From alex.mozejko at databiology.com  Thu Jul  2 03:07:33 2020
From: alex.mozejko at databiology.com (Alex Mozejko)
Date: Thu, 2 Jul 2020 10:07:33 +0000
Subject: [bioontology-support] Databiology: Default web portal credentials
Message-ID: <BN8PR20MB25637EFE0C1C88D16D254542916D0@BN8PR20MB2563.namprd20.prod.outlook.com>

Hello,

We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials:

Username: admin
Password: changemeNOW

Whenever I try I get the error:

?Errors On Form.
Invalid account name/password combination?

The default ssh user credentials worked and I can confirm ssh access.

I can also confirm that creating a new user and uploading an ontology works, so good news there ?

The process I followed to deploy this appliance is as follows:


  1.  Download OVA image from https://bioportal.bioontology.org/virtual_appliance
  2.  Copy OVA to s3 bucket
  3.  Use aws cli to convert image to AMI as detailed here<https://docs.aws.amazon.com/vm-import/latest/userguide/vmimport-image-import.html>
  4.  Launched virtual machine using the converted AMI
  5.  Navigate to portal
  6.  Try to login as admin
  7.  Get error

Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password?

Thanks,
Alex.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200702/bd3f3c27/attachment.html>

From alex.skrenchuk at stanford.edu  Thu Jul  2 14:42:28 2020
From: alex.skrenchuk at stanford.edu (Alex Skrenchuk)
Date: Thu, 2 Jul 2020 21:42:28 +0000
Subject: [bioontology-support] Databiology: Default web portal
	credentials
Message-ID: <AE8E0812-F37B-4F3D-AE03-43B9663E142B@stanford.edu>

HI Alex,

We have not yet experimented with importing OVA to AWS because we are counting that the majority of users will deploy OntoPortal from the AWS marketplace.   We were recently been made aware that version 3.0.1 of the appliance sometimes doesn?t initialize properly in AWS during the first boot which could be usually resolved with a second reboot.

During the very first boot of the appliance we have a firstboot script that resets API keys for the Web UI and Admin user.  If it detects that appliance is running in AWS then it will also resets Admin password to match the instance-id of your EC2 instance.

First I would try to use the EC2 instance-id for admin password and if that doesn?t work then you could try to force re-run of the firstboot script.

ssh to instance as centos user and:

sudo touch /srv/ontoportal/firstboot
sudo chown ontoportal /srv/ontoportal/firstboot
sudo reboot


-Alex


From: bioontology-support <bioontology-support-bounces at lists.stanford.edu> on behalf of Alex Mozejko <alex.mozejko at databiology.com>
Date: Thursday, July 2, 2020 at 8:00 AM
To: "support at bioontology.org" <support at bioontology.org>
Subject: [bioontology-support] Databiology: Default web portal credentials

Hello,

We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials:

Username: admin
Password: changemeNOW

Whenever I try I get the error:

?Errors On Form.
Invalid account name/password combination?

The default ssh user credentials worked and I can confirm ssh access.

I can also confirm that creating a new user and uploading an ontology works, so good news there ?

The process I followed to deploy this appliance is as follows:


  1.  Download OVA image from https://bioportal.bioontology.org/virtual_appliance
  2.  Copy OVA to s3 bucket
  3.  Use aws cli to convert image to AMI as detailed here<https://docs.aws.amazon.com/vm-import/latest/userguide/vmimport-image-import.html>
  4.  Launched virtual machine using the converted AMI
  5.  Navigate to portal
  6.  Try to login as admin
  7.  Get error

Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password?

Thanks,
Alex.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200702/d93789fe/attachment.html>

From jonquet at lirmm.fr  Mon Jul  6 02:16:35 2020
From: jonquet at lirmm.fr (Clement Jonquet)
Date: Mon, 6 Jul 2020 11:16:35 +0200
Subject: [bioontology-support] Remove MEDRA
Message-ID: <7BB1BD09-1F3B-4225-993E-7DDDF8C34FB3@lirmm.fr>

This ontology is empty and create confusion with the real Meddra: 

http://bioportal.bioontology.org/ontologies/MEDRA/?p=summary <http://bioportal.bioontology.org/ontologies/MEDRA/?p=summary>

I would suggest to remove it from BioPortal. 


Bye
Clement

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200706/95f2b100/attachment.html>

From vk396 at njit.edu  Mon Jul  6 11:45:23 2020
From: vk396 at njit.edu (Kuttichi Keloth, Vipina)
Date: Mon, 6 Jul 2020 14:45:23 -0400
Subject: [bioontology-support] Processing two ontologies
Message-ID: <CAGFJoxc04pwzTWhhm6tV-y6Aym6Xk+A7wcfoE=krz=4+Htnjtw@mail.gmail.com>

Hi,

Could you please process two ontologies (CIDIO_AUX and ACT_COVID) uploaded
on BioPortal?
It was uploaded on July 1st.

Thank you.
Vipina
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200706/cbda5ae3/attachment.html>

From vk396 at njit.edu  Mon Jul  6 14:26:24 2020
From: vk396 at njit.edu (Kuttichi Keloth, Vipina)
Date: Mon, 6 Jul 2020 17:26:24 -0400
Subject: [bioontology-support] Processing two ontologies
In-Reply-To: <CAGFJoxc04pwzTWhhm6tV-y6Aym6Xk+A7wcfoE=krz=4+Htnjtw@mail.gmail.com>
References: <CAGFJoxc04pwzTWhhm6tV-y6Aym6Xk+A7wcfoE=krz=4+Htnjtw@mail.gmail.com>
Message-ID: <CAGFJoxd-YMFHaPahEm5hHCk1oUHv6gLfpnwrPHP=ONbkpA3M+w@mail.gmail.com>

The ACT_COVID has been processed.

But CIDIO_AUX is not giving any annotations when using the Annotator to
annotate text.
Could you please look into this?

Thank you.
Vipina

On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina <vk396 at njit.edu>
wrote:

> Hi,
>
> Could you please process two ontologies (CIDIO_AUX and ACT_COVID)
> uploaded on BioPortal?
> It was uploaded on July 1st.
>
> Thank you.
> Vipina
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200706/871a26a4/attachment.html>

From mdorf at stanford.edu  Mon Jul  6 14:39:45 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Mon, 6 Jul 2020 21:39:45 +0000
Subject: [bioontology-support] Processing two ontologies
In-Reply-To: <CAGFJoxd-YMFHaPahEm5hHCk1oUHv6gLfpnwrPHP=ONbkpA3M+w@mail.gmail.com>
References: <CAGFJoxc04pwzTWhhm6tV-y6Aym6Xk+A7wcfoE=krz=4+Htnjtw@mail.gmail.com>
 <CAGFJoxd-YMFHaPahEm5hHCk1oUHv6gLfpnwrPHP=ONbkpA3M+w@mail.gmail.com>
Message-ID: <C1E23DEB-BDF5-494E-87BB-58A2AB2F0880@stanford.edu>

Hi Vipina,

I am working on reprocessing both ontologies. I?ll keep you posted once the process completes.

Thank you for your patience.

Michael


On Jul 6, 2020, at 2:26 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:

The ACT_COVID has been processed.

But CIDIO_AUX is not giving any annotations when using the Annotator to annotate text.
Could you please look into this?

Thank you.
Vipina

On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:
Hi,

Could you please process two ontologies (CIDIO_AUX and ACT_COVID) uploaded on BioPortal?
It was uploaded on July 1st.

