email on how to reset your password.

John


On Jul 17, 2018, at 6:25 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

<image001.png>

========================
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 msgolec at yahoo.com  Tue Jul 17 08:21:18 2018
From: msgolec at yahoo.com (Marcin Golec)
Date: Tue, 17 Jul 2018 15:21:18 +0000 (UTC)
Subject: [bioontology-support] Hypersensitivity Pneumonitis Ontology
	(HP_O)
In-Reply-To: <B9539C6F-58D4-4522-A4CC-3AC986D0F296@stanford.edu>
References: <1575438302.5560846.1531815557299.ref@mail.yahoo.com>
 <1575438302.5560846.1531815557299@mail.yahoo.com>
 <B9539C6F-58D4-4522-A4CC-3AC986D0F296@stanford.edu>
Message-ID: <106948503.5719004.1531840878569@mail.yahoo.com>

 Jennifer,
thank you for your prompt reply.
It still does not work. When I click on "purlbioontology..." link it shows the following communicate:


How we will proceed now?
Perhaps I may upload it again (how?) or I may send you the owl file and you will upload it?
Best regards,
Marcin    On Tuesday, July 17, 2018, 4:02:59 PM GMT+2, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:  
 
 Hello Marcin,


On Jul 17, 2018, at 1:19 AM, Marcin Golec <msgolec at yahoo.com> wrote:
Jennifer,
following our e-mail echange earlier this year, I have uploaded ourHypersensitivity Pneumonitis Ontology (HP_O) to the Bioportal, however, it seems that the ontology is not accessible (i.e. when I click on Bioportal purl there is a communicate saying "We are sorry but something has gone wrong?).


I looked at our system log files and there appears to have been an error on the first attempt to process the ontology. I manually reprocessed your ontology and cleared our application caches. I?m able to access the ontology now without errors. Let me know if you?re seeing the same.
Apologies for the inconvenience.
Kind regards,Jennifer





  
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From mconlon at ufl.edu  Tue Jul 17 08:47:21 2018
From: mconlon at ufl.edu (Conlon, Mike)
Date: Tue, 17 Jul 2018 15:47:21 +0000
Subject: [bioontology-support] your registration to BioPortal
In-Reply-To: <FD44957C-1E11-4FCD-966F-0FEF708128F1@stanford.edu>
References: <FD44957C-1E11-4FCD-966F-0FEF708128F1@stanford.edu>
Message-ID: <A1487A98-2CC9-4888-BDAB-D3AAAFAC5517@ufl.edu>

Hi John,

I tried to use the link in the password reset to reset my password.  Error message attached:

[cid:image001.png at 01D41DC3.EB559630]

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: John Graybeal <jgraybeal at stanford.edu>
Date: Tuesday, July 17, 2018 at 10:54 AM
To: "Conlon, Mike" <mconlon at ufl.edu>
Cc: NCBO User Support <support at bioontology.org>
Subject: your registration to BioPortal

Hello Mike,

I just tried to register and it seemed to go OK. There may have been an ongoing outage when you tried it, I'm not sure.

I've requested a password reset, you should have instructions in your email on how to reset your password.

John


On Jul 17, 2018, at 6:25 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

<image001.png>

========================
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 vendetti at stanford.edu  Tue Jul 17 10:56:26 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 17 Jul 2018 17:56:26 +0000
Subject: [bioontology-support] Hypersensitivity Pneumonitis Ontology
	(HP_O)
In-Reply-To: <336993832.5813493.1531847024190@mail.yahoo.com>
References: <1575438302.5560846.1531815557299.ref@mail.yahoo.com>
 <1575438302.5560846.1531815557299@mail.yahoo.com>
 <B9539C6F-58D4-4522-A4CC-3AC986D0F296@stanford.edu>
 <106948503.5719004.1531840878569@mail.yahoo.com>
 <336993832.5813493.1531847024190@mail.yahoo.com>
Message-ID: <5524328A-E4A8-44F4-9046-BCF743352EBC@stanford.edu>

Hello Marcin,

I just got indication from the person that does our IT support that a large amount of logging filled up the disk space on one of our UI servers. The side effect was that a number of ontology pages in the BioPortal UI weren?t accessible. I?m under the impression this has been fixed now. Apologies for that inconvenience. Please let us know if you have further issues.

Best,
Jennifer



On Jul 17, 2018, at 10:03 AM, Marcin Golec <msgolec at yahoo.com<mailto:msgolec at yahoo.com>> wrote:

Jennifer,

I have just looked at it again and it seems that it works now.

Thank you for your help.

Best regards,

Marcin

----- Forwarded Message -----
From: Marcin Golec <msgolec at yahoo.com<mailto:msgolec at yahoo.com>>
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: Bioontology Support <support at bioontology.org<mailto:support at bioontology.org>>
Sent: Tuesday, July 17, 2018, 5:21:18 PM GMT+2
Subject: Re: Hypersensitivity Pneumonitis Ontology (HP_O)

Jennifer,

thank you for your prompt reply.

It still does not work. When I click on "purlbioontology..." link it shows the following communicate:

<1531840809991blob.jpg>

How we will proceed now?

Perhaps I may upload it again (how?) or I may send you the owl file and you will upload it?

Best regards,

Marcin
On Tuesday, July 17, 2018, 4:02:59 PM GMT+2, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:


Hello Marcin,


On Jul 17, 2018, at 1:19 AM, Marcin Golec <msgolec at yahoo.com<mailto:msgolec at yahoo.com>> wrote:

Jennifer,

following our e-mail echange earlier this year, I have uploaded our Hypersensitivity Pneumonitis Ontology (HP_O) to the Bioportal, however, it seems that the ontology is not accessible (i.e. when I click on Bioportal purl there is a communicate saying "We are sorry but something has gone wrong?).


I looked at our system log files and there appears to have been an error on the first attempt to process the ontology. I manually reprocessed your ontology and cleared our application caches. I?m able to access the ontology now without errors. Let me know if you?re seeing the same.

Apologies for the inconvenience.

Kind regards,
Jennifer



<Screenshot 2018-07-17 07.00.48.png>



<1531840809991blob.jpg><Screenshot 2018-07-17 07.00.48.png>

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From vendetti at stanford.edu  Tue Jul 17 11:18:33 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 17 Jul 2018 18:18:33 +0000
Subject: [bioontology-support] your registration to BioPortal
In-Reply-To: <A1487A98-2CC9-4888-BDAB-D3AAAFAC5517@ufl.edu>
References: <FD44957C-1E11-4FCD-966F-0FEF708128F1@stanford.edu>
 <A1487A98-2CC9-4888-BDAB-D3AAAFAC5517@ufl.edu>
Message-ID: <F1566FA2-EB13-4F22-990C-522745DCB98D@stanford.edu>

Hi Mike,

I?m picking up this thread from John. Another BioPortal user sent us the same screenshot this morning. I was notified by the person that does our IT support that one of our UI servers ran out of disk space and a number of pages in the BioPortal application were inaccessible. I just went through a test cycle of account creation and resetting a password and the system behaved as expected. It may work for you now if you?re willing to try again. If not, could you please forward me privately your password reset email (vendetti at stanford.edu<http://stanford.edu>) so that I can test the link in my local development environment?

Thanks for your continued patience with us.

Kind regards,
Jennifer



On Jul 17, 2018, at 8:47 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Hi John,

I tried to use the link in the password reset to reset my password.  Error message attached:

<image001.png>

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Tuesday, July 17, 2018 at 10:54 AM
To: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
Cc: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: your registration to BioPortal

Hello Mike,

I just tried to register and it seemed to go OK. There may have been an ongoing outage when you tried it, I'm not sure.

I've requested a password reset, you should have instructions in your email on how to reset your password.

John


On Jul 17, 2018, at 6:25 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

<image001.png>

========================
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 mconlon at ufl.edu  Tue Jul 17 11:28:17 2018
From: mconlon at ufl.edu (Conlon, Mike)
Date: Tue, 17 Jul 2018 18:28:17 +0000
Subject: [bioontology-support] your registration to BioPortal
In-Reply-To: <F1566FA2-EB13-4F22-990C-522745DCB98D@stanford.edu>
References: <FD44957C-1E11-4FCD-966F-0FEF708128F1@stanford.edu>
 <A1487A98-2CC9-4888-BDAB-D3AAAFAC5517@ufl.edu>
 <F1566FA2-EB13-4F22-990C-522745DCB98D@stanford.edu>
Message-ID: <FDDE8AA8-6A5A-4C18-A20F-10F645ACBF0B@ufl.edu>

Jennifer,

I was able to reset my password, sign off and sign back on.  All good.

I was unable to visit the VIVO ontology page ?We?re sorry, something has gone wrong.:

Can you please authorize me as the caretaker for the VIVO ontology?  I?d also like to see VIVO added to the Bibliographic group as well as the CTSA group it is now.

Thanks for all the help.  I sure this will all settle down.

Mike

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Tuesday, July 17, 2018 at 2:18 PM
To: "Conlon, Mike" <mconlon at ufl.edu>
Cc: John Graybeal <jgraybeal at stanford.edu>, NCBO User Support <support at bioontology.org>
Subject: Re: [bioontology-support] your registration to BioPortal

Hi Mike,

I?m picking up this thread from John. Another BioPortal user sent us the same screenshot this morning. I was notified by the person that does our IT support that one of our UI servers ran out of disk space and a number of pages in the BioPortal application were inaccessible. I just went through a test cycle of account creation and resetting a password and the system behaved as expected. It may work for you now if you?re willing to try again. If not, could you please forward me privately your password reset email (vendetti at stanford.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__stanford.edu&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VbHOYFnkuHfebclr08IB3VpT-l8j1Vn6BL_jdeBgSpQ&s=vlkEQ1BamzDfJX8dwzI0Y4kdmWFcBPbLPLkDI9X9jzc&e=>) so that I can test the link in my local development environment?

Thanks for your continued patience with us.

Kind regards,
Jennifer




On Jul 17, 2018, at 8:47 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Hi John,

I tried to use the link in the password reset to reset my password.  Error message attached:

<image001.png>

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Tuesday, July 17, 2018 at 10:54 AM
To: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
Cc: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: your registration to BioPortal

Hello Mike,

I just tried to register and it seemed to go OK. There may have been an ongoing outage when you tried it, I'm not sure.

I've requested a password reset, you should have instructions in your email on how to reset your password.

John


On Jul 17, 2018, at 6:25 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

<image001.png>

========================
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<https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VbHOYFnkuHfebclr08IB3VpT-l8j1Vn6BL_jdeBgSpQ&s=iPS-OL4BhQRYbqv-NfnTflYCN_IjTNAl-b_QRgqsj94&e=>

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From support at bioontology.org  Tue Jul 17 11:27:09 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 17 Jul 2018 11:27:09 -0700
Subject: [bioontology-support] [BioPortal] Feedback from fawks
Message-ID: <5b4e34fdd74ec_4b593fba4b399348503d@ncbo-prd-app-09.stanford.edu.mail>

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From abdul.ally at thermofisher.com  Tue Jul 17 11:40:17 2018
From: abdul.ally at thermofisher.com (Ally, Abdul)
Date: Tue, 17 Jul 2018 18:40:17 +0000
Subject: [bioontology-support] bioontology-support Digest, Vol 123,
	Issue 41
In-Reply-To: <mailman.44315.1531851587.24310.bioontology-support@lists.stanford.edu>
References: <mailman.44315.1531851587.24310.bioontology-support@lists.stanford.edu>
Message-ID: <A9AD8A44-3890-46F2-B2C3-0147CE6453F9@thermofisher.com>

Got it! 

