From zhu at iastate.edu  Fri Oct  1 08:29:42 2021
From: zhu at iastate.edu (Hu, Zhiliang [AN S])
Date: Fri, 1 Oct 2021 15:29:42 +0000
Subject: [bioontology-support] Help on a small API script
In-Reply-To: <48044B40-F35D-470B-ADFB-54A3D1E0E4BE@stanford.edu>
References: <069BD98E-6F4F-4AB2-8A25-A3B30D0789E2@iastate.edu>
 <48044B40-F35D-470B-ADFB-54A3D1E0E4BE@stanford.edu>
Message-ID: <B0AC0B76-59D2-4728-AEEA-87C8568D5EF3@iastate.edu>

Hi Jennifer,

Thank you for your patience with me. The information are very helpful.
Now I get it to work!

Have a good weekend!

Zhiliang

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Thu, Sep 30, 2021 at 06:26 PM
To: Zhiliang Hu <zhu at iastate.edu>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] Help on a small API script

Hello Zhiliang,

If you want check the version of the latest submission of a particular ontology, you can use the /latest_submission endpoint, e.g., for VT the REST API call would be the following:

http://data.bioontology.org/ontologies/VT/latest_submission

In the JSON results, you can check for the ?version? key/value pair:



[cid:image001.png at 01D7B6AF.3CECE890]

You may also be interested in the /submissions endpoint, which would allow you to retrieve all of the submissions for a particular ontology, e.g.:

http://data.bioontology.org/ontologies/VT/submissions

You can iterate over the collection, looking at the ?version? key/value pair for each ontology submission object.

We have some example code for interacting with our REST API in GitHub:

https://github.com/ncbo/ncbo_rest_sample_code

Kind regards,
Jennifer




On Sep 30, 2021, at 3:34 PM, Hu, Zhiliang [AN S] <zhu at iastate.edu<mailto:zhu at iastate.edu>> wrote:

Greetings,

I have a routine to watch the latest versions of a few ontologies (VT/LPT/CMO/etc).
I tried the following:

use LWP::Simple;
use JSON qw( decode_json );
my $bioprtAPIky = "720f4412-5a96-48cc-a39f-961570c9a94b";
my $url = "http://data.bioontology.org";
  $url .= "/property_search?";
  $url .= "apikey=$bioprtAPIky";
  $url .= "&ontology=VT";
  $url .= "&q=version";
my $get = get("$url");

and get lost at what to extract for.

I was on your doc http://data.bioontology.org/documentation but didn't get much. Could you help with this script? (to get just the latest version number).

Thanks in advance,

Zhiliang

PS:
I used to "get" "https://bioportal.bioontology.org/ontologies/VT/?p=summary" and apparently the scripting "get" is being blocked on your site lately.


_______________________________________________
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 daniel at hopebio.org  Thu Oct  7 10:16:18 2021
From: daniel at hopebio.org (Daniel Chang)
Date: Thu, 7 Oct 2021 17:16:18 +0000
Subject: [bioontology-support] FW: [BioPortal] User Hope Biosciences Stem
 Cell Research Foundation password reset
References: <615f2a08e9efe_d36110d9b09896@ncbo-prd-app-14.stanford.edu.mail>
Message-ID: <CO6PR06MB7234F7C88F3FD197F70B95FEF2B19@CO6PR06MB7234.namprd06.prod.outlook.com>

Hello,

I?m having trouble accessing our account, Hope Biosciences Stem Cell Research Foundation. When we try resetting our password, we are able to receive an email (see below) with a link, but that link displays the following page. Please help. Thank you.

[Graphical user interface, application, Word  Description automatically generated]

From: "admin at bioontology.org" <admin at bioontology.org>
Date: Thursday, October 7, 2021 at 12:10 PM
To: "daniel at hopebio.org" <daniel at hopebio.org>
Subject: [BioPortal] User Hope Biosciences Stem Cell Research Foundation password reset

Someone has requested a password reset for user Hope Biosciences Stem Cell Research Foundation. If this was you, please click on the link below to reset your password. Otherwise, please ignore this email.

https://bioportal.bioontology.org/reset_password?tk=HmJiDPNGcEkxRLSYXa8A7mYNFyh3jQNeeQpP&em=daniel%40hopebio.org&un=Hope+Biosciences+Stem+Cell+Research+Foundation

Thanks,
BioPortal Team
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From vendetti at stanford.edu  Thu Oct  7 17:06:25 2021
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 8 Oct 2021 00:06:25 +0000
Subject: [bioontology-support] [bioontology-admin] [BioPortal] User Hope
 Biosciences Stem Cell Research Foundation password reset
In-Reply-To: <CO6PR06MB7234F7C88F3FD197F70B95FEF2B19@CO6PR06MB7234.namprd06.prod.outlook.com>
References: <615f2a08e9efe_d36110d9b09896@ncbo-prd-app-14.stanford.edu.mail>
 <CO6PR06MB7234F7C88F3FD197F70B95FEF2B19@CO6PR06MB7234.namprd06.prod.outlook.com>
Message-ID: <73BBA1D9-05E0-4B5A-AD34-1C1ADEB609E9@stanford.edu>

Hello Daniel,

Apologies the for the difficulties you?ve had attempting to reset your password. I?ve investigated and reproduced the issue in our production environment. The ability to reset passwords for account names with spaces is broken, which I?ve documented in our issue tracker:

https://github.com/ncbo/bioportal_web_ui/issues/177

I?ll contact you off the support list with information about how to login until this issue is fixed.

Kind regards,
Jennifer



On Oct 7, 2021, at 10:16 AM, Daniel Chang <daniel at hopebio.org<mailto:daniel at hopebio.org>> wrote:

Hello,

I?m having trouble accessing our account, Hope Biosciences Stem Cell Research Foundation. When we try resetting our password, we are able to receive an email (see below) with a link, but that link displays the following page. Please help. Thank you.

<image001.png>

From: "admin at bioontology.org<mailto:admin at bioontology.org>" <admin at bioontology.org<mailto:admin at bioontology.org>>
Date: Thursday, October 7, 2021 at 12:10 PM
To: "daniel at hopebio.org<mailto:daniel at hopebio.org>" <daniel at hopebio.org<mailto:daniel at hopebio.org>>
Subject: [BioPortal] User Hope Biosciences Stem Cell Research Foundation password reset

Someone has requested a password reset for user Hope Biosciences Stem Cell Research Foundation. If this was you, please click on the link below to reset your password. Otherwise, please ignore this email.

https://bioportal.bioontology.org/reset_password?tk=HmJiDPNGcEkxRLSYXa8A7mYNFyh3jQNeeQpP&em=daniel%40hopebio.org&un=Hope+Biosciences+Stem+Cell+Research+Foundation

Thanks,
BioPortal Team
_______________________________________________
bioontology-admin mailing list
bioontology-admin at lists.stanford.edu<mailto:bioontology-admin at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-admin

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From support at bioontology.org  Fri Oct  8 10:28:24 2021
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 08 Oct 2021 10:28:24 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Eric Deutsch
Message-ID: <61607fb88440_24da209345c66324@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Fri Oct  8 10:59:53 2021
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 8 Oct 2021 17:59:53 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Eric Deutsch
In-Reply-To: <61607fb88440_24da209345c66324@ncbo-prd-app-08.stanford.edu.mail>
References: <61607fb88440_24da209345c66324@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <1813073C-51BB-49EA-BAD2-E84B1B875596@stanford.edu>

Hi Eric,


On Oct 8, 2021, at 10:28 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Hi, our ontology "MS" has not been updated at your site for over a year:

https://bioportal.bioontology.org/ontologies/MS

but we have updated it over 20 times in the past year:
https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo

How we arrange it so that the MS ontology is kept up-to-date in BioPortal?