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200706/1dad0beb/attachment-0001.html>

From vk396 at njit.edu  Mon Jul  6 14:40:35 2020
From: vk396 at njit.edu (Kuttichi Keloth, Vipina)
Date: Mon, 6 Jul 2020 17:40:35 -0400
Subject: [bioontology-support] Processing two ontologies
In-Reply-To: <C1E23DEB-BDF5-494E-87BB-58A2AB2F0880@stanford.edu>
References: <CAGFJoxc04pwzTWhhm6tV-y6Aym6Xk+A7wcfoE=krz=4+Htnjtw@mail.gmail.com>
 <CAGFJoxd-YMFHaPahEm5hHCk1oUHv6gLfpnwrPHP=ONbkpA3M+w@mail.gmail.com>
 <C1E23DEB-BDF5-494E-87BB-58A2AB2F0880@stanford.edu>
Message-ID: <CAGFJoxfczSrZn8-ZK8AQqN+b_-dO=BuRDRUYKc3=dUP7DCAs8g@mail.gmail.com>

Ok. Thank you so much.

Vipina

On Mon, Jul 6, 2020 at 5:39 PM Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Vipina,
>
> I am working on reprocessing both ontologies. I?ll keep you posted once
> the process completes.
>
> Thank you for your patience.
>
> Michael
>
>
> On Jul 6, 2020, at 2:26 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu>
> wrote:
>
> The ACT_COVID has been processed.
>
> But CIDIO_AUX is not giving any annotations when using the Annotator to
> annotate text.
> Could you please look into this?
>
> Thank you.
> Vipina
>
> On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina <vk396 at njit.edu>
> wrote:
>
>> Hi,
>>
>> Could you please process two ontologies (CIDIO_AUX and ACT_COVID)
>> uploaded on BioPortal?
>> It was uploaded on July 1st.
>>
>> Thank you.
>> Vipina
>>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200706/e7638c5d/attachment.html>

From mdorf at stanford.edu  Mon Jul  6 16:07:31 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Mon, 6 Jul 2020 23:07:31 +0000
Subject: [bioontology-support] Processing two ontologies
In-Reply-To: <CAGFJoxfczSrZn8-ZK8AQqN+b_-dO=BuRDRUYKc3=dUP7DCAs8g@mail.gmail.com>
References: <CAGFJoxc04pwzTWhhm6tV-y6Aym6Xk+A7wcfoE=krz=4+Htnjtw@mail.gmail.com>
 <CAGFJoxd-YMFHaPahEm5hHCk1oUHv6gLfpnwrPHP=ONbkpA3M+w@mail.gmail.com>
 <C1E23DEB-BDF5-494E-87BB-58A2AB2F0880@stanford.edu>
 <CAGFJoxfczSrZn8-ZK8AQqN+b_-dO=BuRDRUYKc3=dUP7DCAs8g@mail.gmail.com>
Message-ID: <10B9CF24-4620-4BDA-8323-095DB179C88B@stanford.edu>

Hi Vipina,

Both of your ontologies have finished processing. Let me know if you are still seeing any issues.

Thank you!

Michael

On Jul 6, 2020, at 2:40 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:

Ok. Thank you so much.

Vipina

On Mon, Jul 6, 2020 at 5:39 PM Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Vipina,

I am working on reprocessing both ontologies. I?ll keep you posted once the process completes.

Thank you for your patience.

Michael


On Jul 6, 2020, at 2:26 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:

The ACT_COVID has been processed.

But CIDIO_AUX is not giving any annotations when using the Annotator to annotate text.
Could you please look into this?

Thank you.
Vipina

On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:
Hi,

Could you please process two ontologies (CIDIO_AUX and ACT_COVID) uploaded on BioPortal?
It was uploaded on July 1st.

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


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200706/f3379f70/attachment-0001.html>

From vk396 at njit.edu  Mon Jul  6 16:14:22 2020
From: vk396 at njit.edu (Kuttichi Keloth, Vipina)
Date: Mon, 6 Jul 2020 19:14:22 -0400
Subject: [bioontology-support] Processing two ontologies
In-Reply-To: <10B9CF24-4620-4BDA-8323-095DB179C88B@stanford.edu>
References: <CAGFJoxc04pwzTWhhm6tV-y6Aym6Xk+A7wcfoE=krz=4+Htnjtw@mail.gmail.com>
 <CAGFJoxd-YMFHaPahEm5hHCk1oUHv6gLfpnwrPHP=ONbkpA3M+w@mail.gmail.com>
 <C1E23DEB-BDF5-494E-87BB-58A2AB2F0880@stanford.edu>
 <CAGFJoxfczSrZn8-ZK8AQqN+b_-dO=BuRDRUYKc3=dUP7DCAs8g@mail.gmail.com>
 <10B9CF24-4620-4BDA-8323-095DB179C88B@stanford.edu>
Message-ID: <CAGFJoxd7QmiWMMCAM05UKDvjK1hRECegM_TF0K-Sg7Fjgg_nZw@mail.gmail.com>

Thanks a lot.

Vipina

On Mon, Jul 6, 2020 at 7:07 PM Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Vipina,
>
> Both of your ontologies have finished processing. Let me know if you are
> still seeing any issues.
>
> Thank you!
>
> Michael
>
> On Jul 6, 2020, at 2:40 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu>
> wrote:
>
> Ok. Thank you so much.
>
> Vipina
>
> On Mon, Jul 6, 2020 at 5:39 PM Michael Dorf <mdorf at stanford.edu> wrote:
>
>> Hi Vipina,
>>
>> I am working on reprocessing both ontologies. I?ll keep you posted once
>> the process completes.
>>
>> Thank you for your patience.
>>
>> Michael
>>
>>
>> On Jul 6, 2020, at 2:26 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu>
>> wrote:
>>
>> The ACT_COVID has been processed.
>>
>> But CIDIO_AUX is not giving any annotations when using the Annotator to
>> annotate text.
>> Could you please look into this?
>>
>> Thank you.
>> Vipina
>>
>> On Mon, Jul 6, 2020 at 2:45 PM Kuttichi Keloth, Vipina <vk396 at njit.edu>
>> wrote:
>>
>>> Hi,
>>>
>>> Could you please process two ontologies (CIDIO_AUX and ACT_COVID)
>>> uploaded on BioPortal?
>>> It was uploaded on July 1st.
>>>
>>> Thank you.
>>> Vipina
>>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200706/3ecb6066/attachment.html>

From soldatova.larisa at gmail.com  Tue Jul  7 06:02:16 2020
From: soldatova.larisa at gmail.com (Larisa Soldatova)
Date: Tue, 7 Jul 2020 14:02:16 +0100
Subject: [bioontology-support] please remove me from this list
Message-ID: <CABCJnNxBAo8yt-05fDDqkEF_CnPcoPoWBRhFi9NNB=ReY_pnfA@mail.gmail.com>

Hi,

I must have gotten on this list by mistake. Please can you remove me so I
do not receive copies of all your emails?

Thanks,
Larisa
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200707/e5484e90/attachment.html>

From mdorf at stanford.edu  Tue Jul  7 14:41:49 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 7 Jul 2020 21:41:49 +0000
Subject: [bioontology-support] please remove me from this list
In-Reply-To: <CABCJnNxBAo8yt-05fDDqkEF_CnPcoPoWBRhFi9NNB=ReY_pnfA@mail.gmail.com>
References: <CABCJnNxBAo8yt-05fDDqkEF_CnPcoPoWBRhFi9NNB=ReY_pnfA@mail.gmail.com>
Message-ID: <99E16791-338F-472B-BEC9-406C48ADEF82@stanford.edu>

Hi Larisa,

You should receive an email with further instructions on how to unsubscribe from our list. Let us know if you haven?t received one.