Abdul Ally
Area Director, Laboratory Science and Operations

Thermo Fisher Scientific
14665 Rothgeb Drive | Rockville, MD 20850

> On Jul 17, 2018, at 2:19 PM, "bioontology-support-request at lists.stanford.edu" <bioontology-support-request at lists.stanford.edu> wrote:
> 
> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.
> 
> 
> Send bioontology-support mailing list submissions to
>        bioontology-support at lists.stanford.edu
> 
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of bioontology-support digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: Hypersensitivity Pneumonitis Ontology (HP_O)
>      (Jennifer Leigh Vendetti)
>   2. Re: your registration to BioPortal (Jennifer Leigh Vendetti)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 17 Jul 2018 17:56:26 +0000
> From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
> To: Marcin Golec <msgolec at yahoo.com>
> Cc: "bioontology-support at lists.stanford.edu"
>        <bioontology-support at lists.stanford.edu>
> Subject: Re: [bioontology-support] Hypersensitivity Pneumonitis
>        Ontology        (HP_O)
> Message-ID: <5524328A-E4A8-44F4-9046-BCF743352EBC at stanford.edu>
> Content-Type: text/plain; charset="utf-8"
> 
> Hello Marcin,
> 
> I just got indication from the person that does our IT support that a large amount of logging filled up the disk space on one of our UI servers. The side effect was that a number of ontology pages in the BioPortal UI weren?t accessible. I?m under the impression this has been fixed now. Apologies for that inconvenience. Please let us know if you have further issues.
> 
> Best,
> Jennifer
> 
> 
> 
> On Jul 17, 2018, at 10:03 AM, Marcin Golec <msgolec at yahoo.com<mailto:msgolec at yahoo.com>> wrote:
> 
> Jennifer,
> 
> I have just looked at it again and it seems that it works now.
> 
> Thank you for your help.
> 
> Best regards,
> 
> Marcin
> 
> ----- Forwarded Message -----
> From: Marcin Golec <msgolec at yahoo.com<mailto:msgolec at yahoo.com>>
> To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
> Cc: Bioontology Support <support at bioontology.org<mailto:support at bioontology.org>>
> Sent: Tuesday, July 17, 2018, 5:21:18 PM GMT+2
> Subject: Re: Hypersensitivity Pneumonitis Ontology (HP_O)
> 
> Jennifer,
> 
> thank you for your prompt reply.
> 
> It still does not work. When I click on "purlbioontology..." link it shows the following communicate:
> 
> <1531840809991blob.jpg>
> 
> How we will proceed now?
> 
> Perhaps I may upload it again (how?) or I may send you the owl file and you will upload it?
> 
> Best regards,
> 
> Marcin
> On Tuesday, July 17, 2018, 4:02:59 PM GMT+2, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
> 
> 
> Hello Marcin,
> 
> 
> On Jul 17, 2018, at 1:19 AM, Marcin Golec <msgolec at yahoo.com<mailto:msgolec at yahoo.com>> wrote:
> 
> Jennifer,
> 
> following our e-mail echange earlier this year, I have uploaded our Hypersensitivity Pneumonitis Ontology (HP_O) to the Bioportal, however, it seems that the ontology is not accessible (i.e. when I click on Bioportal purl there is a communicate saying "We are sorry but something has gone wrong?).
> 
> 
> I looked at our system log files and there appears to have been an error on the first attempt to process the ontology. I manually reprocessed your ontology and cleared our application caches. I?m able to access the ontology now without errors. Let me know if you?re seeing the same.
> 
> Apologies for the inconvenience.
> 
> Kind regards,
> Jennifer
> 
> 
> 
> <Screenshot 2018-07-17 07.00.48.png>
> 
> 
> 
> <1531840809991blob.jpg><Screenshot 2018-07-17 07.00.48.png>
> 
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> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 17 Jul 2018 18:18:33 +0000
> From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
> To: "Conlon, Mike" <mconlon at ufl.edu>
> Cc: John Graybeal <jgraybeal at stanford.edu>, NCBO User Support
>        <support at bioontology.org>
> Subject: Re: [bioontology-support] your registration to BioPortal
> Message-ID: <F1566FA2-EB13-4F22-990C-522745DCB98D at stanford.edu>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Mike,
> 
> I?m picking up this thread from John. Another BioPortal user sent us the same screenshot this morning. I was notified by the person that does our IT support that one of our UI servers ran out of disk space and a number of pages in the BioPortal application were inaccessible. I just went through a test cycle of account creation and resetting a password and the system behaved as expected. It may work for you now if you?re willing to try again. If not, could you please forward me privately your password reset email (vendetti at stanford.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__stanford.edu&d=DwICAg&c=q6k2DsTcEGCcCb_WtVSz6hhIl8hvYssy7sH8ZwfbbKU&r=34WErv924Zyuu7uIrWyVmfq_VmgZkl9Vr5kWlMjPIdE&m=lZ322HoemrdfLNX7CwLV2nQoe3isTJI1uGjRwIx6YOE&s=1d2EP2Fxq4DeUsj-Hlgmc2zYQ_EMMV-8EDTp0ER5_rI&e=>) so that I can test the link in my local development environment?
> 
> Thanks for your continued patience with us.
> 
> Kind regards,
> Jennifer
> 
> 
> 
> On Jul 17, 2018, at 8:47 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:
> 
> Hi John,
> 
> I tried to use the link in the password reset to reset my password.  Error message attached:
> 
> <image001.png>
> 
> Michael Conlon, PhD
> VIVO Project Director
> Emeritus Faculty
> University of Florida
> 
> 
> 
> From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
> Date: Tuesday, July 17, 2018 at 10:54 AM
> To: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
> Cc: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
> Subject: your registration to BioPortal
> 
> Hello Mike,
> 
> I just tried to register and it seemed to go OK. There may have been an ongoing outage when you tried it, I'm not sure.
> 
> I've requested a password reset, you should have instructions in your email on how to reset your password.
> 
> John
> 
> 
> On Jul 17, 2018, at 6:25 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:
> 
> <image001.png>
> 
> ========================
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwICAg&c=q6k2DsTcEGCcCb_WtVSz6hhIl8hvYssy7sH8ZwfbbKU&r=34WErv924Zyuu7uIrWyVmfq_VmgZkl9Vr5kWlMjPIdE&m=lZ322HoemrdfLNX7CwLV2nQoe3isTJI1uGjRwIx6YOE&s=7ztVKmPuXEmtnb8SvFISe5R8X3NLaxfKqB7JBlMmYeI&e=
> 
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> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwICAg&c=q6k2DsTcEGCcCb_WtVSz6hhIl8hvYssy7sH8ZwfbbKU&r=34WErv924Zyuu7uIrWyVmfq_VmgZkl9Vr5kWlMjPIdE&m=lZ322HoemrdfLNX7CwLV2nQoe3isTJI1uGjRwIx6YOE&s=7ztVKmPuXEmtnb8SvFISe5R8X3NLaxfKqB7JBlMmYeI&e=
> 
> 
> ------------------------------
> 
> End of bioontology-support Digest, Vol 123, Issue 41
> ****************************************************

From vendetti at stanford.edu  Tue Jul 17 11:55:33 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 17 Jul 2018 18:55:33 +0000
Subject: [bioontology-support] your registration to BioPortal
In-Reply-To: <FDDE8AA8-6A5A-4C18-A20F-10F645ACBF0B@ufl.edu>
References: <FD44957C-1E11-4FCD-966F-0FEF708128F1@stanford.edu>
 <A1487A98-2CC9-4888-BDAB-D3AAAFAC5517@ufl.edu>
 <F1566FA2-EB13-4F22-990C-522745DCB98D@stanford.edu>
 <FDDE8AA8-6A5A-4C18-A20F-10F645ACBF0B@ufl.edu>
Message-ID: <CE833E0C-57C9-4CD6-8DE0-6019905AF050@stanford.edu>

Hi Mike,

I added your mconlon account as an administrator for VIVO, and added VIVO to the Bibliographic Materials Group.

With regard to the 500 error on the VIVO page - have you by chance configured your account to use a custom ontology set? This functionality isn?t working for ontologies with views (VIVO has 11 associated views).

So far this morning I haven?t been able to reproduce this on my end. I wonder if there is an issue now with the browser cache. Did you by chance try to refresh the VIVO page using Cmd+Shift R (Mac) or Ctrl+Shift+R (Windows/Linux)? If you let me know what browser you?re using, I could send more specific instructions for selectively clearing BioPortal?s cache.

Best,
Jennifer



[cid:735E5393-8A7A-43EB-87B5-52AAC2E90157 at stanford.edu]




[cid:F5134243-593F-4CF8-9967-34CEC876AC1D at stanford.edu]







On Jul 17, 2018, at 11:28 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Jennifer,

I was able to reset my password, sign off and sign back on.  All good.

I was unable to visit the VIVO ontology page ?We?re sorry, something has gone wrong.:

Can you please authorize me as the caretaker for the VIVO ontology?  I?d also like to see VIVO added to the Bibliographic group as well as the CTSA group it is now.

Thanks for all the help.  I sure this will all settle down.

Mike

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Date: Tuesday, July 17, 2018 at 2:18 PM
To: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
Cc: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>, NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] your registration to BioPortal

Hi Mike,

I?m picking up this thread from John. Another BioPortal user sent us the same screenshot this morning. I was notified by the person that does our IT support that one of our UI servers ran out of disk space and a number of pages in the BioPortal application were inaccessible. I just went through a test cycle of account creation and resetting a password and the system behaved as expected. It may work for you now if you?re willing to try again. If not, could you please forward me privately your password reset email (vendetti at stanford.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__stanford.edu&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VbHOYFnkuHfebclr08IB3VpT-l8j1Vn6BL_jdeBgSpQ&s=vlkEQ1BamzDfJX8dwzI0Y4kdmWFcBPbLPLkDI9X9jzc&e=>) so that I can test the link in my local development environment?

Thanks for your continued patience with us.

Kind regards,
Jennifer




On Jul 17, 2018, at 8:47 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Hi John,

I tried to use the link in the password reset to reset my password.  Error message attached:

<image001.png>

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Tuesday, July 17, 2018 at 10:54 AM
To: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
Cc: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: your registration to BioPortal

Hello Mike,

I just tried to register and it seemed to go OK. There may have been an ongoing outage when you tried it, I'm not sure.

I've requested a password reset, you should have instructions in your email on how to reset your password.

John


On Jul 17, 2018, at 6:25 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

<image001.png>

========================
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<https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VbHOYFnkuHfebclr08IB3VpT-l8j1Vn6BL_jdeBgSpQ&s=iPS-OL4BhQRYbqv-NfnTflYCN_IjTNAl-b_QRgqsj94&e=>

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From vendetti at stanford.edu  Tue Jul 17 11:58:34 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 17 Jul 2018 18:58:34 +0000
Subject: [bioontology-support] [BioPortal] Feedback from fawks
In-Reply-To: <5b4e34fdd74ec_4b593fba4b399348503d@ncbo-prd-app-09.stanford.edu.mail>
References: <5b4e34fdd74ec_4b593fba4b399348503d@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <A4182173-2E02-4535-BB9B-BCFACE783583@stanford.edu>

Hello,

On Jul 17, 2018, at 11:27 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: fawks

Email: fawks14 at gmail.com<mailto:fawks14 at gmail.com>

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

Feedback:

Hi, I am currently working on java application where I need to get all MEDDRA ontologies

This is not enough information for us to help you. What do you mean by ?get all MEDDRA ontologies?? Are you attempting to download the ontology source files for every submission of MEDDRA? Or, are you trying to download all the class data for MEDDRA? Please send a specific example of the API call you?re issuing.


but after approximately 200 parsed values I get connection reset. Apparently server closes the connection to me. Could you please explain to me why that could happen and what I possibly do wrong. Thank you in advance.



Please include the stack trace from your Java program.