I examined the log files for our nightly ontology pull process and found an error related to MS. Our triplestore contained a corrupt ontology submission object that?s preventing creation of new submissions for MS:

E, [2021-10-07T18:05:48.973919 #18479] ERROR -- : Unable to create a new submission in OntologyPull: {:proc_naming=>{:duplicate=>"There is already a persistent resource with id `http://data.bioontology.org/ontologies/MS/submissions/163`?}}

I?ve deleted this corrupt submission object, which should clear the way for the nightly pull process to resume processing new versions of your ontology.

However, there?s something else to be aware of - we?re currently troubleshooting an issue in our production system that?s been preventing our nightly pull process from downloading new versions of a subset of ontologies since September 30th. It?s currently documented here in our issue tracker:

https://github.com/ncbo/bioportal_web_ui/issues/176

I?m not sure if your ontology will be affected by this issue - I?ll know more after our pull process kicks off this evening.

Apologies for the inconvenience.

Kind regards,
Jennifer

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From edeutsch at systemsbiology.org  Fri Oct  8 11:11:28 2021
From: edeutsch at systemsbiology.org (Eric Deutsch)
Date: Fri, 8 Oct 2021 11:11:28 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Eric Deutsch
In-Reply-To: <1813073C-51BB-49EA-BAD2-E84B1B875596@stanford.edu>
References: <61607fb88440_24da209345c66324@ncbo-prd-app-08.stanford.edu.mail>
 <1813073C-51BB-49EA-BAD2-E84B1B875596@stanford.edu>
Message-ID: <a38d08652014e5f53f3e8f9337b63979@mail.gmail.com>

Hi Jennifer, thank you for the prompt response!

Looking forward to seeing if it will be fixed as of tomorrow.



Thanks!

Eric





*From:* Jennifer Leigh Vendetti <vendetti at stanford.edu>
*Sent:* Friday, October 8, 2021 11:00 AM
*To:* support at bioontology.org
*Cc:* edeutsch at systemsbiology.org
*Subject:* Re: [bioontology-support] [BioPortal] Feedback from Eric Deutsch



Hi Eric,





On Oct 8, 2021, at 10:28 AM, support at bioontology.org wrote:



Hi, our ontology "MS" has not been updated at your site for over a year:

https://bioportal.bioontology.org/ontologies/MS

but we have updated it over 20 times in the past year:
https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo

How we arrange it so that the MS ontology is kept up-to-date in BioPortal?







I examined the log files for our nightly ontology pull process and found an
error related to MS. Our triplestore contained a corrupt ontology
submission object that?s preventing creation of new submissions for MS:



E, [2021-10-07T18:05:48.973919 #18479] ERROR -- : Unable to create a new
submission in OntologyPull: {:proc_naming=>{:duplicate=>"There is already a
persistent resource with id `
http://data.bioontology.org/ontologies/MS/submissions/163`?}}



I?ve deleted this corrupt submission object, which should clear the way for
the nightly pull process to resume processing new versions of your ontology.



However, there?s something else to be aware of - we?re currently
troubleshooting an issue in our production system that?s been preventing
our nightly pull process from downloading new versions of a subset of
ontologies since September 30th. It?s currently documented here in our
issue tracker:



https://github.com/ncbo/bioportal_web_ui/issues/176



I?m not sure if your ontology will be affected by this issue - I?ll know
more after our pull process kicks off this evening.



Apologies for the inconvenience.



Kind regards,

Jennifer
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From vendetti at stanford.edu  Sat Oct  9 08:11:36 2021
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Sat, 9 Oct 2021 15:11:36 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Eric Deutsch
In-Reply-To: <a38d08652014e5f53f3e8f9337b63979@mail.gmail.com>
References: <61607fb88440_24da209345c66324@ncbo-prd-app-08.stanford.edu.mail>
 <1813073C-51BB-49EA-BAD2-E84B1B875596@stanford.edu>
 <a38d08652014e5f53f3e8f9337b63979@mail.gmail.com>
Message-ID: <CC515F6E-C2B8-46D1-B25E-05BE5770D851@stanford.edu>

Hi Eric,

I checked our system this morning and it appears that a new version of MS was successfully retrieved and processed.

Kind regards,
Jennifer


[cid:F1661DE5-BABC-4CB9-B2AF-294D137DEF87 at lan]



On Oct 8, 2021, at 11:11 AM, Eric Deutsch <edeutsch at systemsbiology.org<mailto:edeutsch at systemsbiology.org>> wrote:

Hi Jennifer, thank you for the prompt response!
Looking forward to seeing if it will be fixed as of tomorrow.

Thanks!
Eric


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, October 8, 2021 11:00 AM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: edeutsch at systemsbiology.org<mailto:edeutsch at systemsbiology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Eric Deutsch

Hi Eric,



On Oct 8, 2021, at 10:28 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Hi, our ontology "MS" has not been updated at your site for over a year:
https://bioportal.bioontology.org/ontologies/MS
but we have updated it over 20 times in the past year:
https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo
How we arrange it so that the MS ontology is kept up-to-date in BioPortal?



I examined the log files for our nightly ontology pull process and found an error related to MS. Our triplestore contained a corrupt ontology submission object that?s preventing creation of new submissions for MS:

E, [2021-10-07T18:05:48.973919 #18479] ERROR -- : Unable to create a new submission in OntologyPull: {:proc_naming=>{:duplicate=>"There is already a persistent resource with id `http://data.bioontology.org/ontologies/MS/submissions/163`<http://data.bioontology.org/ontologies/MS/submissions/163%60>?}}

I?ve deleted this corrupt submission object, which should clear the way for the nightly pull process to resume processing new versions of your ontology.

However, there?s something else to be aware of - we?re currently troubleshooting an issue in our production system that?s been preventing our nightly pull process from downloading new versions of a subset of ontologies since September 30th. It?s currently documented here in our issue tracker:

https://github.com/ncbo/bioportal_web_ui/issues/176

I?m not sure if your ontology will be affected by this issue - I?ll know more after our pull process kicks off this evening.

Apologies for the inconvenience.

Kind regards,
Jennifer

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From edeutsch at systemsbiology.org  Sun Oct 10 21:25:58 2021
From: edeutsch at systemsbiology.org (Eric Deutsch)
Date: Sun, 10 Oct 2021 21:25:58 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Eric Deutsch
In-Reply-To: <CC515F6E-C2B8-46D1-B25E-05BE5770D851@stanford.edu>
References: <61607fb88440_24da209345c66324@ncbo-prd-app-08.stanford.edu.mail>
 <1813073C-51BB-49EA-BAD2-E84B1B875596@stanford.edu>
 <a38d08652014e5f53f3e8f9337b63979@mail.gmail.com>
 <CC515F6E-C2B8-46D1-B25E-05BE5770D851@stanford.edu>
Message-ID: <97a13cd6bf2f8f5d0fc655c1c658ba52@mail.gmail.com>

Hi Jennifer, many thanks for fixing this. I have tested and it is good, all
up to date.



Thank you!

Eric





*From:* Jennifer Leigh Vendetti <vendetti at stanford.edu>
*Sent:* Saturday, October 9, 2021 8:12 AM
*To:* Eric Deutsch <edeutsch at systemsbiology.org>
*Cc:* support at bioontology.org
*Subject:* Re: [bioontology-support] [BioPortal] Feedback from Eric Deutsch



Hi Eric,



I checked our system this morning and it appears that a new version of MS
was successfully retrieved and processed.