Thanks,

Michael



> On Jul 7, 2020, at 6:02 AM, Larisa Soldatova <soldatova.larisa at gmail.com> wrote:
> 
> Hi,
> 
> I must have gotten on this list by mistake. Please can you remove me so I do not receive copies of all your emails?
> 
> Thanks,
> Larisa
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


From support at bioontology.org  Mon Jul 13 00:21:34 2020
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 13 Jul 2020 00:21:34 -0700
Subject: [bioontology-support] [BioPortal] Feedback from ALQAHATANI SAEED
	FARES
Message-ID: <5f0c0b7e49be6_60a220ebeb896432@ncbo-prd-app-09.stanford.edu.mail>

An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200713/4ca5041c/attachment.html>

From jgraybeal at stanford.edu  Mon Jul 13 07:33:08 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 13 Jul 2020 14:33:08 +0000
Subject: [bioontology-support] [BioPortal] Feedback from ALQAHATANI
	SAEED	FARES
In-Reply-To: <5f0c0b7e49be6_60a220ebeb896432@ncbo-prd-app-09.stanford.edu.mail>
References: <5f0c0b7e49be6_60a220ebeb896432@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <1F07E0C8-8849-4EED-8DE6-88ACD5D84BEA@stanford.edu>

Hello Saeed,

Thanks for your request. I can only offer you the permissions already granted by our terms of use, which can be found at https://ncbo.bioontology.org/terms. Hopefully that is sufficient for your needs.

John

On Jul 13, 2020, at 12:21 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: ALQAHATANI SAEED FARES

Email: dr-s2001 at hotmail.com<mailto:dr-s2001 at hotmail.com>

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

Feedback:

I have a research proposal entitled "Digital intervention development to promote self-management and diagnosis of the knee", so I need to take your permission to take some information from this application.
Thank you for your cooperation

kind regards,
Saeed

_______________________________________________
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



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200713/1843524d/attachment.html>

From Junaid_Bhatti at manulife.com  Tue Jul 14 08:48:16 2020
From: Junaid_Bhatti at manulife.com (Junaid Bhatti)
Date: Tue, 14 Jul 2020 15:48:16 +0000
Subject: [bioontology-support] Queries on REST API call limit and licensing
Message-ID: <8FB65458-D0DD-4D04-9157-D193405DFDDB@mfcgd.com>

Greetings:

I am a Senior Data Scientist at an life insurance company in North America. I have reviewed the website (https://bioportal.bioontology.org/) and it is unclear to me whether there is a limit in usage if you are part of a private company. Specifically, is there a limit on REST API calls? Secondly, is there a requirement to obtain any license or permission restrictions in the use of NCBO portal by private companies?

Thanking you in anticipation for your responses to my queries.

Best regards,

Junaid

Junaid A. Bhatti, PhD, MSc, MBBS.
Sr. Data Scientist | Underwriting COE | Advanced Analytics
Manulife

E    junaid_bhatti at manulife.com<mailto:junaid_bhatti at manulife.com>
T    416 687 3148 (Direct) Internal ext. 273148
M  647 237 6284

250 Bloor St. East, Toronto, ON, M4W 1E5

[cid:image002.png at 01D492D2.F591D670]




STATEMENT OF CONFIDENTIALITY The information contained in this email message and any attachments may be confidential and legally privileged and is intended for the use of the addressee(s) only. If you are not an intended recipient, please: (1) notify me immediately by replying to this message; (2) do not use, disseminate, distribute or reproduce any part of the message or any attachment; and (3) destroy all copies of this message and any attachments.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200714/64102256/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 3895 bytes
Desc: image001.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200714/64102256/attachment.png>

From jgraybeal at stanford.edu  Wed Jul 15 18:53:38 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 16 Jul 2020 01:53:38 +0000
Subject: [bioontology-support] Queries on REST API call limit and
 licensing
In-Reply-To: <8FB65458-D0DD-4D04-9157-D193405DFDDB@mfcgd.com>
References: <8FB65458-D0DD-4D04-9157-D193405DFDDB@mfcgd.com>
Message-ID: <889A5211-CE46-4349-9F7F-4915615C1B89@stanford.edu>

Hello Junaid, thank you for your questions.

There is only one enforced limit on access to BioPortal right now, and that is that API requests are limited to 15 per second (rarely reduced to 5 per second in we have too heavy a load. When this happens you would get an error message as your reply message.

There are practical limits that are enforced if certain calls are overused. Any Recommender query that is long will heavily load the system, as will requests for all terms and their properties from very large ontologies (even though this request is paged). There are some other requests that might be problematic?if you have questions about specific queries you can email them to the support list. Too many heavily loaded queries in a row will cause the system to become non-responsive, and sometimes to fail, forcing us to restart it.

If we find a single entity is making so many calls that causes problems for the system, we will attempt to contact that user to request a modification. If we can not reach the user, or if we determine the user is not complying with our terms, we will blacklist the user's API key, or their IP address if they are querying anonymously.

There are permission restrictions on certain BioPortal ontologies, and as our Terms (https://ncbo.bioontology.org/terms) indicate, it is up to the users of BioPortal to ensure they are following the license requirements of each ontology contained in BioPortal. (These license requirements are specified in the summary metadata, displayed on the summary page of each ontology.)

We do not restrict usage of BioPortal by private companies. However, we find that many companies?typically ones that ask about usage limits :-) ?need to use BioPortal more heavily than the above constraints allow. Also private companies often don't want to risk their queries becoming known publicly.

For that reason, we make available the OntoPortal (https://ontoportal.org/the-ontoportal-virtual-appliance/), which private companies can install locally and populate with whatever ontologies they want to use. (Alternatively, they can make arrangements with our team to provide this service, assuming available resources on our side.)  The instructions for obtaining and installing OntoPortal are at https://ontoportal.github.io/administration, and a registration is required. Registration terms for commercial companies may require discussion with the OntoPortal providers (see the documentation).

I hope this helps with your questions. You can reply with questions to the support list, or contact me directly (jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>) if you want further information about registration costs for OntoPortal.

John




On Jul 14, 2020, at 8:48 AM, Junaid Bhatti <Junaid_Bhatti at manulife.com<mailto:Junaid_Bhatti at manulife.com>> wrote:

Greetings:
I am a Senior Data Scientist at an life insurance company in North America. I have reviewed the website (https://bioportal.bioontology.org/) and it is unclear to me whether there is a limit in usage if you are part of a private company. Specifically, is there a limit on REST API calls? Secondly, is there a requirement to obtain any license or permission restrictions in the use of NCBO portal by private companies?
Thanking you in anticipation for your responses to my queries.
Best regards,
Junaid
 Junaid A. Bhatti, PhD, MSc, MBBS.
Sr. Data Scientist | Underwriting COE | Advanced Analytics
Manulife

========================
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



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/97d4c24a/attachment-0001.html>

From support at bioontology.org  Wed Jul 15 10:57:55 2020
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 15 Jul 2020 10:57:55 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Emma Vos
Message-ID: <5f0f43a380552_8cf27449f480627@ncbo-prd-app-09.stanford.edu.mail>

An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200715/05238f03/attachment-0001.html>

From brodriguez at integraltx.com  Thu Jul 16 07:09:00 2020
From: brodriguez at integraltx.com (Benjamin Rodriguez)
Date: Thu, 16 Jul 2020 10:09:00 -0400
Subject: [bioontology-support] Account details error, seeking API key
Message-ID: <CAOC8+69uaKtybFvruLLViThUSt1CxYsYxyjavD8PKxRWprW=HA@mail.gmail.com>

Dear Support,

I registered for an account under brodriguez. I need to obtain an API key.
I am able to log in, but I receive a "something has gone wrong" error
message when I click link for account details. I assume the API key is
under account details. Can you give me my API key?