Jennifer

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From msgolec at yahoo.com  Tue Jul 17 12:00:33 2018
From: msgolec at yahoo.com (Marcin Golec)
Date: Tue, 17 Jul 2018 19:00:33 +0000 (UTC)
Subject: [bioontology-support] Hypersensitivity Pneumonitis Ontology
	(HP_O)
In-Reply-To: <5524328A-E4A8-44F4-9046-BCF743352EBC@stanford.edu>
References: <1575438302.5560846.1531815557299.ref@mail.yahoo.com>
 <1575438302.5560846.1531815557299@mail.yahoo.com>
 <B9539C6F-58D4-4522-A4CC-3AC986D0F296@stanford.edu>
 <106948503.5719004.1531840878569@mail.yahoo.com>
 <336993832.5813493.1531847024190@mail.yahoo.com>
 <5524328A-E4A8-44F4-9046-BCF743352EBC@stanford.edu>
Message-ID: <558942834.5881634.1531854033057@mail.yahoo.com>

 Jennifer,
thank you.
I am also under impression how fast you, Americans, are acting. My respect.
Best regards from Europe,
Marcin
    On Tuesday, July 17, 2018, 7:56:32 PM GMT+2, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:  
 
 Hello Marcin,
I just got indication from the person that does our IT support that a large amount of logging filled up the disk space on one of our UI servers. The side effect was that a number of ontology pages in the BioPortal UI weren?t accessible. I?m under the impression this has been fixed now. Apologies for that inconvenience. Please let us know if you have further issues.
Best,Jennifer



On Jul 17, 2018, at 10:03 AM, Marcin Golec <msgolec at yahoo.com> wrote:
Jennifer,
I have just looked at it again and it seems that it works now.
Thank you for your help.
Best regards,
Marcin
----- Forwarded Message -----From: Marcin Golec <msgolec at yahoo.com>To: Jennifer Leigh Vendetti <vendetti at stanford.edu>Cc: Bioontology Support <support at bioontology.org>Sent: Tuesday, July 17, 2018, 5:21:18 PM GMT+2Subject: Re: Hypersensitivity Pneumonitis Ontology (HP_O)
Jennifer,
thank you for your prompt reply.
It still does not work. When I click on "purlbioontology..." link it shows the following communicate:
<1531840809991blob.jpg>

How we will proceed now?
Perhaps I may upload it again (how?) or I may send you the owl file and you will upload it?
Best regards,
MarcinOn Tuesday, July 17, 2018, 4:02:59 PM GMT+2, Jennifer Leigh Vendetti <vendetti at stanford.edu> wrote:

Hello Marcin,


On Jul 17, 2018, at 1:19 AM, Marcin Golec <msgolec at yahoo.com> wrote:
Jennifer,
following our e-mail echange earlier this year, I have uploaded ourHypersensitivity Pneumonitis Ontology (HP_O) to the Bioportal, however, it seems that the ontology is not accessible (i.e. when I click on Bioportal purl there is a communicate saying "We are sorry but something has gone wrong?).


I looked at our system log files and there appears to have been an error on the first attempt to process the ontology. I manually reprocessed your ontology and cleared our application caches. I?m able to access the ontology now without errors. Let me know if you?re seeing the same.
Apologies for the inconvenience.
Kind regards,Jennifer


<Screenshot 2018-07-17 07.00.48.png>


<1531840809991blob.jpg><Screenshot 2018-07-17 07.00.48.png>

  
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From mconlon at ufl.edu  Tue Jul 17 15:06:15 2018
From: mconlon at ufl.edu (Conlon, Mike)
Date: Tue, 17 Jul 2018 22:06:15 +0000
Subject: [bioontology-support] your registration to BioPortal
In-Reply-To: <CE833E0C-57C9-4CD6-8DE0-6019905AF050@stanford.edu>
References: <FD44957C-1E11-4FCD-966F-0FEF708128F1@stanford.edu>
 <A1487A98-2CC9-4888-BDAB-D3AAAFAC5517@ufl.edu>
 <F1566FA2-EB13-4F22-990C-522745DCB98D@stanford.edu>
 <FDDE8AA8-6A5A-4C18-A20F-10F645ACBF0B@ufl.edu>
 <CE833E0C-57C9-4CD6-8DE0-6019905AF050@stanford.edu>
Message-ID: <196134D2-77E4-4546-8E4D-FE129C339C0A@ufl.edu>

Jennifer,

Yes, I configured to use custom ontology set.  I undid that and was able to make progress.  I uploaded our current ontology version, which bioportal is processing.

I?ll check back tomorrow to see how things went.

Thank you for all your help!

Regards,

Mike


Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Tuesday, July 17, 2018 at 2:55 PM
To: "Conlon, Mike" <mconlon at ufl.edu>
Cc: NCBO User Support <support at bioontology.org>
Subject: Re: [bioontology-support] your registration to BioPortal

Hi Mike,

I added your mconlon account as an administrator for VIVO, and added VIVO to the Bibliographic Materials Group.

With regard to the 500 error on the VIVO page - have you by chance configured your account to use a custom ontology set? This functionality isn?t working for ontologies with views (VIVO has 11 associated views).

So far this morning I haven?t been able to reproduce this on my end. I wonder if there is an issue now with the browser cache. Did you by chance try to refresh the VIVO page using Cmd+Shift R (Mac) or Ctrl+Shift+R (Windows/Linux)? If you let me know what browser you?re using, I could send more specific instructions for selectively clearing BioPortal?s cache.

Best,
Jennifer



[cid:735E5393-8A7A-43EB-87B5-52AAC2E90157 at stanford.edu]




[cid:F5134243-593F-4CF8-9967-34CEC876AC1D at stanford.edu]








On Jul 17, 2018, at 11:28 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Jennifer,

I was able to reset my password, sign off and sign back on.  All good.

I was unable to visit the VIVO ontology page ?We?re sorry, something has gone wrong.:

Can you please authorize me as the caretaker for the VIVO ontology?  I?d also like to see VIVO added to the Bibliographic group as well as the CTSA group it is now.

Thanks for all the help.  I sure this will all settle down.

Mike

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Date: Tuesday, July 17, 2018 at 2:18 PM
To: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
Cc: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>, NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] your registration to BioPortal

Hi Mike,

I?m picking up this thread from John. Another BioPortal user sent us the same screenshot this morning. I was notified by the person that does our IT support that one of our UI servers ran out of disk space and a number of pages in the BioPortal application were inaccessible. I just went through a test cycle of account creation and resetting a password and the system behaved as expected. It may work for you now if you?re willing to try again. If not, could you please forward me privately your password reset email (vendetti at stanford.edu<https://urldefense.proofpoint.com/v2/url?u=http-3A__stanford.edu&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VbHOYFnkuHfebclr08IB3VpT-l8j1Vn6BL_jdeBgSpQ&s=vlkEQ1BamzDfJX8dwzI0Y4kdmWFcBPbLPLkDI9X9jzc&e=>) so that I can test the link in my local development environment?

Thanks for your continued patience with us.

Kind regards,
Jennifer





On Jul 17, 2018, at 8:47 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Hi John,

I tried to use the link in the password reset to reset my password.  Error message attached:

<image001.png>

Michael Conlon, PhD
VIVO Project Director
Emeritus Faculty
University of Florida



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Tuesday, July 17, 2018 at 10:54 AM
To: "Conlon, Mike" <mconlon at ufl.edu<mailto:mconlon at ufl.edu>>
Cc: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: your registration to BioPortal

Hello Mike,

I just tried to register and it seemed to go OK. There may have been an ongoing outage when you tried it, I'm not sure.

I've requested a password reset, you should have instructions in your email on how to reset your password.

John


On Jul 17, 2018, at 6:25 AM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

<image001.png>

========================
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<https://urldefense.proofpoint.com/v2/url?u=https-3A__mailman.stanford.edu_mailman_listinfo_bioontology-2Dsupport&d=DwMGaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=0KAeOm4xReLRjGI8tqzw-A&m=VbHOYFnkuHfebclr08IB3VpT-l8j1Vn6BL_jdeBgSpQ&s=iPS-OL4BhQRYbqv-NfnTflYCN_IjTNAl-b_QRgqsj94&e=>

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From vendetti at stanford.edu  Tue Jul 17 15:19:49 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 17 Jul 2018 22:19:49 +0000
Subject: [bioontology-support] your registration to BioPortal
In-Reply-To: <196134D2-77E4-4546-8E4D-FE129C339C0A@ufl.edu>
References: <FD44957C-1E11-4FCD-966F-0FEF708128F1@stanford.edu>
 <A1487A98-2CC9-4888-BDAB-D3AAAFAC5517@ufl.edu>
 <F1566FA2-EB13-4F22-990C-522745DCB98D@stanford.edu>
 <FDDE8AA8-6A5A-4C18-A20F-10F645ACBF0B@ufl.edu>
 <CE833E0C-57C9-4CD6-8DE0-6019905AF050@stanford.edu>
 <196134D2-77E4-4546-8E4D-FE129C339C0A@ufl.edu>
Message-ID: <950619C6-4495-43DE-B16C-CA9B41730401@stanford.edu>


On Jul 17, 2018, at 3:06 PM, Conlon, Mike <mconlon at ufl.edu<mailto:mconlon at ufl.edu>> wrote:

Yes, I configured to use custom ontology set.  I undid that and was able to make progress.


OK. Glad to hear that. We have an issue in our tracker for this problem with custom ontology sets: https://github.com/ncbo/bioportal_web_ui/issues/36.


I uploaded our current ontology version, which bioportal is processing.


It looks like your new submission is fully processed and available now:


[cid:6E18FABF-5A25-41DF-A9B2-C12FC83CDE0B at stanford.edu]


Best,
Jennifer
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From vendetti at stanford.edu  Tue Jul 17 16:21:08 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 17 Jul 2018 23:21:08 +0000
Subject: [bioontology-support] [BioPortal] Feedback from fawks
In-Reply-To: <CADQ7=gU55EPcxFBeu+OD0eLdGOe9wP3b66hBY_T=WwrDW-gh7w@mail.gmail.com>
References: <5b4e34fdd74ec_4b593fba4b399348503d@ncbo-prd-app-09.stanford.edu.mail>
 <A4182173-2E02-4535-BB9B-BCFACE783583@stanford.edu>
 <CADQ7=gU55EPcxFBeu+OD0eLdGOe9wP3b66hBY_T=WwrDW-gh7w@mail.gmail.com>
Message-ID: <4662B9CE-E1B3-4B8C-B7AE-E397B2D21C72@stanford.edu>

Hello Alex,

Thank you for the additional information. We throttle API calls to 15 per second for each user account. Any requests beyond the 15 per second are rejected with an HTTP status code of 429. Have you tried spacing out your API calls?

Also, a couple of points you may want to consider:

1). Do you need to use the descendants endpoint? Or, is the children endpoint sufficient for you? The descendants endpoint will return *all* children, going all the way down the tree. The children endpoint will only return the *direct* children (one level deep).

2). You could modify your API calls for class data to get only the attributes you need via the include parameter, which results in a smaller response. A call to get the preferred label and cui for a MEDDRA class would look like the following:

http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222?include=prefLabel,cui,hasChildren<http://data.bioontology.org/ontologies/MEDDRA/classes/http://purl.bioontology.org/ontology/MEDDRA/10028222?include=prefLabel,cui,hasChildren>

Notice that I also tacked on the ?hasChildren? attribute. Another idea would be to check this value to see if the class has children before making an additional call to retrieve them.

3). You could turn off the hypermedia link serialization with the display_links parameter, again resulting in smaller responses:

http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222?include=prefLabel,cui&display_links=false<http://data.bioontology.org/ontologies/MEDDRA/classes/http://purl.bioontology.org/ontology/MEDDRA/10028222?include=prefLabel,cui&display_links=false>

Hope this information is helpful.

Kind regards,
Jennifer




On Jul 17, 2018, at 12:23 PM, Alex Fawksson <fawks14 at gmail.com<mailto:fawks14 at gmail.com>> wrote:

Thank you for your prompt response. I am making a call to data.bioontology.org/ontologies/MEDDRA/classes<http://data.bioontology.org/ontologies/MEDDRA/classes>. I need to get name, cui and descendants from all classes for MEDDRA to store in db. The descendants are needed to preserve data structure so it could be later correctly displayed on front-end.

I do the call to API using apache HttpClient. Originally I tried to use spring RestTemplate but it had some issues with making calls for descendants.