Kind regards,

Jennifer











On Oct 8, 2021, at 11:11 AM, Eric Deutsch <edeutsch at systemsbiology.org>
wrote:



Hi Jennifer, thank you for the prompt response!

Looking forward to seeing if it will be fixed as of tomorrow.



Thanks!

Eric





*From:* Jennifer Leigh Vendetti <vendetti at stanford.edu>
*Sent:* Friday, October 8, 2021 11:00 AM
*To:* support at bioontology.org
*Cc:* edeutsch at systemsbiology.org
*Subject:* Re: [bioontology-support] [BioPortal] Feedback from Eric Deutsch



Hi Eric,





On Oct 8, 2021, at 10:28 AM, support at bioontology.org wrote:



Hi, our ontology "MS" has not been updated at your site for over a year:

https://bioportal.bioontology.org/ontologies/MS

but we have updated it over 20 times in the past year:
https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo

How we arrange it so that the MS ontology is kept up-to-date in BioPortal?







I examined the log files for our nightly ontology pull process and found an
error related to MS. Our triplestore contained a corrupt ontology
submission object that?s preventing creation of new submissions for MS:



E, [2021-10-07T18:05:48.973919 #18479] ERROR -- : Unable to create a new
submission in OntologyPull: {:proc_naming=>{:duplicate=>"There is already a
persistent resource with id `
http://data.bioontology.org/ontologies/MS/submissions/163`?}}



I?ve deleted this corrupt submission object, which should clear the way for
the nightly pull process to resume processing new versions of your ontology.



However, there?s something else to be aware of - we?re currently
troubleshooting an issue in our production system that?s been preventing
our nightly pull process from downloading new versions of a subset of
ontologies since September 30th. It?s currently documented here in our
issue tracker:



https://github.com/ncbo/bioportal_web_ui/issues/176



I?m not sure if your ontology will be affected by this issue - I?ll know
more after our pull process kicks off this evening.



Apologies for the inconvenience.



Kind regards,

Jennifer
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From support at bioontology.org  Mon Oct 11 05:18:27 2021
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 11 Oct 2021 05:18:27 -0700
Subject: [bioontology-support] [BioPortal] Feedback from k.j.van.der.velde
Message-ID: <61642b9374523_21f028ea5d88595@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Mon Oct 11 08:57:08 2021
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 11 Oct 2021 08:57:08 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Christian Pich
Message-ID: <61645ed42517a_60fd241d834179ee@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Tue Oct 12 12:34:13 2021
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 12 Oct 2021 19:34:13 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
	k.j.van.der.velde
In-Reply-To: <61642b9374523_21f028ea5d88595@ncbo-prd-app-08.stanford.edu.mail>
References: <61642b9374523_21f028ea5d88595@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <90151ED6-46E6-481C-A86A-C1BCAC77445C@stanford.edu>

Hello Joeri,


On Oct 11, 2021, at 5:18 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Dear support,

I have uploaded a new ontology last Friday (https://bioportal.bioontology.org/ontologies/DFO) but in the 'Classes' tab there is an error (Problem retrieving classes). Has it not been indexed yet, or did I do something wrong?

I?ve taken a look at our production log files. It appears that your ontology was ingested into the system and processed, i.e., our REST endpoint is currently serving class data for DFO (screenshot attached).

The BioPortal web application is showing an error message when attempting to display the Classes page because our system is unable to calculate the set of root classes for the ontology. The Classes page needs to know the root classes in order to construct the class tree. I looked briefly at your ontology and noticed that it?s an OWL ontology, but the 2 root classes are declared using an obo prefix. It?s not immediately evident to me if this is what?s causing our system difficulties in calculating the roots. I?ve entered an issue in our tracker so that we can investigate further:

https://github.com/ncbo/bioportal-project/issues/220

Kind regards,
Jennifer



[cid:194864A5-479A-4B80-AC80-D86A32331078 at lan]
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From vendetti at stanford.edu  Tue Oct 12 12:53:19 2021
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 12 Oct 2021 19:53:19 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Christian Pich
In-Reply-To: <61645ed42517a_60fd241d834179ee@ncbo-prd-app-09.stanford.edu.mail>
References: <61645ed42517a_60fd241d834179ee@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <3D53EE1A-A31A-4427-9F15-6769FA52C35E@stanford.edu>

Hi Christian,


On Oct 11, 2021, at 8:57 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Hi, I am getting an error when loading the obo file for the spatial ontology

In BioPortal, we?re hosting the OWL version of this ontology, not the OBO version. The Spatial Ontology entry is configured to retrieve the OWL source file from this GitHub URL:

https://raw.githubusercontent.com/obophenotype/biological-spatial-ontology/master/bspo.owl


because two terms (stanzas) are using a date-only syntax for the created_date for which the ontology parser are expecting a date/time stamp:

[Typedef]
id: BSPO:0000114
name: lateral to
def: "X lateral to y if x is further from the midsagittal plane than y." []
is_transitive: true
inverse_of: BSPO:0000115 ! medial to
created_by: Jennifer Gir?n
creation_date: 2021-04-21

[Typedef]
id: BSPO:0000115
name: medial to
name: X medial to y if x is closer to the midsagittal plane than y.
is_transitive: true
created_by: Jennifer Gir?n
creation_date: 2021-04-21

Is it possible to either remove those two lines or include a sull date and time-stamp like in GO.

Although we host and serve ontologies from BioPortal, we?re often not the ontology authors. If you?d like to request a change to the ontology content, I suggest reaching out to the ontology maintainers. Contact information for ontology maintainers is typically listed on the ontology summary page:

https://bioportal.bioontology.org/ontologies/BSPO

? in the Details pane. The homepage for this ontology is:

https://github.com/obophenotype/biological-spatial-ontology

According to their homepage, you can use their issue tracker to make requests related to content:

https://github.com/obophenotype/biological-spatial-ontology/issues

Kind regards,
Jennifer

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From support at bioontology.org  Thu Oct 14 12:45:19 2021
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 14 Oct 2021 12:45:19 -0700
Subject: [bioontology-support] [BioPortal] Feedback from satyasahoo
Message-ID: <616888cf67cff_1a982125668814bf@ncbo-prd-app-09.stanford.edu.mail>

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From jgraybeal at stanford.edu  Fri Oct 15 13:53:25 2021
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 15 Oct 2021 20:53:25 +0000
Subject: [bioontology-support] [BioPortal] Feedback from satyasahoo
In-Reply-To: <616888cf67cff_1a982125668814bf@ncbo-prd-app-09.stanford.edu.mail>
References: <616888cf67cff_1a982125668814bf@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <985E75F7-E1B2-4C79-8AF7-107E6D5E811D@stanford.edu>

Thank you for your email, sorry I have been slow in responding.

I spent some time looking closely at these circumstances, which are highly unusual, as we can't reproduce the issue outside of BioPortal itself. We will continue to look into it in the next few days and keep updating the ticket you cited.

Our apologies for the difficulty!

John



On Oct 14, 2021, at 12:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: satyasahoo

Email: satyasahoo at ieee.org<mailto:satyasahoo at ieee.org>

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

Feedback:

Good Afternoon,
We continue to experience parsing errors with the Epilepsy and Seizure Ontology (EpSO) OWL file.