Thanks,
Ben

Disclaimer

The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you should delete this message. You are hereby notified that any disclosure, copying, distribution or taking action in relation to the contents of this information is strictly prohibited and may be unlawful.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/1a818933/attachment-0001.html>

From brayanrodbajo at gmail.com  Thu Jul 16 04:48:48 2020
From: brayanrodbajo at gmail.com (Brayan Rodriguez)
Date: Thu, 16 Jul 2020 06:48:48 -0500
Subject: [bioontology-support] Get altLabel and label
Message-ID: <CALicoqhrXcLRka4AMXyYw+Wft10MhD+CCXVHSE7rX7iPz+EV_w@mail.gmail.com>

Hi.
I am writing due to the need for extracting the properties label and
altLabel of a specific term through the API (data.bioontology.org). Do you
know how can I get this information?

Thank you in advance.

Best,
-- 

Brayan Rodr?guez.
Systems Engineer, Universidad del Valle.
Master of Computer Engineering, Universidad Icesi.
Cali, Colombia.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/ff7ff3d6/attachment-0001.html>

From mdorf at stanford.edu  Thu Jul 16 10:58:35 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 16 Jul 2020 17:58:35 +0000
Subject: [bioontology-support] Get altLabel and label
In-Reply-To: <CALicoqhrXcLRka4AMXyYw+Wft10MhD+CCXVHSE7rX7iPz+EV_w@mail.gmail.com>
References: <CALicoqhrXcLRka4AMXyYw+Wft10MhD+CCXVHSE7rX7iPz+EV_w@mail.gmail.com>
Message-ID: <85BDBAD1-15A7-429E-A136-CF6D8FC821A5@stanford.edu>

Hi Brayan,

Thank you for your question. Depending on the ontology you are working with, the fields ?label? and ?altLabel? may or may not exist. Your best solution for extracting these fields is by asking for ALL of the properties of a given class using the ?display=properties? query parameter:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F122040007?include=prefLabel,synonym,definition,cui,semanticType,obsolete,properties<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/122040007?include=prefLabel,synonym,definition,cui,semanticType,obsolete,properties>

http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C34952?include=prefLabel,synonym,definition,cui,semanticType,obsolete,properties<http://data.bioontology.org/ontologies/NCIT/classes/http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C34952?include=prefLabel,synonym,definition,cui,semanticType,obsolete,properties>

If you know the property name that contains the data you need (the names/namespaces can be different for different ontologies), you can extract them from the ?properties? collection.

Let me know if this works for you.

Michael


On Jul 16, 2020, at 4:48 AM, Brayan Rodriguez <brayanrodbajo at gmail.com<mailto:brayanrodbajo at gmail.com>> wrote:

Hi.
I am writing due to the need for extracting the properties label and altLabel of a specific term through the API (data.bioontology.org<http://data.bioontology.org/>). Do you know how can I get this information?

Thank you in advance.

Best,
--

Brayan Rodr?guez.
Systems Engineer, Universidad del Valle.
Master of Computer Engineering, Universidad Icesi.
Cali, Colombia.
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/3bb974b0/attachment.html>

From vk396 at njit.edu  Thu Jul 16 11:45:51 2020
From: vk396 at njit.edu (Kuttichi Keloth, Vipina)
Date: Thu, 16 Jul 2020 14:45:51 -0400
Subject: [bioontology-support] BioPortal not allowing uploads
Message-ID: <CAGFJoxfk-ShU-aMkbfthN7jUhbXjGxFCxo8it=D=-C3WO-tepg@mail.gmail.com>

Hi,

I guess you are notified about the issue. The submit ontology page
returns an error.

Could you please look into this?

Thank you.
Vipina
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/14be5362/attachment-0001.html>

From mdorf at stanford.edu  Thu Jul 16 14:25:12 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 16 Jul 2020 21:25:12 +0000
Subject: [bioontology-support] BioPortal not allowing uploads
In-Reply-To: <CAGFJoxfk-ShU-aMkbfthN7jUhbXjGxFCxo8it=D=-C3WO-tepg@mail.gmail.com>
References: <CAGFJoxfk-ShU-aMkbfthN7jUhbXjGxFCxo8it=D=-C3WO-tepg@mail.gmail.com>
Message-ID: <CF25A14D-0D06-48BC-95F3-6A1B97B65060@stanford.edu>

Hi Vipina,

Thank you for your report. Apologies for that. There was a system glitch that required clearing of our internal cache repositories. The ontology submission page is now back to operational. Let us know if you are still experiencing issues.

Thank you!

Michael

> On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina <vk396 at njit.edu> wrote:
> 
> Hi,
> 
> I guess you are notified about the issue. The submit ontology page returns an error.
> 
> Could you please look into this?
> 
> Thank you.
> Vipina
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

From mdorf at stanford.edu  Thu Jul 16 14:28:47 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 16 Jul 2020 21:28:47 +0000
Subject: [bioontology-support] Account details error, seeking API key
In-Reply-To: <CAOC8+69uaKtybFvruLLViThUSt1CxYsYxyjavD8PKxRWprW=HA@mail.gmail.com>
References: <CAOC8+69uaKtybFvruLLViThUSt1CxYsYxyjavD8PKxRWprW=HA@mail.gmail.com>
Message-ID: <7C8C0DF2-4D13-4478-9469-683B1AA79CA8@stanford.edu>

Hi Benjamin,

Thank you for your report. Please accept my apologies for the downtime. The problem was caused by a system glitch that required clearing of our internal cache repositories. The account details page is now back to operational, and you should be able to retrieve your API key directly from there.

Let us know if you are still experiencing issues.

Thank you!

Michael

On Jul 16, 2020, at 7:09 AM, Benjamin Rodriguez <brodriguez at integraltx.com<mailto:brodriguez at integraltx.com>> wrote:

Dear Support,

I registered for an account under brodriguez. I need to obtain an API key.
I am able to log in, but I receive a "something has gone wrong" error message when I click link for account details. I assume the API key is under account details. Can you give me my API key?

Thanks,
Ben



Disclaimer

The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you should delete this message. You are hereby notified that any disclosure, copying, distribution or taking action in relation to the contents of this information is strictly prohibited and may be unlawful.