The exception stack trace is this

java.net.SocketException: Connection reset
at java.net.SocketInputStream.read(SocketInputStream.java:210)
at java.net.SocketInputStream.read(SocketInputStream.java:141)
at org.apache.http.impl.io.AbstractSessionInputBuffer.fillBuffer(AbstractSessionInputBuffer.java:161)
at org.apache.http.impl.io.SocketInputBuffer.fillBuffer(SocketInputBuffer.java:82)
at org.apache.http.impl.io.AbstractSessionInputBuffer.readLine(AbstractSessionInputBuffer.java:278)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:138)
at org.apache.http.impl.conn.DefaultHttpResponseParser.parseHead(DefaultHttpResponseParser.java:56)
at org.apache.http.impl.io.AbstractMessageParser.parse(AbstractMessageParser.java:259)
at org.apache.http.impl.AbstractHttpClientConnection.receiveResponseHeader(AbstractHttpClientConnection.java:286)
at org.apache.http.impl.conn.DefaultClientConnection.receiveResponseHeader(DefaultClientConnection.java:257)
at org.apache.http.impl.conn.ManagedClientConnectionImpl.receiveResponseHeader(ManagedClientConnectionImpl.java:207)
at org.apache.http.protocol.HttpRequestExecutor.doReceiveResponse(HttpRequestExecutor.java:273)
at org.apache.http.protocol.HttpRequestExecutor.execute(HttpRequestExecutor.java:125)
at org.apache.http.impl.client.DefaultRequestDirector.tryExecute(DefaultRequestDirector.java:684)
at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:486)
at org.apache.http.impl.client.AbstractHttpClient.doExecute(AbstractHttpClient.java:835)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:83)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:108)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:56)
at com.ua.satrumroom.farma.service.MeddraService.getJSON(MeddraService.java:146)
at com.ua.satrumroom.farma.service.MeddraService.parseMedOne(MeddraService.java:90)
at com.ua.satrumroom.farma.service.MeddraService.parseMedOne(MeddraService.java:105)
at com.ua.satrumroom.farma.service.MeddraService.parseMedOne(MeddraService.java:105)
at com.ua.satrumroom.farma.service.MeddraService.parseMedOne(MeddraService.java:116)
at com.ua.satrumroom.farma.service.MeddraService.parseMedOne(MeddraService.java:116)
at com.ua.satrumroom.farma.service.MeddraService$$FastClassBySpringCGLIB$$da2ae9d8.invoke(<generated>)
at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:738)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.aop.aspectj.MethodInvocationProceedingJoinPoint.proceed(MethodInvocationProceedingJoinPoint.java:85)
at com.ua.satrumroom.farma.aop.logging.LoggingAspect.logAround(LoggingAspect.java:85)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethodWithGivenArgs(AbstractAspectJAdvice.java:627)
at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethod(AbstractAspectJAdvice.java:616)
at org.springframework.aop.aspectj.AspectJAroundAdvice.invoke(AspectJAroundAdvice.java:70)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.aspectj.AspectJAfterThrowingAdvice.invoke(AspectJAfterThrowingAdvice.java:62)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:673)
at com.ua.satrumroom.farma.service.MeddraService$$EnhancerBySpringCGLIB$$ea306061.parseMedOne(<generated>)
at com.ua.satrumroom.farma.FarmaBaseApp.initApplication(FarmaBaseApp.java:64)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1622)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.refresh(EmbeddedWebApplicationContext.java:122)
at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:693)
at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:360)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:303)
at com.ua.satrumroom.farma.FarmaBaseApp.main(FarmaBaseApp.java:81)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.boot.devtools.restart.RestartLauncher.run(RestartLauncher.java:49)


On Tue, 17 Jul 2018 21:58 Jennifer Leigh Vendetti, <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello,

On Jul 17, 2018, at 11:27 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: fawks

Email: fawks14 at gmail.com<mailto:fawks14 at gmail.com>

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

Feedback:

Hi, I am currently working on java application where I need to get all MEDDRA ontologies

This is not enough information for us to help you. What do you mean by ?get all MEDDRA ontologies?? Are you attempting to download the ontology source files for every submission of MEDDRA? Or, are you trying to download all the class data for MEDDRA? Please send a specific example of the API call you?re issuing.


but after approximately 200 parsed values I get connection reset. Apparently server closes the connection to me. Could you please explain to me why that could happen and what I possibly do wrong. Thank you in advance.



Please include the stack trace from your Java program.

Jennifer


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From vendetti at stanford.edu  Wed Jul 18 11:18:29 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 18 Jul 2018 18:18:29 +0000
Subject: [bioontology-support] [BioPortal] Feedback from fawks
In-Reply-To: <CADQ7=gU+=gfocBtE6NURTc91jhWasVbftTadBo2Fsc+sDTt5DA@mail.gmail.com>
References: <5b4e34fdd74ec_4b593fba4b399348503d@ncbo-prd-app-09.stanford.edu.mail>
 <A4182173-2E02-4535-BB9B-BCFACE783583@stanford.edu>
 <CADQ7=gU55EPcxFBeu+OD0eLdGOe9wP3b66hBY_T=WwrDW-gh7w@mail.gmail.com>
 <4662B9CE-E1B3-4B8C-B7AE-E397B2D21C72@stanford.edu>
 <CADQ7=gU+=gfocBtE6NURTc91jhWasVbftTadBo2Fsc+sDTt5DA@mail.gmail.com>
Message-ID: <50806984-858E-4777-9111-D03C0FC35F79@stanford.edu>

Hello Alex,


> On Jul 18, 2018, at 10:02 AM, Alex Fawksson <fawks14 at gmail.com> wrote:
> 
> Hello Jennifer, thank you for your advice. Using children instead of descandants is very sound idea. As for modified API calls I tried using it with parameters you recommended but encountered one problem. PrefLabel and Cui worked but hasChildren doesn't seem to work. If I understood correctly it should have only listed elements that have children but it still included childless elements into the list.


Apologies if I didn?t explain the hasChildren attribute in enough detail.

It?s a boolean attached to a class object that simply indicates whether or not a class has children. Including this property when using the classes endpoint won?t filter out classes with no children. You would still need to iterate over the collection of MEDDRA classes, checking the value of hasChildren for each class, and retrieving the children if hasChildren = true.

Let me know if that makes sense.

Kind regards,
Jennifer



From vendetti at stanford.edu  Wed Jul 18 15:47:15 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 18 Jul 2018 22:47:15 +0000
Subject: [bioontology-support] [BioPortal] Feedback from fawks
In-Reply-To: <CADQ7=gVoCdx_YTbPOpqNAX66hmcTpP-4x5+co9QjO-9h_k4JnQ@mail.gmail.com>
References: <5b4e34fdd74ec_4b593fba4b399348503d@ncbo-prd-app-09.stanford.edu.mail>
 <A4182173-2E02-4535-BB9B-BCFACE783583@stanford.edu>
 <CADQ7=gU55EPcxFBeu+OD0eLdGOe9wP3b66hBY_T=WwrDW-gh7w@mail.gmail.com>
 <4662B9CE-E1B3-4B8C-B7AE-E397B2D21C72@stanford.edu>
 <CADQ7=gU+=gfocBtE6NURTc91jhWasVbftTadBo2Fsc+sDTt5DA@mail.gmail.com>
 <50806984-858E-4777-9111-D03C0FC35F79@stanford.edu>
 <CADQ7=gVoCdx_YTbPOpqNAX66hmcTpP-4x5+co9QjO-9h_k4JnQ@mail.gmail.com>
Message-ID: <D6EACDC3-6285-4C11-BAAE-86009326FB0B@stanford.edu>

Hi Alex,

No, that wasn?t a dumb question at all.

It looks like I missed something in my initial reply to you. If you use the hasChildren include parameter when issuing a REST call for a single class, the data will get returned successfully, e.g.:

This call to get a MEDDRA class:

http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222?include=prefLabel,cui,hasChildren<http://data.bioontology.org/ontologies/MEDDRA/classes/http://purl.bioontology.org/ontology/MEDDRA/10028222?include=prefLabel,cui,hasChildren>

? returns the hasChildren boolean:

[cid:96167143-32FA-42F2-ADD3-958703D5A858 at stanford.edu]

However, if you issue a REST call to get all classes for MEDDRA, it appears that the hasChildren include parameter is ignored, i.e.:

This call to get all the classes:

http://data.bioontology.org/ontologies/MEDDRA/classes?include=prefLabel,cui,hasChildren

? results in a collection of classes that don?t have the hasChildren boolean (as you point out below):

[cid:8EF231CE-426F-4F83-9D03-0D53DABC01B5 at stanford.edu]


I think this is a bug in our software. We have code that checks the list of include parameters and returns an HTTP 422 status code for any parameters that aren?t allowed for a particular endpoint:

https://github.com/ncbo/ontologies_api/blob/master/controllers/classes_controller.rb#L233

The 422 response is only returned for the include parameters of all, descendants, and ancestors, e.g.:

[cid:D25CF51E-C8CB-40C5-B073-6E768874F68A at stanford.edu]

I?ve entered an issue in our tracker for this today:

https://github.com/ncbo/ontologies_api/issues/49

Apologies, but until we get that issue sorted out, I think you?ll need to ignore my suggestion to check this property before making calls to get children.

Kind regards,
Jennifer



On Jul 18, 2018, at 11:26 AM, Alex Fawksson <fawks14 at gmail.com<mailto:fawks14 at gmail.com>> wrote:

Ok, that may sound like a really dumb question but where exactly is hasChildren boolean in this?
{

  *   "prefLabel": "Multiple idiopathic hemorrhagic sarcoma",
  *
-
"cui": [
     *   "C0036220"
],
  *   "@id": "http://purl.bioontology.org/ontology/MEDDRA/10028222"<http://purl.bioontology.org/ontology/MEDDRA/10028222>,
  *   "@type": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
  *
-
"links": {
     *   "self": "http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222"<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222>,
     *   "ontology": "http://data.bioontology.org/ontologies/MEDDRA"<http://data.bioontology.org/ontologies/MEDDRA>,
     *   "children": "http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/children"<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/children>,
     *   "parents": "http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/parents"<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/parents>,
     *   "descendants": "http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/descendants"<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/descendants>,
     *   "ancestors": "http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/ancestors"<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/ancestors>,
     *   "instances": "http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/instances"<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/instances>,
     *   "tree": "http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/tree"<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/tree>,
     *   "notes": "http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/notes"<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/notes>,
     *   "mappings": "http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/mappings"<http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222/mappings>,
     *   "ui": "http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222"<http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10028222>,
     *
-
"@context": {
        *   "self": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
        *   "ontology": "http://data.bioontology.org/metadata/Ontology"<http://data.bioontology.org/metadata/Ontology>,
        *   "children": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
        *   "parents": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
        *   "descendants": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
        *   "ancestors": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
        *   "instances": "http://data.bioontology.org/metadata/Instance"<http://data.bioontology.org/metadata/Instance>,
        *   "tree": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
        *   "notes": "http://data.bioontology.org/metadata/Note"<http://data.bioontology.org/metadata/Note>,
        *   "mappings": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>,
        *   "ui": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>
}
},
  *
-
"@context": {
     *   "@vocab": "http://data.bioontology.org/metadata/"<http://data.bioontology.org/metadata/>,
     *   "prefLabel": "http://data.bioontology.org/metadata/skosprefLabel"<http://data.bioontology.org/metadata/skosprefLabel>,
     *   "cui": "http://data.bioontology.org/metadata/umlscui"<http://data.bioontology.org/metadata/umlscui>
}

}

2018-07-18 21:18 GMT+03:00 Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>:
Hello Alex,


> On Jul 18, 2018, at 10:02 AM, Alex Fawksson <fawks14 at gmail.com<mailto:fawks14 at gmail.com>> wrote:
>
> Hello Jennifer, thank you for your advice. Using children instead of descandants is very sound idea. As for modified API calls I tried using it with parameters you recommended but encountered one problem. PrefLabel and Cui worked but hasChildren doesn't seem to work. If I understood correctly it should have only listed elements that have children but it still included childless elements into the list.


Apologies if I didn?t explain the hasChildren attribute in enough detail.

It?s a boolean attached to a class object that simply indicates whether or not a class has children. Including this property when using the classes endpoint won?t filter out classes with no children. You would still need to iterate over the collection of MEDDRA classes, checking the value of hasChildren for each class, and retrieving the children if hasChildren = true.

Let me know if that makes sense.

Kind regards,
Jennifer




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From support at bioontology.org  Thu Jul 19 10:55:24 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 19 Jul 2018 10:55:24 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Ashleigh Lewis
Message-ID: <5b50d08c552ea_66db3f893430e2906867d@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Thu Jul 19 11:24:23 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 19 Jul 2018 18:24:23 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Ashleigh Lewis
In-Reply-To: <5b50d08c552ea_66db3f893430e2906867d@ncbo-prd-app-09.stanford.edu.mail>
References: <5b50d08c552ea_66db3f893430e2906867d@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <175A5406-A778-491D-95A8-E1E905F4A67C@stanford.edu>

Hello Ashleigh,


On Jul 19, 2018, at 10:55 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Ashleigh Lewis

Email: lewisa2 at uw.edu<mailto:lewisa2 at uw.edu>

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

Feedback:

I am having issues with the MDDB and ICD9 ontologies specifically in REDCap. I have tested some of the other ontologies and they are working properly but the MDDB and ICD9 is not loading. Is there anything I can do on my end to fix this issue?