The previous submission also experienced similar BioPortal parsing error documented as Issue#216: https://github.com/ncbo/bioportal-project/issues/216.

The BioPortal issue tracker noted that the EpSO OWL file was correctly parsed in the BioPortal staging environment (https://stage.bioontology.org/ontologies/EPSO?p=classes).

The latest release of EpSO (version 2.1) OWL is experiencing same error "Error Rdf Labels").

We request your help in addressing this error at the earliest as we have received community feedback regarding their inability to visually browse EpSO in the BioPortal "Classes" and "Properties" tabs.

Thank you for your time and consideration!

Sincerely,
Satya Sahoo, PhD FAMIA
CWRU School of Medicine
https://bmhinformatics.case.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  | ORCID  0000-0001-6875-5360



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From jgraybeal at stanford.edu  Sun Oct 17 14:04:18 2021
From: jgraybeal at stanford.edu (John Graybeal)
Date: Sun, 17 Oct 2021 21:04:18 +0000
Subject: [bioontology-support] [BioPortal] Feedback from satyasahoo
In-Reply-To: <616888cf67cff_1a982125668814bf@ncbo-prd-app-09.stanford.edu.mail>
References: <616888cf67cff_1a982125668814bf@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <716C70D6-F90C-457C-AEF0-84FA27F327DD@stanford.edu>

Hello Dr. Sahoo,

Thank you for your patience with this problem.  We have fixed the ontology and it is now correctly visible in BioPortal.

Details about the problem can be found in the ticket https://github.com/ncbo/bioportal-project/issues/216. In brief, the customized default property setting fields are meant to be specialized settings that are IRIs (unique identifiers), but they had been filled with regular text strings. (Examples of the unique identifiers can be found in the help text below each field.)

These invalid settings were causing the final parsing stage (using rapper) to fail. When we removed them we were able to parse the ontology successfully.

John

On Oct 14, 2021, at 12:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: satyasahoo

Email: satyasahoo at ieee.org<mailto:satyasahoo at ieee.org>

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

Feedback:

Good Afternoon,
We continue to experience parsing errors with the Epilepsy and Seizure Ontology (EpSO) OWL file.

The previous submission also experienced similar BioPortal parsing error documented as Issue#216: https://github.com/ncbo/bioportal-project/issues/216.

The BioPortal issue tracker noted that the EpSO OWL file was correctly parsed in the BioPortal staging environment (https://stage.bioontology.org/ontologies/EPSO?p=classes).

The latest release of EpSO (version 2.1) OWL is experiencing same error "Error Rdf Labels").

We request your help in addressing this error at the earliest as we have received community feedback regarding their inability to visually browse EpSO in the BioPortal "Classes" and "Properties" tabs.

Thank you for your time and consideration!

Sincerely,
Satya Sahoo, PhD FAMIA
CWRU School of Medicine
https://bmhinformatics.case.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  | ORCID  0000-0001-6875-5360



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From elizabeth at hopebio.org  Fri Oct 15 09:04:14 2021
From: elizabeth at hopebio.org (Elizabeth Oh)
Date: Fri, 15 Oct 2021 11:04:14 -0500
Subject: [bioontology-support] Inquiry About Search Specificity
Message-ID: <CAK+8Z+G2zDfEEL49KcrXmfDdFd5ZpLCf9RUAoP4PEvrEqE_AKg@mail.gmail.com>

Good Morning,

I am from the data management team at Hope Biosciences Stem Cell Research
Foundation and was wondering if there was a way to limit a search to only
the lowest level terms for MedDRA in our Redcap integration.

If that is not available is there any way to automatically fill and
complete corresponding fields such as preferred term, high level term, and
organ system (PT, HLT, HLGT, SOC) using the original search?

-- 
Sincerely,

Elizabeth Oh, B.S. (she/her/hers)
Clinical Data Specialist
elizabeth at hopebio.org <yasmany at hopebio.org>
( <http://www.hopebio.org>281) 740-3087

CONFIDENTIALITY NOTE: This message may contain confidential or legally
privileged information. If you are not the intended recipient, you
are hereby notified that any disclosure, copying, distribution, or taking
any action in reliance on these contents is strictly prohibited and may be
unlawful. If you have received this communication in error, please notify
us immediately by responding to this e-mail and then delete it from your
system.
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From satya_sanket at hotmail.com  Mon Oct 18 06:39:53 2021
From: satya_sanket at hotmail.com (Satya Sahoo)
Date: Mon, 18 Oct 2021 13:39:53 +0000
Subject: [bioontology-support] [BioPortal] Feedback from satyasahoo
In-Reply-To: <716C70D6-F90C-457C-AEF0-84FA27F327DD@stanford.edu>
References: <616888cf67cff_1a982125668814bf@ncbo-prd-app-09.stanford.edu.mail>
 <716C70D6-F90C-457C-AEF0-84FA27F327DD@stanford.edu>
Message-ID: <TU4PR8401MB09288F6DC977734624E70346E8BC9@TU4PR8401MB0928.NAMPRD84.PROD.OUTLOOK.COM>

Good Morning, John:
Thank you for resolving this issue! We will work on revising the customized local property to use IRI instead of just text. The visualization of the classes in BioPortal works now.

If possible, can you please clarify if BioPortal can use the entity prefixIRI instead of the rdfs:Label to generate the class names (similar to Protege rendering option using Entity )?

We have consistently used the prefixIRI to assign class names in EpSO and rdfs:Label to model synonyms/alternate names of the classes.

I appreciate your time and help!

Sincerely,
Satya


________________________________
From: John Graybeal <jgraybeal at stanford.edu>
Sent: Sunday, October 17, 2021 5:04 PM
To: support at bioontology.org <support at bioontology.org>
Cc: satyasahoo at ieee.org <satyasahoo at ieee.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from satyasahoo

Hello Dr. Sahoo,

Thank you for your patience with this problem.  We have fixed the ontology and it is now correctly visible in BioPortal.

Details about the problem can be found in the ticket https://github.com/ncbo/bioportal-project/issues/216. In brief, the customized default property setting fields are meant to be specialized settings that are IRIs (unique identifiers), but they had been filled with regular text strings. (Examples of the unique identifiers can be found in the help text below each field.)

These invalid settings were causing the final parsing stage (using rapper) to fail. When we removed them we were able to parse the ontology successfully.

John

On Oct 14, 2021, at 12:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: satyasahoo

Email: satyasahoo at ieee.org<mailto:satyasahoo at ieee.org>

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

Feedback:

Good Afternoon,
We continue to experience parsing errors with the Epilepsy and Seizure Ontology (EpSO) OWL file.

The previous submission also experienced similar BioPortal parsing error documented as Issue#216: https://github.com/ncbo/bioportal-project/issues/216.

The BioPortal issue tracker noted that the EpSO OWL file was correctly parsed in the BioPortal staging environment (https://stage.bioontology.org/ontologies/EPSO?p=classes).

The latest release of EpSO (version 2.1) OWL is experiencing same error "Error Rdf Labels").

We request your help in addressing this error at the earliest as we have received community feedback regarding their inability to visually browse EpSO in the BioPortal "Classes" and "Properties" tabs.

Thank you for your time and consideration!