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/660f368f/attachment-0001.html>

From vk396 at njit.edu  Thu Jul 16 14:29:43 2020
From: vk396 at njit.edu (Kuttichi Keloth, Vipina)
Date: Thu, 16 Jul 2020 17:29:43 -0400
Subject: [bioontology-support] BioPortal not allowing uploads
In-Reply-To: <CF25A14D-0D06-48BC-95F3-6A1B97B65060@stanford.edu>
References: <CAGFJoxfk-ShU-aMkbfthN7jUhbXjGxFCxo8it=D=-C3WO-tepg@mail.gmail.com>
 <CF25A14D-0D06-48BC-95F3-6A1B97B65060@stanford.edu>
Message-ID: <CAGFJoxfYWCqCMse91uodN=NM175U0rZm++EUGuU=hG=sYHK=YA@mail.gmail.com>

Thank you. I was able to upload some time back ( CIDIT_V1_2). But I guess
there is a processing error.
It shows under the submissions - uploaded,* Error rdf.*

*Could you please reprocess it?*

*Thank you.*
*Vipina*

On Thu, Jul 16, 2020 at 5:25 PM Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Vipina,
>
> Thank you for your report. Apologies for that. There was a system glitch
> that required clearing of our internal cache repositories. The ontology
> submission page is now back to operational. Let us know if you are still
> experiencing issues.
>
> Thank you!
>
> Michael
>
> > On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina <vk396 at njit.edu>
> wrote:
> >
> > Hi,
> >
> > I guess you are notified about the issue. The submit ontology page
> returns an error.
> >
> > Could you please look into this?
> >
> > Thank you.
> > Vipina
> > _______________________________________________
> > bioontology-support mailing list
> > bioontology-support at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/5e9fe0c8/attachment.html>

From mdorf at stanford.edu  Thu Jul 16 14:35:49 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Thu, 16 Jul 2020 21:35:49 +0000
Subject: [bioontology-support] BioPortal not allowing uploads
In-Reply-To: <CAGFJoxfYWCqCMse91uodN=NM175U0rZm++EUGuU=hG=sYHK=YA@mail.gmail.com>
References: <CAGFJoxfk-ShU-aMkbfthN7jUhbXjGxFCxo8it=D=-C3WO-tepg@mail.gmail.com>
 <CF25A14D-0D06-48BC-95F3-6A1B97B65060@stanford.edu>
 <CAGFJoxfYWCqCMse91uodN=NM175U0rZm++EUGuU=hG=sYHK=YA@mail.gmail.com>
Message-ID: <A1C1C147-50AE-48B2-A6CA-9BE5A0B2619E@stanford.edu>

Hi Vipina,

I am seeing parsing errors during the processing of your ontology, which I need some time to investigate. I?ll keep you posted on my findings.

Thanks,

Michael


On Jul 16, 2020, at 2:29 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:

Thank you. I was able to upload some time back ( CIDIT_V1_2). But I guess there is a processing error.
It shows under the submissions - uploaded, Error rdf.

Could you please reprocess it?

Thank you.
Vipina

On Thu, Jul 16, 2020 at 5:25 PM Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Vipina,

Thank you for your report. Apologies for that. There was a system glitch that required clearing of our internal cache repositories. The ontology submission page is now back to operational. Let us know if you are still experiencing issues.

Thank you!

Michael

> On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:
>
> Hi,
>
> I guess you are notified about the issue. The submit ontology page returns an error.
>
> Could you please look into this?
>
> Thank you.
> Vipina
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/71d31971/attachment-0001.html>

From vendetti at stanford.edu  Thu Jul 16 14:39:53 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 16 Jul 2020 21:39:53 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Emma Vos
In-Reply-To: <5f0f43a380552_8cf27449f480627@ncbo-prd-app-09.stanford.edu.mail>
References: <5f0f43a380552_8cf27449f480627@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <CD6ACC8B-DC3B-4630-AB0B-65DC83DA6A03@stanford.edu>

Hello Emma,


On Jul 15, 2020, at 10:57 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


I wanted to annotate some cell types (e.g. "monocyte") with Cell Ontology terms, using the Annotator tool. Unfortunately, this didn't work. When browsing through the Cell Ontology, I saw that part of the ontology is missing in BioPortal. For example, Cell Ontology contains a term for "monocyte": http://purl.obolibrary.org/obo/CL_0000576 . But this term is not included in the Cell Ontology on BioPortal. Hence why I couldn't annotate this "monocyte" properly using the Annotator tool.

Another issue I had was with downloading the CSV file of Cell Ontology. I get the following error:
"Cannot read latest submission upload file: /srv/ncbo/repository/CL/73/CL.csv.gz"



Apologies for the inconvenience. It appears there was an error that occurred during the processing of the latest submission of the Cell Ontology. I reprocessed the ontology and the issues you reported are resolved - the CSV file is downloadable again, and the classes page appears normal.

Kind regards,
Jennifer



[cid:5B3100B2-FB05-4940-8D61-C4EC0351EE9E at stanford.edu]
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/189d30a6/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-07-16 14.36.38.png
Type: image/png
Size: 289481 bytes
Desc: Screenshot 2020-07-16 14.36.38.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200716/189d30a6/attachment-0001.png>

From vendetti at stanford.edu  Thu Jul 16 20:57:01 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 17 Jul 2020 03:57:01 +0000
Subject: [bioontology-support] BioPortal not allowing uploads
In-Reply-To: <CAGFJoxfYWCqCMse91uodN=NM175U0rZm++EUGuU=hG=sYHK=YA@mail.gmail.com>
References: <CAGFJoxfk-ShU-aMkbfthN7jUhbXjGxFCxo8it=D=-C3WO-tepg@mail.gmail.com>
 <CF25A14D-0D06-48BC-95F3-6A1B97B65060@stanford.edu>
 <CAGFJoxfYWCqCMse91uodN=NM175U0rZm++EUGuU=hG=sYHK=YA@mail.gmail.com>
Message-ID: <1778A813-CE93-4DB0-8AEE-B67BF3115E82@stanford.edu>

Hello Vipina,

There are 2,535 occurrences in your ontology source file where the value of rdf:about has a leading space character. One such example can be seen on line 156,587:

<owl:Class rdf:about=" http://purl.obolibrary.org/obo/CIDO_UMLS_C5203670?>

The ontology parsing library we use internally considers these leading space characters illegal:


Detailed logs:
--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser at 985696
    Stack trace:
org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=156589:column=79] IRI ' http://purl.obolibrary.org/obo/CIDO_UMLS_C5203670' cannot be resolved against current base IRI http://purl.obolibrary.org/obo/cido.owl reason is: Illegal character in scheme name at index 0: %20http://purl.obolibrary.org/obo/CIDO_UMLS_C5203670<http://purl.obolibrary.org/obo/CIDO_UMLS_C5203670>        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:221)


I ran a search and replace over the file to remove these leading space characters and uploaded the modified version of your ontology as a new submission. It?s fully processed and available in BioPortal now. If you want to submit updates, you?ll need to correct these leading space characters in your original source file.

Kind regards,
Jennifer



On Jul 16, 2020, at 2:29 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:

Thank you. I was able to upload some time back ( CIDIT_V1_2). But I guess there is a processing error.
It shows under the submissions - uploaded, Error rdf.

Could you please reprocess it?

Thank you.
Vipina

On Thu, Jul 16, 2020 at 5:25 PM Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Vipina,

Thank you for your report. Apologies for that. There was a system glitch that required clearing of our internal cache repositories. The ontology submission page is now back to operational. Let us know if you are still experiencing issues.

Thank you!

Michael

> On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina <vk396 at njit.edu<mailto:vk396 at njit.edu>> wrote:
>
> Hi,
>
> I guess you are notified about the issue. The submit ontology page returns an error.
>
> Could you please look into this?
>
> Thank you.
> Vipina
> _______________________________________________
> 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200717/8ac532fc/attachment.html>

From vk396 at njit.edu  Fri Jul 17 07:15:12 2020
From: vk396 at njit.edu (Kuttichi Keloth, Vipina)
Date: Fri, 17 Jul 2020 10:15:12 -0400
Subject: [bioontology-support] BioPortal not allowing uploads
In-Reply-To: <1778A813-CE93-4DB0-8AEE-B67BF3115E82@stanford.edu>
References: <CAGFJoxfk-ShU-aMkbfthN7jUhbXjGxFCxo8it=D=-C3WO-tepg@mail.gmail.com>
 <CF25A14D-0D06-48BC-95F3-6A1B97B65060@stanford.edu>
 <CAGFJoxfYWCqCMse91uodN=NM175U0rZm++EUGuU=hG=sYHK=YA@mail.gmail.com>
 <1778A813-CE93-4DB0-8AEE-B67BF3115E82@stanford.edu>
Message-ID: <CAGFJoxdYRxLFnS-G=bpC5cJH36A5bmMYcNXZ21C4iUPVcec_2g@mail.gmail.com>

Hi Jennifer,

Thank you so much. I was not aware of this. I loaded it in Protege and
there were no issues.
I will make sure to correct these in future uploads.