You?ve reached the support list for the BioPortal application. We don?t develop and/or maintain REDCap.

I confirmed that BioPortal's REST API is successfully returning data for both MDDB ICD9CM. We only have ICD9CM in our application, so I?m not sure if that?s what you?re referring to above by ?ICD9?. I would suggest contacting the REDCap developers. If they believe the problem is somehow on our end, we?d need more specifics, preferably in the form of detailed error messages. As far as I can tell though, there?s no issue at the moment with either of these ontologies in BioPortal.

Kind regards,
Jennifer



[cid:9D353F15-D344-4B14-BAE3-3B594EBECF89 at stanford.edu]
[cid:CF80D206-A1D3-4B6F-A1E8-F53E7A8B8301 at stanford.edu]
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From vendetti at stanford.edu  Thu Jul 19 16:29:41 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 19 Jul 2018 23:29:41 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Ashleigh Lewis
In-Reply-To: <D3D8ED7B-BBDC-4272-A84C-938A565406FC@uw.edu>
References: <5b50d08c552ea_66db3f893430e2906867d@ncbo-prd-app-09.stanford.edu.mail>
 <175A5406-A778-491D-95A8-E1E905F4A67C@stanford.edu>
 <D3D8ED7B-BBDC-4272-A84C-938A565406FC@uw.edu>
Message-ID: <96EA3F83-C169-4F52-B593-09AC1907B19B@stanford.edu>

Hello Ashleigh,

Thank you for providing additional detail.


On Jul 19, 2018, at 1:47 PM, Ashleigh Lewis <lewisa2 at uw.edu<mailto:lewisa2 at uw.edu>> wrote:

Hi Jennifer,

Thank you for your email and checking on those ontologies. I did do some initial troubleshooting with our servers prior to contacting you as well as testing on another version of the REDCap software to determine it was not isolated to a certain software version at which I would have contacted the REDCap Developers. I believe this is still a Bioportal malfunction specific to the MDDB (Master Drug Data Base Clinical Drugs) ontology. When I look at the class here:
https://bioportal.bioontology.org/ontologies/MDDB?p=classes&conceptid=bp_fake_root

This does not show the drug codes and names it once did. This should be a pharmaceutical lookup list but when you type in for example Cetirizine HCl Tab 10 MG which used to show up with code 09133 no longer shows up. You can get it to search the table which now contains different codes such as ?body system?.

I think I thought originally it was an issue not pulling any of the table list because I was searching for pharmaceuticals but it does filter but only when you type in the new list items it has so working properly just what I believe is not the correct look up table.

I noticed that the most recent submission was uploaded on 7/6/2018 so I am wondering if this ontology has now changed and no longer actually is a Master Drug Data Base Clinical Drugs or if there was some error in the most recent upload.


OK - I think this is the root of the issue. MDDB is one of a group of ontologies made available by the National Library of Medicine as part of their UMLS distribution [1]. Twice per year we do bulk imports of their new releases. It looks like MDDB was included in the UMLS 2017AA release, but has been removed from the two subsequent releases (2017AB and 2018AA). I think we missed the fact that MDDB was removed from the UMLS distribution and our import process created two new submissions in BioPortal for 2017AA and 2018AA that were mostly void of content. I deleted those last two submissions, and reverted the system to serve content from the 2017AA release. I verified that the example class you listed above is accessible via our REST endpoint:


[cid:7C21CAF0-B666-4918-9A4A-638533982B13 at stanford.edu]

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/



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From support at bioontology.org  Fri Jul 20 15:45:13 2018
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 20 Jul 2018 15:45:13 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Barbara safka
Message-ID: <5b5265f94265c_160f3ff27348186844495@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Fri Jul 20 15:48:47 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 20 Jul 2018 22:48:47 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Barbara safka
In-Reply-To: <5b5265f94265c_160f3ff27348186844495@ncbo-prd-app-08.stanford.edu.mail>
References: <5b5265f94265c_160f3ff27348186844495@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <957E822F-8080-41B1-9061-F578DB7A6783@stanford.edu>

Hello Barbara,


On Jul 20, 2018, at 3:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Barbara safka

Email: gsafka at cox.net<mailto:gsafka at cox.net>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3D55530

Feedback:

I would like to get some more information on CPT.I live in Virginia.Thank you



CPT is imported into BioPortal from the UMLS Metathesaurus. You can see a synopsis of CPT here: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CPT/.

Jennifer


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From gjscnc at mst.edu  Fri Jul 20 19:20:03 2018
From: gjscnc at mst.edu (George Shannon)
Date: Fri, 20 Jul 2018 22:20:03 -0400
Subject: [bioontology-support] Request for information - API key for
 bio-ontology annotator and technical information
Message-ID: <CAJWrVhMj5HgFrNY9xMn8kuNcn6u1+LKyTC1XGk9oXpep4SUVwA@mail.gmail.com>

I am a volunteer research member of the Systems Engineering Dept. and the
Applied Computational Intelligence Lab at the Missouri University of
Science and Technology (MST).

I am investigating entity recognition methods, and wish to perform
comparisons of existing methods against an innovative approach we have
developed biomedical text. We use an ontology-based approach, principally
SNOMED-CT.

I'm contacting you for technical information regarding use of the annotator
REST-full service.

As I understand it, this service is the Open Biomedical Annotator as
described in Jonquet C, Shah NH, Musen MA. The Open Biomedical Annotator.
Summit on Translational Bioinformatics. 2009;2009:56-60.  This papers notes
use of the MGrep method for identifying medical entities in text.

Would you mind helping me in three area: 1) confirm use of the MGrep entity
recognizer, 2) can I obtain an API key for use of the annotator via the
REST interface, and 3) does a parameter exist in the API for limiting
results to a particular ontology?

I would greatly appreciate your help.

Best Regards,

George

-- 
George J. Shannon, PhD SE
Missouri University of Science and Technology
(314) 550-5589 (cell)
gjscnc at mst.edu
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From jgraybeal at stanford.edu  Fri Jul 20 22:03:01 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Sat, 21 Jul 2018 05:03:01 +0000
Subject: [bioontology-support] Request for information - API key for
 bio-ontology annotator and technical information
In-Reply-To: <CAJWrVhMj5HgFrNY9xMn8kuNcn6u1+LKyTC1XGk9oXpep4SUVwA@mail.gmail.com>
References: <CAJWrVhMj5HgFrNY9xMn8kuNcn6u1+LKyTC1XGk9oXpep4SUVwA@mail.gmail.com>
Message-ID: <SN6PR02MB4639D0CC479376B676740521DA500@SN6PR02MB4639.namprd02.prod.outlook.com>

A few quick thoughts before disappearing for the weekend:
1) yes, though there might have been an improvement or two since then.
2) when you register for BioPortal you get an API key that works for all tools (on your profile page).
3) yes. If you search for ?BioPortal api? I think the first hit is the API documentation.

You might want to review the support archives on nabble (search google again) for related topics, and the BioPortal release notes (google?) re annotator upgrades.

Sorry, can?t provide examples, pilot says I must go now!

John

________________________________
From: bioontology-support <bioontology-support-bounces at lists.stanford.edu> on behalf of George Shannon <gjscnc at mst.edu>
Sent: Friday, July 20, 2018 7:20:03 PM
To: support at bioontology.org
Cc: Corns, Steven; Donald C. Wunsch
Subject: [bioontology-support] Request for information - API key for bio-ontology annotator and technical information

I am a volunteer research member of the Systems Engineering Dept. and the Applied Computational Intelligence Lab at the Missouri University of Science and Technology (MST).

I am investigating entity recognition methods, and wish to perform comparisons of existing methods against an innovative approach we have developed biomedical text. We use an ontology-based approach, principally SNOMED-CT.

I'm contacting you for technical information regarding use of the annotator REST-full service.

As I understand it, this service is the Open Biomedical Annotator as described in Jonquet C, Shah NH, Musen MA. The Open Biomedical Annotator. Summit on Translational Bioinformatics. 2009;2009:56-60.  This papers notes use of the MGrep method for identifying medical entities in text.

Would you mind helping me in three area: 1) confirm use of the MGrep entity recognizer, 2) can I obtain an API key for use of the annotator via the REST interface, and 3) does a parameter exist in the API for limiting results to a particular ontology?

I would greatly appreciate your help.

Best Regards,

George

--
George J. Shannon, PhD SE
Missouri University of Science and Technology
(314) 550-5589 (cell)
gjscnc at mst.edu
<mailto:gjscnc at mst.edu>
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From kushida at biosciencedbc.jp  Mon Jul 23 03:22:45 2018
From: kushida at biosciencedbc.jp (Tatsuya Kushida)
Date: Mon, 23 Jul 2018 19:22:45 +0900
Subject: [bioontology-support] Ontology mapping
In-Reply-To: <CAJuGyWkvv_uDM9J2=RiA4C5_MNZhrVj7+r0+9oUokHEf3QsCOQ@mail.gmail.com>
References: <CAJuGyWnmbDzOboNw+3TdyYE5JUYYVk3vP6wBF3vd=+9UY28Q+Q@mail.gmail.com>
 <54BBD023-519D-4D54-81C9-316856CCF33D@stanford.edu>
 <CAJuGyWkvv_uDM9J2=RiA4C5_MNZhrVj7+r0+9oUokHEf3QsCOQ@mail.gmail.com>
Message-ID: <CAJuGyW=DTM3-V=mcME9tu+d_i=zvboDw2bFppNdHm-Jk=L12sQ@mail.gmail.com>

Hello Jennifer,

I'm sorry.
There was an error in the previous email so I will resend it.


Thank you so much for useful information.

I'd like to get the total count of mappings between IOBC and MESH.
So, I ran the following API,
http://data.bioontology.org/mappings/?ontologies=IOBC,MESH .
However the result was "totalCount: 0".

On the other hand, I ran the following API,
http://data.bioontology.org/ontologies/IOBC/classes/http%3A%2F%2Fpurl.jp%2Fbio%2F4%2Fid%2F200906053522984593/mappings
.
As a result, I found one mapping between IOBC and MESH, namely
"http://purl.jp/bio/4/id/200906053522984593", and
"http://purl.bioontology.org/ontology/MESH/D019853".

How can I get the total count of mappings between IOBC and MESH all at once?



2018-07-23 19:03 GMT+09:00 Tatsuya Kushida <kushida at biosciencedbc.jp>:
> Hello Jennifer,
>
> Thank you so much for useful information.
>
> I'd like to get the total count of mappings between IOBC and MESH.
> So, I ran the following API,
> http://data.bioontology.org/mappings/?ontologies=IOBC,MESH .
> However the result was "totalCount: 0".
>
> On the other hand, I ran the following API,
> http://data.bioontology.org/ontologies/IOBC/classes/http%3A%2F%2Fpurl.jp%2Fbio%2F4%2Fid%2F200906026623112891/mappings
> .
> As a result, I found one mapping between IOBC and MESH, namely
> "http://purl.jp/bio/4/id/200906053522984593" and
> "http://purl.bioontology.org/ontology/MESH/D019853".
>
> How can I get the total count of mappings between IOBC and MESH all at once?
>
> Best regards,
> Tatsuya
>
>
> --
> Tatsuya Kushida, Ph.D.
> National Bioscience Database Center (NBDC),
> Japan SCIENCE AND TECHNOLOGY AGENCY (JST)
> 5-3, Yonbancho, Chiyoda-ku, Tokyo 102-0081, JAPAN
> Phone: +81 3 5214 8491 FAX: 81 3 5214 8470
> http://www.jst.go.jp/EN/index.html
> http://biosciencedbc.jp/en/
> t2kushida at jst.go.jp
> kushida at biosciencedbc.jp
>
>
>
>
> 2018-07-10 1:38 GMT+09:00 Jennifer Leigh Vendetti <vendetti at stanford.edu>:
>> Hello Tatsuya,
>>
>>
>> On Jul 8, 2018, at 4:40 PM, Tatsuya Kushida <kushida at biosciencedbc.jp>
>> wrote:
>>
>> Dear BioPortal staffs,
>>
>> I'm a developer of IOBC (http://purl.bioontology.org/ontology/IOBC).
>> Can I ask you a question? How can I do mapping my ontology terms to
>> other ontology ones?
>>
>>
>>
>> Mappings are automatically generated when you submit an ontology to
>> BioPortal. You can also manually create mappings using our REST API:
>>
>> http://data.bioontology.org/documentation#Mapping
>>
>> We have example code for programmatically creating mappings in our GitHub
>> sample code repository:
>>
>> https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/CreateMapping.java
>>
>>
>>
>> I worry that my ontology mapping fully has not
>> been done yet
>> (https://bioportal.bioontology.org/ontologies/IOBC/?p=mappings).
>>
>>
>>
>> If you let us know what you think is missing, we could perhaps better
>> comment on this point.
>>
>> Kind regards,
>> Jennifer
>>
>>