Sincerely,
Satya Sahoo, PhD FAMIA
CWRU School of Medicine
https://bmhinformatics.case.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  | ORCID  0000-0001-6875-5360



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From support at bioontology.org  Fri Oct 15 00:34:02 2021
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 15 Oct 2021 00:34:02 -0700
Subject: [bioontology-support] =?utf-8?q?=5BBioPortal=5D_Feedback_from_?=
	=?utf-8?b?6K64?=
Message-ID: <61692eea1d4a5_7a4d2580320296b@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Mon Oct 18 11:32:47 2021
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 18 Oct 2021 18:32:47 +0000
Subject: [bioontology-support] [BioPortal] Feedback from satyasahoo
In-Reply-To: <TU4PR8401MB09288F6DC977734624E70346E8BC9@TU4PR8401MB0928.NAMPRD84.PROD.OUTLOOK.COM>
References: <616888cf67cff_1a982125668814bf@ncbo-prd-app-09.stanford.edu.mail>
 <716C70D6-F90C-457C-AEF0-84FA27F327DD@stanford.edu>
 <TU4PR8401MB09288F6DC977734624E70346E8BC9@TU4PR8401MB0928.NAMPRD84.PROD.OUTLOOK.COM>
Message-ID: <2E84E3EA-2FB4-4AE2-9310-409CD6A0CF2B@stanford.edu>

Hello Satya,


On Oct 18, 2021, at 6:39 AM, Satya Sahoo <satya_sanket at hotmail.com<mailto:satya_sanket at hotmail.com>> wrote:

Thank you for resolving this issue! We will work on revising the customized local property to use IRI instead of just text. The visualization of the classes in BioPortal works now.

If possible, can you please clarify if BioPortal can use the entity prefixIRI instead of the rdfs:Label to generate the class names (similar to Protege rendering option using Entity )?


The Protege application has a vast array of options for displaying entity names. Could you clarify if you?re referring to the View -> "Render by entity IRI short name (id)" menu item?



[cid:099CD854-A212-4B3F-A642-A6D4083FFE18 at lan]





We have consistently used the prefixIRI to assign class names in EpSO and rdfs:Label to model synonyms/alternate names of the classes.



Kind regards,
Jennifer


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From jgraybeal at stanford.edu  Tue Oct 19 17:07:49 2021
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 20 Oct 2021 00:07:49 +0000
Subject: [bioontology-support] Inquiry About Search Specificity
In-Reply-To: <CAK+8Z+G2zDfEEL49KcrXmfDdFd5ZpLCf9RUAoP4PEvrEqE_AKg@mail.gmail.com>
References: <CAK+8Z+G2zDfEEL49KcrXmfDdFd5ZpLCf9RUAoP4PEvrEqE_AKg@mail.gmail.com>
Message-ID: <2B49A186-AFBB-4973-8A12-692CBDC54EDD@stanford.edu>

Hi Elizabeth,

I think you are asking quesrtions about what RedCAP does with BioPortal. These questions would best be asked of your RedCAP administrator.

We are not aware of any solutions that directly meet your needs. BioPortal APIs do provide the ability to ask for *all* information about a term, and so the information could be obtained by RedCAP through the API if that is desirable.

Sorry we can't be more help,

John

On Oct 15, 2021, at 9:04 AM, Elizabeth Oh <elizabeth at hopebio.org<mailto:elizabeth at hopebio.org>> wrote:

Good Morning,

I am from the data management team at Hope Biosciences Stem Cell Research Foundation and was wondering if there was a way to limit a search to only the lowest level terms for MedDRA in our Redcap integration.

If that is not available is there any way to automatically fill and complete corresponding fields such as preferred term, high level term, and organ system (PT, HLT, HLGT, SOC) using the original search?

--
Sincerely,

Elizabeth Oh, B.S. (she/her/hers)
Clinical Data Specialist
elizabeth at hopebio.org<mailto:yasmany at hopebio.org>
(<http://www.hopebio.org/>281) 740-3087

CONFIDENTIALITY NOTE: This message may contain confidential or legally privileged information. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or taking any action in reliance on these contents is strictly prohibited and may be unlawful. If you have received this communication in error, please notify us immediately by responding to this e-mail and then delete it from your system.
_______________________________________________
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  | ORCID  0000-0001-6875-5360



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From jgraybeal at stanford.edu  Tue Oct 19 17:10:42 2021
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 20 Oct 2021 00:10:42 +0000
Subject: [bioontology-support] =?utf-8?q?=5BBioPortal=5D_Feedback_from_?=
 =?utf-8?b?6K64?=
In-Reply-To: <61692eea1d4a5_7a4d2580320296b@ncbo-prd-app-08.stanford.edu.mail>
References: <61692eea1d4a5_7a4d2580320296b@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <CDDDF935-AC50-48B3-9685-86D5E0EBBBEB@stanford.edu>

Hello,

I'm sorry, we who provide BioPortal support do not have a deep knowledge of the ontologies in it, so we can not help you with this question.

In general you can use the search and other APs I to obtain information about specific concepts, but I do not know if MedDRA contains the necessary semantic information to make this straightforward.

Perhaps someone else on the list can provide more information on this request?

John

On Oct 15, 2021, at 12:34 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: ?

Email: 291549190 at qq.com<mailto:291549190 at qq.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FMEDDRA%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FMEDDRA%252F10042613

Feedback:

How can I use the MedDRA dictionary in BioPortal to classify the adverse reactions in the entire document to see which SOCs they belong to

_______________________________________________
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  | ORCID  0000-0001-6875-5360



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From jgraybeal at stanford.edu  Thu Oct 21 15:02:02 2021
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 21 Oct 2021 22:02:02 +0000
Subject: [bioontology-support] [BioPortal] Feedback from satyasahoo
In-Reply-To: <TU4PR8401MB09288F6DC977734624E70346E8BC9@TU4PR8401MB0928.NAMPRD84.PROD.OUTLOOK.COM>
References: <616888cf67cff_1a982125668814bf@ncbo-prd-app-09.stanford.edu.mail>
 <716C70D6-F90C-457C-AEF0-84FA27F327DD@stanford.edu>
 <TU4PR8401MB09288F6DC977734624E70346E8BC9@TU4PR8401MB0928.NAMPRD84.PROD.OUTLOOK.COM>
Message-ID: <63B4F886-F93B-4B9B-88F8-B746B5D32E77@stanford.edu>

Hello Satya,

BioPortal creates the class names by default based on skos:prefLabel. If it can not find skos:prefLabel, it will use rdfs:label if it is present (*not* 'rdfs:Label', I expect that will not work). If that is not present, it uses the short local identifier component at the end of the IRI as the label.

The only adjustment you can make to that is to specify the preferred label identifier as whatever IRI you want. So if you defined a property in your ontology called http://mydomain.example/prefixIRI, and declared for each term
 <myOnt:thisTerm> http://mydomain.example/prefixIRI "My label string" .
then that would work.

But I think that I may be misunderstanding your use of "prefixIRI"  in this context. You may be referring to what I would call the 'fragment' or 'IRI fragment', the final part of the IRI that is the unique phrase occurring after the final separator (typically the '#' or '/') at the end of the II prefix. This expression 'fragment' is common in IRI and URL parsing and web references, so I'll use it here.

As you can see in my description above, if nothing else is available as the preferred label, BioPortal will use the IRI fragment as the label. This only works if BioPortal does not see any rdfs:label at all (so, no skos:prefLabel and no skos:altLabe can be present, because they are both rdfs:labels). There is no way to specify the fragment be used as the label.

Based on my understanding of the SKOS W3C standard, I do not recommend using rdfs:label for synonyms/alternate names of the classes. SKOS has design a pattern expressly for this purpose: skos:prefLabel for the preferred name (if any), and skos:altLabel for any other names including synonyms. I believe that most semantic tools will adopt this usage as they present preferred and alternate names for ontology terms, and this pattern works nicely with internationalization as well as using language tags. Reference https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#seclabel for a clear and detailed definition.