Thank you.
Vipina


On Thu, Jul 16, 2020 at 11:57 PM Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Vipina,
>
> There are 2,535 occurrences in your ontology source file where the value
> of rdf:about has a leading space character. One such example can be seen on
> line 156,587:
>
> <owl:Class rdf:about=" http://purl.obolibrary.org/obo/CIDO_UMLS_C5203670?>
>
> The ontology parsing library we use internally considers these leading
> space characters illegal:
>
>
> Detailed logs:
>
> --------------------------------------------------------------------------------
> Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser at 985696
>     Stack trace:
> org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException:
> [line=156589:column=79] IRI '
> http://purl.obolibrary.org/obo/CIDO_UMLS_C5203670' cannot be resolved
> against current base IRI http://purl.obolibrary.org/obo/cido.owl reason
> is: Illegal character in scheme name at index 0: %20http://
> purl.obolibrary.org/obo/CIDO_UMLS_C5203670
>  org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76)
>
> uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:221)
>
>
> I ran a search and replace over the file to remove these leading space
> characters and uploaded the modified version of your ontology as a new
> submission. It?s fully processed and available in BioPortal now. If you
> want to submit updates, you?ll need to correct these leading space
> characters in your original source file.
>
> Kind regards,
> Jennifer
>
>
>
> On Jul 16, 2020, at 2:29 PM, Kuttichi Keloth, Vipina <vk396 at njit.edu>
> wrote:
>
> Thank you. I was able to upload some time back ( CIDIT_V1_2). But I guess
> there is a processing error.
> It shows under the submissions - uploaded,* Error rdf.*
>
> *Could you please reprocess it?*
>
> *Thank you.*
> *Vipina*
>
> On Thu, Jul 16, 2020 at 5:25 PM Michael Dorf <mdorf at stanford.edu> wrote:
>
>> Hi Vipina,
>>
>> Thank you for your report. Apologies for that. There was a system glitch
>> that required clearing of our internal cache repositories. The ontology
>> submission page is now back to operational. Let us know if you are still
>> experiencing issues.
>>
>> Thank you!
>>
>> Michael
>>
>> > On Jul 16, 2020, at 11:45 AM, Kuttichi Keloth, Vipina <vk396 at njit.edu>
>> wrote:
>> >
>> > Hi,
>> >
>> > I guess you are notified about the issue. The submit ontology page
>> returns an error.
>> >
>> > Could you please look into this?
>> >
>> > Thank you.
>> > Vipina
>> > _______________________________________________
>> > bioontology-support mailing list
>> > bioontology-support at lists.stanford.edu
>> > https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200717/b7c284e0/attachment-0001.html>

From soldatova.larisa at gmail.com  Mon Jul 20 07:29:16 2020
From: soldatova.larisa at gmail.com (Larisa Soldatova)
Date: Mon, 20 Jul 2020 15:29:16 +0100
Subject: [bioontology-support] problems with submitting a new ontology
Message-ID: <CABCJnNxxxXLPko9=LrSG85CzHxmNCwbh3XmBRiSt2Fs1fOnGZw@mail.gmail.com>

Dear Support Team,

I am trying to submit an ontology - TML, and I am getting error messages
after filling in metadata for this ontology. So I am unable to actually
submit a file.

Today I tried to do this again, and I got a message that 'TML' is already
taken. I assume that metadata actually were created, but it did not go any
further.

Please can you check what is wrong?

I need to submit this ontology, it is important for our publication.

Thank you,
Larisa
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200720/cbe0d854/attachment.html>

From vendetti at stanford.edu  Mon Jul 20 10:17:56 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 20 Jul 2020 17:17:56 +0000
Subject: [bioontology-support] problems with submitting a new ontology
In-Reply-To: <CABCJnNxxxXLPko9=LrSG85CzHxmNCwbh3XmBRiSt2Fs1fOnGZw@mail.gmail.com>
References: <CABCJnNxxxXLPko9=LrSG85CzHxmNCwbh3XmBRiSt2Fs1fOnGZw@mail.gmail.com>
Message-ID: <3EEEF389-CC9E-4633-9E55-AFBA610DE48C@stanford.edu>

Hello Larisa,


On Jul 20, 2020, at 7:29 AM, Larisa Soldatova <soldatova.larisa at gmail.com<mailto:soldatova.larisa at gmail.com>> wrote:

I am trying to submit an ontology - TML, and I am getting error messages after filling in metadata for this ontology. So I am unable to actually submit a file.

Today I tried to do this again, and I got a message that 'TML' is already taken. I assume that metadata actually were created, but it did not go any further.


Apologies for the inconvenience. We?re aware of this problem and are currently troubleshooting.

In the mean time, you should be able to submit an ontology file by navigating to your ontology entry page:

http://bioportal.bioontology.org/ontologies/TML

? and clicking the ?Add submission? button at the top of the Submissions table. I had to flush our application caches to make your ontology entry visible. You may need to refresh your browser page / cache to see the entry now.


Kind regards,
Jennifer


[cid:A0B94090-97C4-4B5C-9A4D-50A52E84D7F4 at lan]
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200720/f4324e98/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-07-20 10.15.14.png
Type: image/png
Size: 104524 bytes
Desc: Screenshot 2020-07-20 10.15.14.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200720/f4324e98/attachment-0001.png>

From support at bioontology.org  Tue Jul 21 11:34:20 2020
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 21 Jul 2020 11:34:20 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Melissa Locke
Message-ID: <5f17352c48da4_725226cd174753b4@ncbo-prd-app-08.stanford.edu.mail>

An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200721/3e8f3f6a/attachment.html>

From jgraybeal at stanford.edu  Tue Jul 21 13:40:50 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 21 Jul 2020 20:40:50 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Melissa Locke
In-Reply-To: <5f17352c48da4_725226cd174753b4@ncbo-prd-app-08.stanford.edu.mail>
References: <5f17352c48da4_725226cd174753b4@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <9D82FE6D-466C-4426-885E-3EF51268AB08@stanford.edu>

Hi Melissa,

For online use, I'd suggest you link to the web site (https://bioontology.org) and/or the application (https://bioportal.bioontology.org).

However, we sadly note that the CPT term descriptions are going to go away soon. At the request of the ontology providers, we are going to be removing the ontology contents from BioPortal with our next UMLS release, which will happen in a few weeks. There will still be a summary page, but the ontology terms will no longer be on the site.

John

On Jul 21, 2020, at 11:34 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Melissa Locke

Email: mlocke at cleverleyassociates.com<mailto:mlocke at cleverleyassociates.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FCPT%3Fp%3Dclasses%26conceptid%3D0001U

Feedback:

Hi! We would like to use the BioPortal CPT descriptions to help our clients comply with new CMS disclosure guidelines. We saw your "how to cite" page, but wanted to verify that this is the preferred way for citing your site on a website (not a research paper).

Is the "how to cite" the preferred online citation?

Thanks!