--
Tatsuya Kushida, Ph.D.
National Bioscience Database Center (NBDC),
Japan SCIENCE AND TECHNOLOGY AGENCY (JST)
5-3, Yonbancho, Chiyoda-ku, Tokyo 102-0081, JAPAN
Phone: +81 3 5214 8491 FAX: 81 3 5214 8470
http://www.jst.go.jp/EN/index.html
http://biosciencedbc.jp/en/
t2kushida at jst.go.jp
kushida at biosciencedbc.jp

From vendetti at stanford.edu  Mon Jul 23 15:31:12 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 23 Jul 2018 22:31:12 +0000
Subject: [bioontology-support] Ontology mapping
In-Reply-To: <CAJuGyW=DTM3-V=mcME9tu+d_i=zvboDw2bFppNdHm-Jk=L12sQ@mail.gmail.com>
References: <CAJuGyWnmbDzOboNw+3TdyYE5JUYYVk3vP6wBF3vd=+9UY28Q+Q@mail.gmail.com>
 <54BBD023-519D-4D54-81C9-316856CCF33D@stanford.edu>
 <CAJuGyWkvv_uDM9J2=RiA4C5_MNZhrVj7+r0+9oUokHEf3QsCOQ@mail.gmail.com>
 <CAJuGyW=DTM3-V=mcME9tu+d_i=zvboDw2bFppNdHm-Jk=L12sQ@mail.gmail.com>
Message-ID: <CAFF05D8-709A-438F-96BE-18BA77B7F011@stanford.edu>

Hello Tatsuya,

On Jul 23, 2018, at 3:22 AM, Tatsuya Kushida <kushida at biosciencedbc.jp<mailto:kushida at biosciencedbc.jp>> wrote:

I'd like to get the total count of mappings between IOBC and MESH.
So, I ran the following API,
http://data.bioontology.org/mappings/?ontologies=IOBC,MESH .
However the result was "totalCount: 0".

On the other hand, I ran the following API,
http://data.bioontology.org/ontologies/IOBC/classes/http%3A%2F%2Fpurl.jp%2Fbio%2F4%2Fid%2F200906053522984593/mappings
.
As a result, I found one mapping between IOBC and MESH, namely
"http://purl.jp/bio/4/id/200906053522984593", and
"http://purl.bioontology.org/ontology/MESH/D019853".

How can I get the total count of mappings between IOBC and MESH all at once?


The first API call that you list above is the correct one for getting all mappings between IOBC and MESH.

Apologies, but after some initial investigation, it?s not immediately clear to me why you?re getting different results from the /mappings and /classes endpoints.

I noticed something else that seems unusual about BioPortal?s handling of IOBC. The class you refer to above with ID of "http://purl.jp/bio/4/id/200906053522984593?, is accessible via the REST endpoint, but doesn?t show up anywhere in the class tree in the BioPortal UI.

I entered an issue in our tracker [1], as we?ll need to investigate further. Apologies for the inconvenience.

Kind regards,
Jennifer

[1] https://github.com/ncbo/ontologies_api/issues/50


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From support at bioontology.org  Tue Jul 24 06:59:59 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 24 Jul 2018 06:59:59 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Hanamick Andrey
Message-ID: <5b5730df87b45_101e3fb41bd271d43567@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Tue Jul 24 08:13:08 2018
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 24 Jul 2018 08:13:08 -0700
Subject: [bioontology-support] [BioPortal] Feedback from RSNA Test
Message-ID: <5b5742048a965_3f573fc2a3a4d1d452914@ncbo-prd-app-09.stanford.edu.mail>

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From jgraybeal at stanford.edu  Tue Jul 24 11:03:16 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 24 Jul 2018 18:03:16 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Hanamick Andrey
In-Reply-To: <5b5730df87b45_101e3fb41bd271d43567@ncbo-prd-app-09.stanford.edu.mail>
References: <5b5730df87b45_101e3fb41bd271d43567@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <FB5763C0-A6B3-4BB6-B61C-CAC1F2FB0327@stanford.edu>

Hello Hanamick,

The user manual that we offer is at https://www.bioontology.org/wiki/BioPortal_Help. I apologize that it is a little thin on details, but it does give the basics of using the system.

You are welcome to contact this list with specific questions, or search the archives of this list (http://ncbo-support.2288202.n4.nabble.com/) for questions/answers on specific topics.

John




On Jul 24, 2018, at 6:59 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Hanamick Andrey

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

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

Feedback:

i am a beginer and i very want to learn about bioport "how to use "
Can you put a user manual side that i can search <3

_______________________________________________
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 jgraybeal at stanford.edu  Tue Jul 24 12:37:30 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 24 Jul 2018 19:37:30 +0000
Subject: [bioontology-support] [BioPortal] Feedback from RSNA Test
In-Reply-To: <5b5742048a965_3f573fc2a3a4d1d452914@ncbo-prd-app-09.stanford.edu.mail>
References: <5b5742048a965_3f573fc2a3a4d1d452914@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <6D4E9B24-C00F-48C6-9F1B-9606029E17AD@stanford.edu>

Michael,

Thanks for this input. I've created a ticket for this issue: https://github.com/ncbo/bioportal-project/issues/82, as I spent some time looking over the ontologies and can't see anything there that would explain it.

We'll have a look in the code in BioPortal and see if we can figure out what is going on here.

John

On Jul 24, 2018, at 8:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: RSNA Test

Email: mcrabtree at rsna.org<mailto:mcrabtree at rsna.org>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fwww.radlex.org<http://252Fwww.radlex.org>%252FRID%252F%2523RID10312

Feedback:

email: mcrabtree at rsna.org<mailto:mcrabtree at rsna.org>
URL: https://bioportal.bioontology.org/ontologies/RAD/?p=classes&conceptid=http%3A%2F%2Fradlex.org%2FRID%2FRID30413&jump_to_nav=true

For some classes the prefixIRI has two values. Like in the url above the value is
RID:RID30413
RID30413

when it should only be RID30413.

So we had a few questions.
1. Do you know why this seems to be only happening on some of the classes and is it something we can fix on our end.

2. Is the prefixIRI slot attached by BioPortal because we don't think it's a field we have.

_______________________________________________
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 jgraybeal at stanford.edu  Wed Jul 25 17:52:14 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 26 Jul 2018 00:52:14 +0000
Subject: [bioontology-support] Request for information - API key for
 bio-ontology annotator and technical information
In-Reply-To: <SN6PR02MB4639D0CC479376B676740521DA500@SN6PR02MB4639.namprd02.prod.outlook.com>
References: <CAJWrVhMj5HgFrNY9xMn8kuNcn6u1+LKyTC1XGk9oXpep4SUVwA@mail.gmail.com>
 <SN6PR02MB4639D0CC479376B676740521DA500@SN6PR02MB4639.namprd02.prod.outlook.com>
Message-ID: <5E1C592E-09B1-401B-9417-DD0EE4F7D46E@stanford.edu>

George, all,

Following up with a bit more detail.

Please note you can find a few more recent articles about the annotator, or mentioning updates to the annotator, by searching https://scholar.google.com for 'ncbo annotator'.

The support archives are on Nabble at http://ncbo-support.2288202.n4.nabble.com.

1) There have been a large number of changes in the Annotator since 2009, by a significant number of people. For example see the Contributors in GitHub at https://github.com/ncbo/ncbo_annotator/graphs/contributors and the history tab at  https://github.com/ncbo/ncbo_annotator/commits/master/lib. I think it would be difficult to summarize the changes, especially in this moment, since the principles are mostly in other positions or on vacation. But the Release Notes (and pointers to earlier release notes) are at https://www.bioontology.org/wiki/BioPortal_Release_Notes, and you can search in your browser for 'annotat' to find many of the major changes summarized there. If you have more advanced questions after reviewing that material, contact us and we can try to put you in touch with the right people.

2) There are instructions for getting an API key on the BioPortal wiki:
https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key

3) The API documentation is indeed at http://data.bioontology.org/documentation. Note the first section entries apply to many other sections.

John


On Jul 20, 2018, at 10:03 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

A few quick thoughts before disappearing for the weekend:
1) yes, though there might have been an improvement or two since then.
2) when you register for BioPortal you get an API key that works for all tools (on your profile page).
3) yes. If you search for ?BioPortal api? I think the first hit is the API documentation.

You might want to review the support archives on nabble (search google again) for related topics, and the BioPortal release notes (google?) re annotator upgrades.

Sorry, can?t provide examples, pilot says I must go now!

John

________________________________
From: bioontology-support <bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>> on behalf of George Shannon <gjscnc at mst.edu<mailto:gjscnc at mst.edu>>
Sent: Friday, July 20, 2018 7:20:03 PM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Corns, Steven; Donald C. Wunsch
Subject: [bioontology-support] Request for information - API key for bio-ontology annotator and technical information

I am a volunteer research member of the Systems Engineering Dept. and the Applied Computational Intelligence Lab at the Missouri University of Science and Technology (MST).

I am investigating entity recognition methods, and wish to perform comparisons of existing methods against an innovative approach we have developed biomedical text. We use an ontology-based approach, principally SNOMED-CT.

I'm contacting you for technical information regarding use of the annotator REST-full service.

As I understand it, this service is the Open Biomedical Annotator as described in Jonquet C, Shah NH, Musen MA. The Open Biomedical Annotator. Summit on Translational Bioinformatics. 2009;2009:56-60.  This papers notes use of the MGrep method for identifying medical entities in text.

Would you mind helping me in three area: 1) confirm use of the MGrep entity recognizer, 2) can I obtain an API key for use of the annotator via the REST interface, and 3) does a parameter exist in the API for limiting results to a particular ontology?

I would greatly appreciate your help.

Best Regards,

George

--
George J. Shannon, PhD SE
Missouri University of Science and Technology
(314) 550-5589 (cell)
gjscnc at mst.edu
<mailto:gjscnc at mst.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

========================
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 spelmen at gmail.com  Wed Jul 25 21:43:08 2018
From: spelmen at gmail.com (spellz .)
Date: Thu, 26 Jul 2018 10:13:08 +0530
Subject: [bioontology-support] Reg:sending of query about the annotator
Message-ID: <CACqU87E010RVnwoRQa9ahU05dPYDS4FYBNetKRnERwKDDB8yKw@mail.gmail.com>

Dear sir,
                  I have done all the works programticaly but it took more
time to write as xml file.

for ex: for writing 600 kb of xml file it took more than 4 hours


Thanks & Regards,
SPELMEN VIMALRAJ S
Ph.D Research Scholar
Department Of Computer Science
Bharathiar University
coimbatore-46
Ph: *8807650056*
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From wynner at mail.nih.gov  Thu Jul 26 07:47:08 2018
From: wynner at mail.nih.gov (Wynne, Robert (NIH/NCI) [C])
Date: Thu, 26 Jul 2018 14:47:08 +0000
Subject: [bioontology-support] RRF conversion
Message-ID: <BL0PR0901MB244991EE67236878B9659FC2FB2B0@BL0PR0901MB2449.namprd09.prod.outlook.com>

Hi all,

We're interested in converting an RRF subset from MetaMorphosys to something our Triplestore could consume (ttl/owl/rdf, etc).  Is a most recent script available for this?  Possibly in Github?

Thanks,
Rob
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From jgraybeal at stanford.edu  Thu Jul 26 18:25:23 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 27 Jul 2018 01:25:23 +0000
Subject: [bioontology-support] RRF conversion
In-Reply-To: <BL0PR0901MB244991EE67236878B9659FC2FB2B0@BL0PR0901MB2449.namprd09.prod.outlook.com>
References: <BL0PR0901MB244991EE67236878B9659FC2FB2B0@BL0PR0901MB2449.namprd09.prod.outlook.com>
Message-ID: <267AA14C-C00A-4346-B088-0A010634DAEF@stanford.edu>

Hello Rob,

Our process is as follows:
1) download the UMLS full release in whatever format they provide
2) run Metamorphosys application which generates the RRF files and mysql load script
3) run the generated mysql load script to load data from RRF files
4) run our python umls2rdf script to generate TTL files

The only part of this you don't already have access to (if you're running the UMLS MetaMorphosys) is the umls2rdf script, which is in GitHub at https://github.com/ncbo/umls2rdf.