John

On Oct 18, 2021, at 6:39 AM, Satya Sahoo <satya_sanket at hotmail.com<mailto:satya_sanket at hotmail.com>> wrote:

Good Morning, John:
Thank you for resolving this issue! We will work on revising the customized local property to use IRI instead of just text. The visualization of the classes in BioPortal works now.

If possible, can you please clarify if BioPortal can use the entity prefixIRI instead of the rdfs:Label to generate the class names (similar to Protege rendering option using Entity )?

We have consistently used the prefixIRI to assign class names in EpSO and rdfs:Label to model synonyms/alternate names of the classes.

I appreciate your time and help!

Sincerely,
Satya


________________________________
From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Sunday, October 17, 2021 5:04 PM
To: support at bioontology.org<mailto:support at bioontology.org> <support at bioontology.org<mailto:support at bioontology.org>>
Cc: satyasahoo at ieee.org<mailto:satyasahoo at ieee.org> <satyasahoo at ieee.org<mailto:satyasahoo at ieee.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from satyasahoo

Hello Dr. Sahoo,

Thank you for your patience with this problem.  We have fixed the ontology and it is now correctly visible in BioPortal.

Details about the problem can be found in the ticket https://github.com/ncbo/bioportal-project/issues/216. In brief, the customized default property setting fields are meant to be specialized settings that are IRIs (unique identifiers), but they had been filled with regular text strings. (Examples of the unique identifiers can be found in the help text below each field.)

These invalid settings were causing the final parsing stage (using rapper) to fail. When we removed them we were able to parse the ontology successfully.

John

On Oct 14, 2021, at 12:45 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: satyasahoo
Email: satyasahoo at ieee.org<mailto:satyasahoo at ieee.org>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FEPSO

Feedback:
Good Afternoon,
We continue to experience parsing errors with the Epilepsy and Seizure Ontology (EpSO) OWL file.
The previous submission also experienced similar BioPortal parsing error documented as Issue#216: https://github.com/ncbo/bioportal-project/issues/216.
The BioPortal issue tracker noted that the EpSO OWL file was correctly parsed in the BioPortal staging environment (https://stage.bioontology.org/ontologies/EPSO?p=classes).
The latest release of EpSO (version 2.1) OWL is experiencing same error "Error Rdf Labels").
We request your help in addressing this error at the earliest as we have received community feedback regarding their inability to visually browse EpSO in the BioPortal "Classes" and "Properties" tabs.
Thank you for your time and consideration!
Sincerely,
Satya Sahoo, PhD FAMIA
CWRU School of Medicine
https://bmhinformatics.case.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  | ORCID  0000-0001-6875-5360

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



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From support at bioontology.org  Fri Oct 22 08:40:18 2021
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 22 Oct 2021 08:40:18 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Matt Diller
Message-ID: <6172db62da696_3a7910d47f09178f@ncbo-prd-app-08.stanford.edu.mail>

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From danielle.n.ndi at vumc.org  Wed Oct 27 10:10:30 2021
From: danielle.n.ndi at vumc.org (Ndi, Danielle N)
Date: Wed, 27 Oct 2021 17:10:30 +0000
Subject: [bioontology-support] ICD-10 Updated Needed
In-Reply-To: <98DE7C94-2A7A-4523-AFDD-97EE9A2AA26B@stanford.edu>
References: <MN2PR12MB4453C75ED40F9DFCA01B25C0AC5A9@MN2PR12MB4453.namprd12.prod.outlook.com>
 <MN2PR12MB4453E30B572CD2602C1E25AEAC599@MN2PR12MB4453.namprd12.prod.outlook.com>
 <98DE7C94-2A7A-4523-AFDD-97EE9A2AA26B@stanford.edu>
Message-ID: <BN9PR12MB533982D6B5F6D56EA05C6E88AC859@BN9PR12MB5339.namprd12.prod.outlook.com>

Hi John,

I'm just following up to see if you have any updates you can share on when the next UMLS release will be? We're finding that COVID-related ICD codes released by the CDC in Jan 2021 (https://www.cdc.gov/nchs/data/icd/Announcement-New-ICD-code-for-coronavirus-19-508.pdf) still aren't pulling up when using the Bioportal ICD10CM ontology in REDCap.

I look forward to hearing from you.

Thank you,
Danielle
New ICD-10-CM code for the In March 2020 the Novel Coronavirus Disease, COVID-19, was declared a pandemic by the<https://www.cdc.gov/nchs/data/icd/Announcement-New-ICD-code-for-coronavirus-19-508.pdf>
New ICD-10-CM code for the 2019 Novel Coronavirus (COVID-19), December 3, 2020 Effective: January 1, 2021 In March 2020 the Novel Coronavirus Disease, COVID-19, was declared a pandemic by the
www.cdc.gov
?



________________________________
From: John Graybeal <jgraybeal at stanford.edu>
Sent: Wednesday, May 5, 2021 3:16 PM
To: Ndi, Danielle N <danielle.n.ndi at vumc.org>
Cc: support at bioontology.org <support at bioontology.org>; Markus, Tiffanie M <tiffanie.m.markus at vumc.org>; Ujwok, John A <john.a.ujwok at vumc.org>
Subject: Re: [bioontology-support] ICD-10 Updated Needed

Hello Danielle,

Thank you for this question.

We uppdate all the UMLS vocabularies (our ICD10-CM is from UMLS)  as soon as we can after the UMLS update is released. I see that the UMLS 2021AA release happened just Monday, so we will look at scheduling that as soon as possible.

Unfortunately, it appears ICD10-CM is not updated in the 2021AA UMLS release, per the page https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nlm.nih.gov%2Fresearch%2Fumls%2Fsourcereleasedocs%2Findex.html&data=04%7C01%7Cdanielle.n.ndi%40vumc.org%7Cfb3cf4fb7d8943ed57ff08d91002a4c5%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637558425806731271%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eb0p7M4Uv%2BrwRecinVgpeIrN5mGHWjCyl9X0PjL1tVE%3D&reserved=0>. I don't know why this would be, but if that's the case, we may not have any other means to get the latest ICD10-CM.

I will do a little more investigation and let you know if I can find more positive news.

John


On May 5, 2021, at 8:21 AM, Ndi, Danielle N <danielle.n.ndi at vumc.org<mailto:danielle.n.ndi at vumc.org>> wrote:

Hello,
Please see question below.

Thank you,
Danielle

________________________________
From: Ndi, Danielle N
Sent: Tuesday, May 4, 2021 9:41 AM
To: support at bioportal.org<mailto:support at bioportal.org> <support at bioportal.org<mailto:support at bioportal.org>>
Cc: Ujwok, John A <john.a.ujwok at vumc.org<mailto:john.a.ujwok at vumc.org>>; Markus, Tiffanie M <tiffanie.m.markus at vumc.org<mailto:tiffanie.m.markus at vumc.org>>
Subject: ICD-10 Updated Needed

Hello,
I use the ICD10-CM ontology through REDCap. We are collecting COVID-19 data and have noticed the newest ICD10 updates, including COVID-19 codes added November 30, 2020, are not reflected in the ICD10-CM version you are using. Is there a plan to make this update?