_______________________________________________
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



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200721/eb174231/attachment.html>

From alex.mozejko at databiology.com  Wed Jul 22 23:02:15 2020
From: alex.mozejko at databiology.com (Alex Mozejko)
Date: Thu, 23 Jul 2020 06:02:15 +0000
Subject: [bioontology-support] Databiology: Default web portal
	credentials
In-Reply-To: <AE8E0812-F37B-4F3D-AE03-43B9663E142B@stanford.edu>
References: <AE8E0812-F37B-4F3D-AE03-43B9663E142B@stanford.edu>
Message-ID: <BN8PR20MB2563ECCFC4E9A6279B51F24091760@BN8PR20MB2563.namprd20.prod.outlook.com>

Hi Alex,

Apologies for taking so long to get back to you on this.

Thank you very much to the ?firstboot? tip, that worked a treat.

A couple of weeks ago I created a request at https://license.ontoportal.org/licenses for appliance id d8d04b7b-577b-4d09-b40a-82ccc0a12b99<https://license.ontoportal.org/licenses%20for%20appliance%20id%20d8d04b7b-577b-4d09-b40a-82ccc0a12b99>. Can you please double check that this hasn?t been lost? I?m happy to provide additional information if required.

Also we?re having issues loading new Ontologies, we can use the portal to upload a file and it appears in the list however when clicking into the Ontology, the summary tab shows:

Metrics
We have not yet calculated metrics for ONTOLOGY

Visits
We are still collecting data for ONTOLOGY

And the ?classes? tab reports:

?Problem retrieving classes?
Does any of this sound familiar? Or can you suggest some logs to read which might point us in a right direction to solve?

Apologies again for taking so long to respond.

Thanks,
Alex.

From: Alex Skrenchuk <alex.skrenchuk at stanford.edu>
Sent: Friday, 3 July 2020 5:42 AM
To: Alex Mozejko <alex.mozejko at databiology.com>; support at bioontology.org
Subject: Re: [bioontology-support] Databiology: Default web portal credentials

HI Alex,

We have not yet experimented with importing OVA to AWS because we are counting that the majority of users will deploy OntoPortal from the AWS marketplace.   We were recently been made aware that version 3.0.1 of the appliance sometimes doesn?t initialize properly in AWS during the first boot which could be usually resolved with a second reboot.

During the very first boot of the appliance we have a firstboot script that resets API keys for the Web UI and Admin user.  If it detects that appliance is running in AWS then it will also resets Admin password to match the instance-id of your EC2 instance.

First I would try to use the EC2 instance-id for admin password and if that doesn?t work then you could try to force re-run of the firstboot script.

ssh to instance as centos user and:

sudo touch /srv/ontoportal/firstboot
sudo chown ontoportal /srv/ontoportal/firstboot
sudo reboot


-Alex


From: bioontology-support <bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>> on behalf of Alex Mozejko <alex.mozejko at databiology.com<mailto:alex.mozejko at databiology.com>>
Date: Thursday, July 2, 2020 at 8:00 AM
To: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: [bioontology-support] Databiology: Default web portal credentials

Hello,

We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials:

Username: admin
Password: changemeNOW

Whenever I try I get the error:

?Errors On Form.
Invalid account name/password combination?

The default ssh user credentials worked and I can confirm ssh access.

I can also confirm that creating a new user and uploading an ontology works, so good news there ?

The process I followed to deploy this appliance is as follows:


  1.  Download OVA image from https://bioportal.bioontology.org/virtual_appliance
  2.  Copy OVA to s3 bucket
  3.  Use aws cli to convert image to AMI as detailed here<https://docs.aws.amazon.com/vm-import/latest/userguide/vmimport-image-import.html>
  4.  Launched virtual machine using the converted AMI
  5.  Navigate to portal
  6.  Try to login as admin
  7.  Get error

Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password?

Thanks,
Alex.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200723/cb145a14/attachment-0001.html>

From jgraybeal at stanford.edu  Thu Jul 23 09:06:42 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 23 Jul 2020 16:06:42 +0000
Subject: [bioontology-support] Databiology: Default web
	portal	credentials
In-Reply-To: <BN8PR20MB2563ECCFC4E9A6279B51F24091760@BN8PR20MB2563.namprd20.prod.outlook.com>
References: <AE8E0812-F37B-4F3D-AE03-43B9663E142B@stanford.edu>
 <BN8PR20MB2563ECCFC4E9A6279B51F24091760@BN8PR20MB2563.namprd20.prod.outlook.com>
Message-ID: <7D167CAD-398C-478F-9727-C063F6972F4E@stanford.edu>

Hi Alex,

Thanks for the note about the license key, I've approved your license. Please let me know if you don't get the email, we're working through some email issues.

It sounds like the ontology parsing didn't complete successfully. The guidance in the Submitting Ontologies<https://ontoportal.github.io/administration/ontologies/submitting_ontologies/> and Troubleshooting Submissions<https://ontoportal.github.io/administration/ontologies/troubleshooting_submissions/> sections of our Administration guide might help you to narrow down the problem. (The most common problem we see in BioPortal is that the ontology isn't parseable, and that can be checked with Protege, but you may have checked that already.)

If that doesn't work, let us know where you get stuck.

John

On Jul 22, 2020, at 11:02 PM, Alex Mozejko <alex.mozejko at databiology.com<mailto:alex.mozejko at databiology.com>> wrote:

Hi Alex,

Apologies for taking so long to get back to you on this.

Thank you very much to the ?firstboot? tip, that worked a treat.

A couple of weeks ago I created a request at https://license.ontoportal.org/licenses for appliance id d8d04b7b-577b-4d09-b40a-82ccc0a12b99<https://license.ontoportal.org/licenses%20for%20appliance%20id%20d8d04b7b-577b-4d09-b40a-82ccc0a12b99>. Can you please double check that this hasn?t been lost? I?m happy to provide additional information if required.

Also we?re having issues loading new Ontologies, we can use the portal to upload a file and it appears in the list however when clicking into the Ontology, the summary tab shows:

Metrics
We have not yet calculated metrics for ONTOLOGY

Visits
We are still collecting data for ONTOLOGY

And the ?classes? tab reports:

?Problem retrieving classes?
Does any of this sound familiar? Or can you suggest some logs to read which might point us in a right direction to solve?

Apologies again for taking so long to respond.

Thanks,
Alex.

From: Alex Skrenchuk <alex.skrenchuk at stanford.edu<mailto:alex.skrenchuk at stanford.edu>>
Sent: Friday, 3 July 2020 5:42 AM
To: Alex Mozejko <alex.mozejko at databiology.com<mailto:alex.mozejko at databiology.com>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Databiology: Default web portal credentials

HI Alex,

We have not yet experimented with importing OVA to AWS because we are counting that the majority of users will deploy OntoPortal from the AWS marketplace.   We were recently been made aware that version 3.0.1 of the appliance sometimes doesn?t initialize properly in AWS during the first boot which could be usually resolved with a second reboot.

During the very first boot of the appliance we have a firstboot script that resets API keys for the Web UI and Admin user.  If it detects that appliance is running in AWS then it will also resets Admin password to match the instance-id of your EC2 instance.

First I would try to use the EC2 instance-id for admin password and if that doesn?t work then you could try to force re-run of the firstboot script.

ssh to instance as centos user and:

sudo touch /srv/ontoportal/firstboot
sudo chown ontoportal /srv/ontoportal/firstboot
sudo reboot


-Alex


From: bioontology-support <bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>> on behalf of Alex Mozejko <alex.mozejko at databiology.com<mailto:alex.mozejko at databiology.com>>
Date: Thursday, July 2, 2020 at 8:00 AM
To: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: [bioontology-support] Databiology: Default web portal credentials

Hello,

We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials:

Username: admin
Password: changemeNOW

Whenever I try I get the error:

?Errors On Form.
Invalid account name/password combination?