The

On Jul 26, 2018, at 7:47 AM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi all,

We?re interested in converting an RRF subset from MetaMorphosys to something our Triplestore could consume (ttl/owl/rdf, etc).  Is a most recent script available for this?  Possibly in Github?

Thanks,
Rob
_______________________________________________
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 Laura.Baakman at siemens-healthineers.com  Fri Jul 27 08:39:45 2018
From: Laura.Baakman at siemens-healthineers.com (Baakman, Laura)
Date: Fri, 27 Jul 2018 15:39:45 +0000
Subject: [bioontology-support] ODIE Corpus
Message-ID: <A4CCA5F7E4538B47BCAD0380251D5AF757F486@USTXCA0EM24MSX.ww017.siemens.net>

Dear Sir or Madam,

My name is Laura Baakman, I am currently an intern at Siemens Healthineers. During my internship my goal is to build a coreference resolver for clinical data, such a discharge summaries. While researching existing coreference solvers I have encountered numerous papers that use the ODIE dataset. I would like to train and test my resolver on this corpus too. However I cannot find out how and where to download it. Could you point me in the right direction?

I should note, that since I can only use the corpus if it is licensed for commercial use, since Siemens Healthineers might use the resolver in one of the healthcare products they sell.

Thank you for your  help!

Kind regards,

Laura Baakman

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From vendetti at stanford.edu  Fri Jul 27 12:10:48 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 27 Jul 2018 19:10:48 +0000
Subject: [bioontology-support] [BioPortal] Feedback from RSNA Test
In-Reply-To: <5b5742048a965_3f573fc2a3a4d1d452914@ncbo-prd-app-09.stanford.edu.mail>
References: <5b5742048a965_3f573fc2a3a4d1d452914@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <5A6CFA7D-0513-4E21-8CFA-26C88D6CB717@stanford.edu>

Hi Michael,


On Jul 24, 2018, at 8:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

URL: https://bioportal.bioontology.org/ontologies/RAD/?p=classes&conceptid=http%3A%2F%2Fradlex.org%2FRID%2FRID30413&jump_to_nav=true

For some classes the prefixIRI has two values. Like in the url above the value is
RID:RID30413
RID30413

when it should only be RID30413.

So we had a few questions.
1. Do you know why this seems to be only happening on some of the classes and is it something we can fix on our end.



I looked at our source code and the content of the two ontology files that are part of your latest submission. The two values in the prefixIRI property appear to be the result of the use of OWL punning. The class you list above (?wall of left renal pelvis?, with ID http://radlex.org/RID/RID30413) is declared as an entity in RadLex.owl on line 583,219:

<owl:Class rdf:about="http://radlex.org/RID/RID30413">

? and in pun_RadLex.owl on line 145,308:

<owl:NamedIndividual rdf:about="http://radlex.org/RID/RID30413?>

One of the values in the prefixIRI property is prepended with ?RID:? because that prefix is declared in pun_RadLex.owl:

<rdf:RDF xmlns="http://radlex.org/RID/"
     xml:base="http://radlex.org/RID/"
     xmlns:RID="http://radlex.org/RID/"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">

? but not in RadLex.owl.

Your ontology files are valid OWL, and it may be the case that we shouldn?t have two values in the prefixIRI property. However, I?m not aware of any issues this is causing with regard to BioPortal?s functionality.


2. Is the prefixIRI slot attached by BioPortal because we don't think it's a field we have.



Yes, this is an annotation property that we attach to classes when we ingest ontologies. We allow end users to submit ontologies in OWL, OBO, and SKOS, all of which have their own formats for knowledge representation. We store class IDs in annotation properties like prefixIRI to facilitate the ability to search for terms across all ontologies in BioPortal, regardless of format.

In the future, if you want to check the source of a property, you can issue a REST call with the ?properties? include parameter, e.g.:

http://data.bioontology.org/ontologies/RAD/classes/http%3A%2F%2Fradlex.org%2FRID%2FRID30413?include=prefLabel,properties&display_links=false<http://data.bioontology.org/ontologies/RAD/classes/http://radlex.org/RID/RID30413?include=prefLabel,properties&display_links=false>

In the resulting JSON, the prefixIRI property is visible as part of the data.bioontology.org/metadata<http://data.bioontology.org/metadata> namespace:


[cid:05089E39-9936-4481-B712-2464A0040ECE at stanford.edu]

Best,
Jennifer




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From jgraybeal at stanford.edu  Fri Jul 27 15:28:11 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 27 Jul 2018 22:28:11 +0000
Subject: [bioontology-support] ODIE Corpus
In-Reply-To: <A4CCA5F7E4538B47BCAD0380251D5AF757F486@USTXCA0EM24MSX.ww017.siemens.net>
References: <A4CCA5F7E4538B47BCAD0380251D5AF757F486@USTXCA0EM24MSX.ww017.siemens.net>
Message-ID: <452CF678-957B-4548-AC32-95F01F44F8B5@stanford.edu>

I'm sorry, I have no knowledge of the ODIE dataset, and this is not the type of content that BioPortal manages. I'm afraid we can not help you with this query.

John

On Jul 27, 2018, at 8:39 AM, Baakman, Laura <Laura.Baakman at siemens-healthineers.com<mailto:Laura.Baakman at siemens-healthineers.com>> wrote:

Dear Sir or Madam,

My name is Laura Baakman, I am currently an intern at Siemens Healthineers. During my internship my goal is to build a coreference resolver for clinical data, such a discharge summaries. While researching existing coreference solvers I have encountered numerous papers that use the ODIE dataset. I would like to train and test my resolver on this corpus too. However I cannot find out how and where to download it. Could you point me in the right direction?

I should note, that since I can only use the corpus if it is licensed for commercial use, since Siemens Healthineers might use the resolver in one of the healthcare products they sell.

Thank you for your  help!

Kind regards,

Laura Baakman

_______________________________________________
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



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From markampa at pennmedicine.upenn.edu  Fri Jul 27 12:45:15 2018
From: markampa at pennmedicine.upenn.edu (Miller, Mark)
Date: Fri, 27 Jul 2018 19:45:15 +0000
Subject: [bioontology-support] bulk download of mapping data?
Message-ID: <BYAPR04MB40698C753F98ECBB24F45914F72A0@BYAPR04MB4069.namprd04.prod.outlook.com>

I'm user markampa

I would like to download a large number of your high-quality term mappings.  I think I see how to do it thought the API, but would prefer downloading a static file or retrieving the mappings with a SPARQL query.

I see https://www.bioontology.org/wiki/SPARQL_BioPortal but can't seem to get the sample queries to work.

I created a query file like this

mark at office:~/apache-jena-3.8.0/bin$ cat > ~/bpmap.rq
PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT
*
WHERE {
        ?mapping map:target <http://purl.bioontology.org/ontology/CSP/0468-5952> .
        ?mapping map:source ?source .
    }

And submitted it with Jena's remote query command like this, but got an error.

mark at office:~/apache-jena-3.8.0/bin$ ./rsparql --service 'http://sparql.bioontology.org/mappings/sparql/?apikey=9cf735c3-a44a-404f-8b2f-c49d48b2b8b2' --query  ~/bpmap.rq
HTTP Exeception
HttpException: 500 HTTP 500 error making the query: INTERNAL SERVER ERROR
        at org.apache.jena.sparql.engine.http.HttpQuery.rewrap(HttpQuery.java:370)
        at org.apache.jena.sparql.engine.http.HttpQuery.execGet(HttpQuery.java:336)
        at org.apache.jena.sparql.engine.http.HttpQuery.exec(HttpQuery.java:288)
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execResultSetInner(QueryEngineHTTP.java:352)
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execSelect(QueryEngineHTTP.java:344)
        at org.apache.jena.sparql.util.QueryExecUtils.doSelectQuery(QueryExecUtils.java:196)
        at org.apache.jena.sparql.util.QueryExecUtils.executeQuery(QueryExecUtils.java:79)
        at arq.rsparql.exec(rsparql.java:76)
        at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
        at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
        at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
        at arq.rsparql.main(rsparql.java:44)
mark at office:~/apache-jena-3.8.0/bin$
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From support at bioontology.org  Mon Jul 30 05:57:55 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 30 Jul 2018 05:57:55 -0700
Subject: [bioontology-support] =?utf-8?q?=5BBioPortal=5D_Feedback_from_Fer?=
	=?utf-8?q?nanda_D=C3=B3rea?=
Message-ID: <5b5f0b53832fb_66a03fba0ff2ca34990bb@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Mon Jul 30 09:08:58 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 30 Jul 2018 16:08:58 +0000
Subject: [bioontology-support] bulk download of mapping data?
In-Reply-To: <BYAPR04MB40698C753F98ECBB24F45914F72A0@BYAPR04MB4069.namprd04.prod.outlook.com>
References: <BYAPR04MB40698C753F98ECBB24F45914F72A0@BYAPR04MB4069.namprd04.prod.outlook.com>
Message-ID: <87C00012-5FB1-46F8-9301-FCBFC334C288@stanford.edu>

Hello Mark,


On Jul 27, 2018, at 12:45 PM, Miller, Mark <markampa at pennmedicine.upenn.edu<mailto:markampa at pennmedicine.upenn.edu>> wrote:

I?m user markampa

I would like to download a large number of your high-quality term mappings.  I think I see how to do it thought the API, but would prefer downloading a static file or retrieving the mappings with a SPARQL query.


The open SPARQL endpoint is a beta service that we published a number of years ago, but haven?t had the resources to maintain. The data is entirely out of date. Current ontology data is only available via our REST API.

Apologies that we also don?t make the mappings available as static files.

If you let me know what mappings you?re trying to retrieve, I can help with which API calls to use.

Kind regards,
Jennifer




I see https://www.bioontology.org/wiki/SPARQL_BioPortal but can?t seem to get the sample queries to work.

I created a query file like this

mark at office:~/apache-jena-3.8.0/bin$ cat > ~/bpmap.rq
PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT
*
WHERE {
        ?mapping map:target <http://purl.bioontology.org/ontology/CSP/0468-5952> .
        ?mapping map:source ?source .
    }

And submitted it with Jena?s remote query command like this, but got an error.

mark at office:~/apache-jena-3.8.0/bin$ ./rsparql --service 'http://sparql.bioontology.org/mappings/sparql/?apikey=9cf735c3-a44a-404f-8b2f-c49d48b2b8b2' --query  ~/bpmap.rq
HTTP Exeception
HttpException: 500 HTTP 500 error making the query: INTERNAL SERVER ERROR
        at org.apache.jena.sparql.engine.http.HttpQuery.rewrap(HttpQuery.java:370)
        at org.apache.jena.sparql.engine.http.HttpQuery.execGet(HttpQuery.java:336)
        at org.apache.jena.sparql.engine.http.HttpQuery.exec(HttpQuery.java:288)
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execResultSetInner(QueryEngineHTTP.java:352)
        at org.apache.jena.sparql.engine.http.QueryEngineHTTP.execSelect(QueryEngineHTTP.java:344)
        at org.apache.jena.sparql.util.QueryExecUtils.doSelectQuery(QueryExecUtils.java:196)
        at org.apache.jena.sparql.util.QueryExecUtils.executeQuery(QueryExecUtils.java:79)
        at arq.rsparql.exec(rsparql.java:76)
        at jena.cmd.CmdMain.mainMethod(CmdMain.java:93)
        at jena.cmd.CmdMain.mainRun(CmdMain.java:58)
        at jena.cmd.CmdMain.mainRun(CmdMain.java:45)
        at arq.rsparql.main(rsparql.java:44)
mark at office:~/apache-jena-3.8.0/bin$
_______________________________________________
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 Jul 30 09:12:05 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 30 Jul 2018 16:12:05 +0000
Subject: [bioontology-support]
 =?utf-8?q?=5BBioPortal=5D_Feedback_from_Fer?=
 =?utf-8?q?nanda_D=C3=B3rea?=
In-Reply-To: <5b5f0b53832fb_66a03fba0ff2ca34990bb@ncbo-prd-app-08.stanford.edu.mail>
References: <5b5f0b53832fb_66a03fba0ff2ca34990bb@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <AB81176F-1E76-413E-A25B-D6E5C6E2C857@stanford.edu>

Hello Fernanda,


On Jul 30, 2018, at 5:57 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Fernanda D?rea

Email: fernanda.dorea at sva.se<mailto:fernanda.dorea at sva.se>

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

Feedback:

Hi, I work for the National Veterinary Institute in Sweden and we have been developing an ontology of Animal Health Surveillance:

https://w3id.org/ahso

I would like to know if it is possible to have the ontology listed in the BioPortal, and what are the requirements and procedures in order to do so.