Thank you,
Danielle

_______________________________________________
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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=04%7C01%7Cdanielle.n.ndi%40vumc.org%7Cfb3cf4fb7d8943ed57ff08d91002a4c5%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637558425806736255%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=rCkhmhEx1YUHGUrWwi0VMz%2BsSbBEPXNi6CXGZSJ6czU%3D&reserved=0>

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



[ WARNING : This email came from an external source. Please treat this message with additional caution.]
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From vendetti at stanford.edu  Wed Oct 27 14:09:03 2021
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 27 Oct 2021 21:09:03 +0000
Subject: [bioontology-support] AFO Error Diff
In-Reply-To: <633CA398-5968-4A61-931D-7E6E0A8251D4@stanford.edu>
References: <5f4387325d003_187c27ee53051630@ncbo-prd-app-08.stanford.edu.mail>
 <cb88702f033a40b495c2bc07add19b3e@osthus.com>
 <5A5E822B-1F9E-4850-9249-FE65654EBE6C@stanford.edu>
 <c7d0784d6f324b17b01723dcec4c9181@osthus.com>
 <01155AF5-B2FD-488B-9394-5E8A05E90858@stanford.edu>
 <ec081aec1f6d4e83bfbeaf31d6a75327@osthus.com>
 <633CA398-5968-4A61-931D-7E6E0A8251D4@stanford.edu>
Message-ID: <91651746-C91B-4D71-AC1D-D5CF27A19282@stanford.edu>

Hi Karin,

Apologies for the late reply.

I manually regenerated a diff file in our system for your last two submissions (both uploaded on Oct. 14th) and reset some statuses. I think the system is in a state now where the diffs should succeed going forward. If possible, please let me know the next time you upload a new version if you experience issues again.

The diff file I generated shows no class changes / additions / deletions. Does this seem correct to you? I noticed that the last two uploads have the same version number of "REC/2021/09?.

Kind regards,
Jennifer


On Oct 11, 2021, at 5:45 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Karin,


On Oct 11, 2021, at 10:01 AM, Karin Colsman <karin.colsman.contractor at osthus.com<mailto:karin.colsman.contractor at osthus.com>> wrote:

 Hi Jennifer,

we are still having problems with getting the AFO to conform to the BioPortal tooling ? the upload result says ? Error Diff?. I am experimenting with using a newer OWL API version in our tooling, but it?s not giving us any errors.

Are you using any Open Source tools on your end that are producing the error? If so, it would be of great help to us to know which ones they are, so that I can try to reproduce the problem.


We use a 3rd party Java library to perform the diffs called Bubastis:

https://github.com/EBISPOT/bubastis

It?s unfortunately somewhat of an outdated library. We?ve discussed moving to ROBOT instead:

http://robot.obolibrary.org/diff

? but haven?t been able to find the resources for that yet.

I?ve entered an issue in our tracker for the failing diff for AFO so that we can investigate:

https://github.com/ncbo/bioportal-project/issues/219

At first glance, I don?t know if the error is in our code or from Bubastis.

Kind regards,
Jennifer


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From jgraybeal at stanford.edu  Wed Oct 27 14:26:01 2021
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 27 Oct 2021 21:26:01 +0000
Subject: [bioontology-support] ICD-10 Updated Needed
In-Reply-To: <BN9PR12MB533982D6B5F6D56EA05C6E88AC859@BN9PR12MB5339.namprd12.prod.outlook.com>
References: <MN2PR12MB4453C75ED40F9DFCA01B25C0AC5A9@MN2PR12MB4453.namprd12.prod.outlook.com>
 <MN2PR12MB4453E30B572CD2602C1E25AEAC599@MN2PR12MB4453.namprd12.prod.outlook.com>
 <98DE7C94-2A7A-4523-AFDD-97EE9A2AA26B@stanford.edu>
 <BN9PR12MB533982D6B5F6D56EA05C6E88AC859@BN9PR12MB5339.namprd12.prod.outlook.com>
Message-ID: <F6C16549-F8DC-46A1-A331-C4F6E5DC3B6C@stanford.edu>

Danielle,

I would expect these to be included in their (UMLS) November release, which we will try to get into BioPortal within a month of the release. So, early December.

John

On Oct 27, 2021, at 10:10 AM, Ndi, Danielle N <danielle.n.ndi at vumc.org<mailto:danielle.n.ndi at vumc.org>> wrote:

Hi John,

I'm just following up to see if you have any updates you can share on when the next UMLS release will be? We're finding that COVID-related ICD codes released by the CDC in Jan 2021 (https://www.cdc.gov/nchs/data/icd/Announcement-New-ICD-code-for-coronavirus-19-508.pdf) still aren't pulling up when using the Bioportal ICD10CM ontology in REDCap.

I look forward to hearing from you.

Thank you,
Danielle
New ICD-10-CM code for the In March 2020 the Novel Coronavirus Disease, COVID-19, was declared a pandemic by the<https://www.cdc.gov/nchs/data/icd/Announcement-New-ICD-code-for-coronavirus-19-508.pdf>
New ICD-10-CM code for the 2019 Novel Coronavirus (COVID-19), December 3, 2020 Effective: January 1, 2021 In March 2020 the Novel Coronavirus Disease, COVID-19, was declared a pandemic by the
www.cdc.gov<http://www.cdc.gov/>
?



________________________________
From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Wednesday, May 5, 2021 3:16 PM
To: Ndi, Danielle N <danielle.n.ndi at vumc.org<mailto:danielle.n.ndi at vumc.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org> <support at bioontology.org<mailto:support at bioontology.org>>; Markus, Tiffanie M <tiffanie.m.markus at vumc.org<mailto:tiffanie.m.markus at vumc.org>>; Ujwok, John A <john.a.ujwok at vumc.org<mailto:john.a.ujwok at vumc.org>>
Subject: Re: [bioontology-support] ICD-10 Updated Needed

Hello Danielle,

Thank you for this question.

We uppdate all the UMLS vocabularies (our ICD10-CM is from UMLS)  as soon as we can after the UMLS update is released. I see that the UMLS 2021AA release happened just Monday, so we will look at scheduling that as soon as possible.

Unfortunately, it appears ICD10-CM is not updated in the 2021AA UMLS release, per the pagehttps://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nlm.nih.gov%2Fresearch%2Fumls%2Fsourcereleasedocs%2Findex.html&data=04%7C01%7Cdanielle.n.ndi%40vumc.org%7Cfb3cf4fb7d8943ed57ff08d91002a4c5%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637558425806731271%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eb0p7M4Uv%2BrwRecinVgpeIrN5mGHWjCyl9X0PjL1tVE%3D&reserved=0>. I don't know why this would be, but if that's the case, we may not have any other means to get the latest ICD10-CM.

I will do a little more investigation and let you know if I can find more positive news.

John


On May 5, 2021, at 8:21 AM, Ndi, Danielle N <danielle.n.ndi at vumc.org<mailto:danielle.n.ndi at vumc.org>> wrote:

Hello,
Please see question below.

Thank you,
Danielle

________________________________
From: Ndi, Danielle N
Sent: Tuesday, May 4, 2021 9:41 AM
To: support at bioportal.org<mailto:support at bioportal.org> <support at bioportal.org<mailto:support at bioportal.org>>
Cc: Ujwok, John A <john.a.ujwok at vumc.org<mailto:john.a.ujwok at vumc.org>>; Markus, Tiffanie M <tiffanie.m.markus at vumc.org<mailto:tiffanie.m.markus at vumc.org>>
Subject: ICD-10 Updated Needed

Hello,
I use the ICD10-CM ontology through REDCap. We are collecting COVID-19 data and have noticed the newest ICD10 updates, including COVID-19 codes added November 30, 2020, are not reflected in the ICD10-CM version you are using. Is there a plan to make this update?