Yes, you?re welcome to submit your ontology to BioPortal. We have instructions for doing so on our wiki:

https://www.bioontology.org/wiki/BioPortal_Help#Submitting_an_ontology

Let us know if you run into any issues during the process.

Kind regards,
Jennifer

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From hoppesyd at umich.edu  Mon Jul 30 12:59:16 2018
From: hoppesyd at umich.edu (Sydney Hoppe)
Date: Mon, 30 Jul 2018 14:59:16 -0500
Subject: [bioontology-support] Issue on Github
Message-ID: <CACcE1G9N+169Xk37e9eab8o3pdZdyyWYs2F1gecBzLTmD-=-aw@mail.gmail.com>

Hello,

I am working on a local virtual appliance (V2.4) and have run into the
exact issue outline in this github issue.
https://github.com/ncbo/bioportal-project/issues/21. At the end it was
stated "Documented necessary deletion command in internal github pages".
Would you be able to share what commands you used inorder to delete the
corrupt submissions?

Thanks!

-- 
*Sydney Hoppe*
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu | 614.282.1314
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From vendetti at stanford.edu  Mon Jul 30 16:13:48 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 30 Jul 2018 23:13:48 +0000
Subject: [bioontology-support] Issue on Github
In-Reply-To: <CACcE1G9N+169Xk37e9eab8o3pdZdyyWYs2F1gecBzLTmD-=-aw@mail.gmail.com>
References: <CACcE1G9N+169Xk37e9eab8o3pdZdyyWYs2F1gecBzLTmD-=-aw@mail.gmail.com>
Message-ID: <0D7695E9-92F7-4642-9679-A04D8D73D754@stanford.edu>

Hello Sydney,

Yes - I?ll respond offline with instructions.

Kind regards,
Jennifer


On Jul 30, 2018, at 12:59 PM, Sydney Hoppe <hoppesyd at umich.edu<mailto:hoppesyd at umich.edu>> wrote:

Hello,

I am working on a local virtual appliance (V2.4) and have run into the exact issue outline in this github issue. https://github.com/ncbo/bioportal-project/issues/21. At the end it was stated "Documented necessary deletion command in internal github pages". Would you be able to share what commands you used inorder to delete the corrupt submissions?

Thanks!

--
Sydney Hoppe
University of Michigan, Ann Arbor
B.S.E. in Engineering, 2019
hoppesyd at umich.edu<mailto:hoppesyd at umich.edu> | 614.282.1314
_______________________________________________
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 Jul 30 19:30:54 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 30 Jul 2018 19:30:54 -0700
Subject: [bioontology-support] [BioPortal] Feedback from mkalas
Message-ID: <5b5fc9de85413_4a383f8b2502b1ac8005@ncbo-prd-app-08.stanford.edu.mail>

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From Matus.Kalas at uib.no  Mon Jul 30 19:37:19 2018
From: Matus.Kalas at uib.no (Matus Kalas)
Date: Tue, 31 Jul 2018 04:37:19 +0200
Subject: [bioontology-support] [BioPortal] Feedback from mkalas
In-Reply-To: <5b5fc9de85413_4a383f8b2502b1ac8005@ncbo-prd-app-08.stanford.edu.mail>
References: <5b5fc9de85413_4a383f8b2502b1ac8005@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <fe0b2c8bc577633033fd19db3de09913@webmail.uib.no>

Update: Now the "old" browser has started doing the save as the new 
browsers, i.e. it shows the first upload of this version of the 
ontology. But not the last.

Cheers,
Matus


On 2018-07-31 04:30, support at bioontology.org wrote:
> Name: mkalas
> 
>  Email: matus.kalas at bccs.uib.no
> 
>  Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FEDAM
> 
> FEEDBACK:
> 
> Hi!
> 
> We're releasing a new version of the EDAM ontology now (during today
> and tomorrow).
> 
> I must say that I'm impressed that most of the previous problems with
> updating have been solved. Awesome!
> 
> There is still a problem, though:
> 
> After I updated the new version with a new uploaded OWL file (fixing
> an error), I get some leftovers of the previous troublesome behavior:
> - Clicking "1.21" returns "We're sorry but something has gone wrong.
> We have been notified of this error." in a usual web browser.
> - Clicking "Classes" returns "Problem retrieving classes"
> - In a new web browser, those return a view of the FIRST UPLOADED
> "version" of this particular, that is NOT THE FIXED ONE
> - CSV download also returns the FIRST UPLOADED "version" of this
> particular, that is NOT THE FIXED ONE
> 
> We need to get those updated ASAP, so please help!
> 
> A billion thanks!!!
> Matus

From vendetti at stanford.edu  Mon Jul 30 20:02:30 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 31 Jul 2018 03:02:30 +0000
Subject: [bioontology-support] [BioPortal] Feedback from mkalas
In-Reply-To: <5b5fc9de85413_4a383f8b2502b1ac8005@ncbo-prd-app-08.stanford.edu.mail>
References: <5b5fc9de85413_4a383f8b2502b1ac8005@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <44578F69-1BFD-4B39-9B72-6A0CA86ADEA9@stanford.edu>

Hi Matus,


On Jul 30, 2018, at 7:30 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

We're releasing a new version of the EDAM ontology now (during today and tomorrow).

I must say that I'm impressed that most of the previous problems with updating have been solved. Awesome!

There is still a problem, though:

After I updated the new version with a new uploaded OWL file (fixing an error), I get some leftovers of the previous troublesome behavior:

 I didn?t quite follow what you did. Are you saying that you created a new submission (version 1.21) with one OWL file, then edited the submission to upload a second version of the OWL file because the first one had an error?


- Clicking "1.21" returns "We're sorry but something has gone wrong. We have been notified of this error." in a usual web browser.
- Clicking "Classes" returns "Problem retrieving classes"

I looked at the parsing log files for your ontology and I didn?t see any errors, although I did notice that the system was reporting no metrics for this latest version. I ran a script to reprocess the metrics data and reset the application caches so that they?re now visible in the UI. So far I?m not able to reproduce either the 500 error, or the error about retrieving classes.

Are these still occurring for you after that adjustment I made? If so, could you let me know what browser you?re using?


- In a new web browser, those return a view of the FIRST UPLOADED "version" of this particular, that is NOT THE FIXED ONE
- CSV download also returns the FIRST UPLOADED "version" of this particular, that is NOT THE FIXED ONE



I can test this on my end and look at the files on our production server, but I?ll need you to give me some kind of indication of how I would know if we?re seeing your ?fixed? OWL file, e.g., is there some specific text I can search for?

Kind regards,
Jennifer

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From Matus.Kalas at uib.no  Tue Jul 31 09:09:05 2018
From: Matus.Kalas at uib.no (Matus Kalas)
Date: Tue, 31 Jul 2018 18:09:05 +0200
Subject: [bioontology-support] [BioPortal] Feedback from mkalas
In-Reply-To: <44578F69-1BFD-4B39-9B72-6A0CA86ADEA9@stanford.edu>
References: <5b5fc9de85413_4a383f8b2502b1ac8005@ncbo-prd-app-08.stanford.edu.mail>
 <44578F69-1BFD-4B39-9B72-6A0CA86ADEA9@stanford.edu>
Message-ID: <7d7786a72cefe3fa16bae6759ed01fa5@webmail.uib.no>

Thank you so much, Jennifer!

The problem is now fixed after your adjustments.

You understood the problem exactly right.

The first version of the EDAM_1.21.owl had a typo in 2 super-class URIs 
stating http://edamohntology.org/topic_0077 instead of 
http://edamontology.org/topic_0077. Searching for "RNA" in the GUI and 
selecting the one with "RNA" in capitals, without any other words (or 
alternatively just going to 
conceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0099), will show up as 
hanging underneath a non-labelled class topic_0077.

The second version of EDAM_1.21.owl fixes this, and "RNA" 
(conceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0099) appears correctly 
underneath "Nucleic acids".

A million thanks again for your prompt help!
Matus


On 2018-07-31 05:02, Jennifer Leigh Vendetti wrote:
> Hi Matus,
> 
>> On Jul 30, 2018, at 7:30 PM, support at bioontology.org wrote:
>> 
>> We're releasing a new version of the EDAM ontology now (during today
>> and tomorrow).
>> 
>> I must say that I'm impressed that most of the previous problems
>> with updating have been solved. Awesome!
>> 
>> There is still a problem, though:
>> 
>> After I updated the new version with a new uploaded OWL file (fixing
>> an error), I get some leftovers of the previous troublesome
>> behavior:
> 
>  I didn?t quite follow what you did. Are you saying that you created
> a new submission (version 1.21) with one OWL file, then edited the
> submission to upload a second version of the OWL file because the
> first one had an error?
> 
>> - Clicking "1.21" returns "We're sorry but something has gone wrong.
>> We have been notified of this error." in a usual web browser.
>> - Clicking "Classes" returns "Problem retrieving classes"
> 
> I looked at the parsing log files for your ontology and I didn?t see
> any errors, although I did notice that the system was reporting no
> metrics for this latest version. I ran a script to reprocess the
> metrics data and reset the application caches so that they?re now
> visible in the UI. So far I?m not able to reproduce either the 500
> error, or the error about retrieving classes.
> 
> Are these still occurring for you after that adjustment I made? If so,
> could you let me know what browser you?re using?
> 
>> - In a new web browser, those return a view of the FIRST UPLOADED
>> "version" of this particular, that is NOT THE FIXED ONE
>> - CSV download also returns the FIRST UPLOADED "version" of this
>> particular, that is NOT THE FIXED ONE
> 
> I can test this on my end and look at the files on our production
> server, but I?ll need you to give me some kind of indication of how
> I would know if we?re seeing your ?fixed? OWL file, e.g., is
> there some specific text I can search for?
> 
> Kind regards,
> Jennifer

From wynner at mail.nih.gov  Tue Jul 31 14:19:56 2018
From: wynner at mail.nih.gov (Wynne, Robert (NIH/NCI) [C])
Date: Tue, 31 Jul 2018 21:19:56 +0000
Subject: [bioontology-support] RRF conversion
In-Reply-To: <267AA14C-C00A-4346-B088-0A010634DAEF@stanford.edu>
References: <BL0PR0901MB244991EE67236878B9659FC2FB2B0@BL0PR0901MB2449.namprd09.prod.outlook.com>
 <267AA14C-C00A-4346-B088-0A010634DAEF@stanford.edu>
Message-ID: <BL0PR0901MB2449DCCEA1D3A19977857F1BFB2E0@BL0PR0901MB2449.namprd09.prod.outlook.com>

Hi John,

Thank you!  We?ll give this a try.

Rob

From: John Graybeal <jgraybeal at stanford.edu>
Sent: Thursday, July 26, 2018 9:25 PM
To: Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov>
Cc: support at bioontology.org; Remennik, Lyubov (NIH/NCI) [E] <lyubov.remennik at nih.gov>
Subject: Re: [bioontology-support] RRF conversion

Hello Rob,

Our process is as follows:
1) download the UMLS full release in whatever format they provide
2) run Metamorphosys application which generates the RRF files and mysql load script
3) run the generated mysql load script to load data from RRF files
4) run our python umls2rdf script to generate TTL files

The only part of this you don't already have access to (if you're running the UMLS MetaMorphosys) is the umls2rdf script, which is in GitHub at https://github.com/ncbo/umls2rdf.

The

On Jul 26, 2018, at 7:47 AM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi all,

We?re interested in converting an RRF subset from MetaMorphosys to something our Triplestore could consume (ttl/owl/rdf, etc).  Is a most recent script available for this?  Possibly in Github?

Thanks,
Rob
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========================
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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