Thank you,
Danielle

_______________________________________________
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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=04%7C01%7Cdanielle.n.ndi%40vumc.org%7Cfb3cf4fb7d8943ed57ff08d91002a4c5%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637558425806736255%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=rCkhmhEx1YUHGUrWwi0VMz%2BsSbBEPXNi6CXGZSJ6czU%3D&reserved=0>

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



[ WARNING : This email came from an external source. Please treat this message with additional caution.]

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



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From jgraybeal at stanford.edu  Wed Oct 27 21:58:18 2021
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 28 Oct 2021 04:58:18 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Matt Diller
In-Reply-To: <6172db62da696_3a7910d47f09178f@ncbo-prd-app-08.stanford.edu.mail>
References: <6172db62da696_3a7910d47f09178f@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <BYAPR02MB469682D8E92FA75E98F90287DA869@BYAPR02MB4696.namprd02.prod.outlook.com>

Thank you Matt for these observations, appreciate the information.

We are contacting the owner of the first ontology and will remedy the situation shortly.

Your example of NXDX looks like an ontology for me. I am seeing an ontology there that is well-formed and meaningful (see screenshot). I did clean up a few other ontologies that were private (so you shouldn't have been able to see them), and made another ontology private (so now you can't see it). But I didn't see ontologies that matched your description.

Can you please let me know more precisely what you are seeing that is different than what I am seeing? Thank you,

John



________________________________
From: bioontology-support <bioontology-support-bounces at lists.stanford.edu> on behalf of support at bioontology.org <support at bioontology.org>
Sent: Friday, October 22, 2021 8:40 AM
To: support at bioontology.org <support at bioontology.org>; diller17 at ufl.edu <diller17 at ufl.edu>
Subject: [bioontology-support] [BioPortal] Feedback from Matt Diller


Name: Matt Diller

Email: diller17 at ufl.edu

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

Feedback:

To whom it may concern,

The Bioportal page (https://bioportal.bioontology.org/ontologies/NPI) for Non-Pharmacological Interventions (NPI) contains a link to the ontology's homepage that redirects to the website of a gentleman's club. There are also a number of ontologies on Bioportal that aren't ontologies at all (e.g., NXDX https://bioportal.bioontology.org/ontologies/NXDX). If type 'test' into the ontology search bar, you should be able to find nearly all of them.
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From diller17 at ufl.edu  Thu Oct 28 08:10:09 2021
From: diller17 at ufl.edu (Diller,Matthew A)
Date: Thu, 28 Oct 2021 15:10:09 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Matt Diller
In-Reply-To: <BYAPR02MB469682D8E92FA75E98F90287DA869@BYAPR02MB4696.namprd02.prod.outlook.com>
References: <6172db62da696_3a7910d47f09178f@ncbo-prd-app-08.stanford.edu.mail>
 <BYAPR02MB469682D8E92FA75E98F90287DA869@BYAPR02MB4696.namprd02.prod.outlook.com>
Message-ID: <9A6230AC-CA6C-49EF-97ED-9AFEE119FE84@ufl.edu>

Hi John,

Yes, so there are several ontologies that have in their description that they are ?tests for submission? or something to that effect. TEST_CBI and mini fast test are examples. There is also DELETE, which just seems to be an blank BioPortal page. I managed to find these by going to https://bioportal.bioontology.org/ontologies and typing ?test? into the search bar.

Best,

Matt Diller

On Oct 28, 2021, at 12:58 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

[External Email]
Thank you Matt for these observations, appreciate the information.

We are contacting the owner of the first ontology and will remedy the situation shortly.

Your example of NXDX looks like an ontology for me. I am seeing an ontology there that is well-formed and meaningful (see screenshot). I did clean up a few other ontologies that were private (so you shouldn't have been able to see them), and made another ontology private (so now you can't see it). But I didn't see ontologies that matched your description.

Can you please let me know more precisely what you are seeing that is different than what I am seeing? Thank you,

John



________________________________
From: bioontology-support <bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>> on behalf of support at bioontology.org<mailto:support at bioontology.org> <support at bioontology.org<mailto:support at bioontology.org>>
Sent: Friday, October 22, 2021 8:40 AM
To: support at bioontology.org<mailto:support at bioontology.org> <support at bioontology.org<mailto:support at bioontology.org>>; diller17 at ufl.edu<mailto:diller17 at ufl.edu> <diller17 at ufl.edu<mailto:diller17 at ufl.edu>>
Subject: [bioontology-support] [BioPortal] Feedback from Matt Diller

Name: Matt Diller
Email: diller17 at ufl.edu<mailto:diller17 at ufl.edu>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FNPI

Feedback:
To whom it may concern,
The Bioportal page (https://bioportal.bioontology.org/ontologies/NPI<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_NPI&d=DwQFAw&c=sJ6xIWYx-zLMB3EPkvcnVg&r=3a_Hf8mwX7P7aLccwGXP_A&m=AteGM9IxGzm1ddbbCOM4FOks2T3PMUgdLCjNvBEL7_4&s=zEse17sPGoZc29jDztFhrYrf7TmBppQLFdKt5ncrJ2M&e=>) for Non-Pharmacological Interventions (NPI) contains a link to the ontology's homepage that redirects to the website of a gentleman's club. There are also a number of ontologies on Bioportal that aren't ontologies at all (e.g., NXDX https://bioportal.bioontology.org/ontologies/NXDX<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_ontologies_NXDX&d=DwQFAw&c=sJ6xIWYx-zLMB3EPkvcnVg&r=3a_Hf8mwX7P7aLccwGXP_A&m=AteGM9IxGzm1ddbbCOM4FOks2T3PMUgdLCjNvBEL7_4&s=uY06127afNdyFGk-4S7gnvsflx3vZxEuVeNvHlcdKE4&e=>). If type 'test' into the ontology search bar, you should be able to find nearly all of them.

<Screen Shot 2021-10-27 at 9.51.54 PM.png>

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From support at bioontology.org  Fri Oct 29 07:49:56 2021
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 29 Oct 2021 07:49:56 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Krishna Udaiwal
Message-ID: <617c0a14a7f9f_4d67167e930578fc@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Fri Oct 29 11:03:17 2021
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 29 Oct 2021 18:03:17 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Krishna Udaiwal
In-Reply-To: <617c0a14a7f9f_4d67167e930578fc@ncbo-prd-app-08.stanford.edu.mail>
References: <617c0a14a7f9f_4d67167e930578fc@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <AD7C3256-38C0-4342-9A70-9308D8674851@stanford.edu>

Hi Krishna,


On Oct 29, 2021, at 7:49 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


I'm a curator of the Agronomy Ontology (AgrO) project, and wanted to ask if there is a particular issue breaking the AgrO page here:

https://bioportal.bioontology.org/ontologies/AGRO

Seems there are historical versions ("Uploaded: 4/3/20") and is searchable on the 'ontologies' page.

Please let me or our team know via reply or on our github at https://github.com/AgriculturalSemantics/agro/issues



Yes, I found an issue with the data in our triplestore for the latest submission of your ontology. I?ve corrected the issue and reprocessed the last release from July 1st. You should be able to see the summary page for AGRO now.

I noticed that we don?t have anyone from your team listed as having admin privileges to maintain your ontology entry in BioPortal. If there is anyone with a BioPortal account, please let me know the account name so that I can grant you admin privileges.

Kind regards,
Jennifer



[cid:25D60A67-FCC2-44D1-8017-96B5361AB2E1 at lan]
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