The default ssh user credentials worked and I can confirm ssh access.

I can also confirm that creating a new user and uploading an ontology works, so good news there ?

The process I followed to deploy this appliance is as follows:


  1.  Download OVA image from https://bioportal.bioontology.org/virtual_appliance
  2.  Copy OVA to s3 bucket
  3.  Use aws cli to convert image to AMI as detailed here<https://docs.aws.amazon.com/vm-import/latest/userguide/vmimport-image-import.html>
  4.  Launched virtual machine using the converted AMI
  5.  Navigate to portal
  6.  Try to login as admin
  7.  Get error


Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password?

Thanks,
Alex.
_______________________________________________
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



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200723/8f57275d/attachment-0001.html>

From clair.kronk at gmail.com  Thu Jul 23 12:58:00 2020
From: clair.kronk at gmail.com (superraptor2)
Date: Thu, 23 Jul 2020 14:58:00 -0500 (CDT)
Subject: [bioontology-support] Getting IDs to resolve correctly with the GSSO
Message-ID: <1595534280745-0.post@n4.nabble.com>

Hi! I'm attempting to log the GSSO with a prefix at identifiers.org and part
of that process requires agnostic identifiers.

Basically, when I applied, the GSSO resolved individual identifiers with
URLs such as
http://purl.bioontology.org/ontology/GSSO?p=classes&conceptid=http://purl.bioontology.org/ontology/GSSO/000096
instead of http://purl.bioontology.org/ontology/GSSO/GSSO:000096. 

I attempted to update this from 2.0.0 to 2.0.1, changing the IDs from
http://purl.bioontology.org/ontology/GSSO/000096 to
http://purl.bioontology.org/ontology/GSSO/GSSO_006778, in order to mimic
those at the Gene Ontology, but it still requires something like
http://bioportal.bioontology.org/ontologies/GSSO/?p=classes&conceptid=http://purl.bioontology.org/ontology/GSSO/GSSO_006778
instead of http://bioportal.bioontology.org/ontologies/GSSO/GSSO:006778 or
http://bioportal.bioontology.org/ontologies/GSSO/GSSO_006778.

What's the best/fastest way to resolve these URLs? i.e. what do I need to
change within the annotations themselves for this to work? I'm editing
~12,000 entries via Protege, so anything I can do non-manually and in bulk
would be incredibly useful!

Thanks so much!



--
Sent from: http://ncbo-support.2288202.n4.nabble.com/

From alex.mozejko at databiology.com  Fri Jul 24 03:00:41 2020
From: alex.mozejko at databiology.com (Alex Mozejko)
Date: Fri, 24 Jul 2020 10:00:41 +0000
Subject: [bioontology-support] Databiology: Default web
	portal	credentials
In-Reply-To: <7D167CAD-398C-478F-9727-C063F6972F4E@stanford.edu>
References: <AE8E0812-F37B-4F3D-AE03-43B9663E142B@stanford.edu>
 <BN8PR20MB2563ECCFC4E9A6279B51F24091760@BN8PR20MB2563.namprd20.prod.outlook.com>
 <7D167CAD-398C-478F-9727-C063F6972F4E@stanford.edu>
Message-ID: <BN8PR20MB2563E091A6C0796C9AEDFD5891770@BN8PR20MB2563.namprd20.prod.outlook.com>

Hi John,

Thanks for organising the license. I can confirm that the email came through (albeit to ?junk? ?) and that the license was able to be applied successfully.

Thanks also for the troubleshooting tips, I haven?t had a chance to look through these today but hopefully will be able to early next week.

Thanks,
Alex.

From: John Graybeal <jgraybeal at stanford.edu>
Sent: Friday, 24 July 2020 12:07 AM
To: Alex Mozejko <alex.mozejko at databiology.com>
Cc: Alex Skrenchuk <alex.skrenchuk at stanford.edu>; support at bioontology.org; Georges Heiter <georges.heiter at databiology.com>
Subject: Re: [bioontology-support] Databiology: Default web portal credentials

Hi Alex,

Thanks for the note about the license key, I've approved your license. Please let me know if you don't get the email, we're working through some email issues.

It sounds like the ontology parsing didn't complete successfully. The guidance in the Submitting Ontologies<https://ontoportal.github.io/administration/ontologies/submitting_ontologies/> and Troubleshooting Submissions<https://ontoportal.github.io/administration/ontologies/troubleshooting_submissions/> sections of our Administration guide might help you to narrow down the problem. (The most common problem we see in BioPortal is that the ontology isn't parseable, and that can be checked with Protege, but you may have checked that already.)

If that doesn't work, let us know where you get stuck.

John


On Jul 22, 2020, at 11:02 PM, Alex Mozejko <alex.mozejko at databiology.com<mailto:alex.mozejko at databiology.com>> wrote:

Hi Alex,

Apologies for taking so long to get back to you on this.

Thank you very much to the ?firstboot? tip, that worked a treat.

A couple of weeks ago I created a request at https://license.ontoportal.org/licenses for appliance id d8d04b7b-577b-4d09-b40a-82ccc0a12b99<https://license.ontoportal.org/licenses%20for%20appliance%20id%20d8d04b7b-577b-4d09-b40a-82ccc0a12b99>. Can you please double check that this hasn?t been lost? I?m happy to provide additional information if required.

Also we?re having issues loading new Ontologies, we can use the portal to upload a file and it appears in the list however when clicking into the Ontology, the summary tab shows:

Metrics
We have not yet calculated metrics for ONTOLOGY

Visits
We are still collecting data for ONTOLOGY

And the ?classes? tab reports:

?Problem retrieving classes?
Does any of this sound familiar? Or can you suggest some logs to read which might point us in a right direction to solve?

Apologies again for taking so long to respond.

Thanks,
Alex.

From: Alex Skrenchuk <alex.skrenchuk at stanford.edu<mailto:alex.skrenchuk at stanford.edu>>
Sent: Friday, 3 July 2020 5:42 AM
To: Alex Mozejko <alex.mozejko at databiology.com<mailto:alex.mozejko at databiology.com>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Databiology: Default web portal credentials

HI Alex,

We have not yet experimented with importing OVA to AWS because we are counting that the majority of users will deploy OntoPortal from the AWS marketplace.   We were recently been made aware that version 3.0.1 of the appliance sometimes doesn?t initialize properly in AWS during the first boot which could be usually resolved with a second reboot.

During the very first boot of the appliance we have a firstboot script that resets API keys for the Web UI and Admin user.  If it detects that appliance is running in AWS then it will also resets Admin password to match the instance-id of your EC2 instance.

First I would try to use the EC2 instance-id for admin password and if that doesn?t work then you could try to force re-run of the firstboot script.

ssh to instance as centos user and:

sudo touch /srv/ontoportal/firstboot
sudo chown ontoportal /srv/ontoportal/firstboot
sudo reboot


-Alex


From: bioontology-support <bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>> on behalf of Alex Mozejko <alex.mozejko at databiology.com<mailto:alex.mozejko at databiology.com>>
Date: Thursday, July 2, 2020 at 8:00 AM
To: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: [bioontology-support] Databiology: Default web portal credentials

Hello,

We have recently deployed the Bioportal appliance to one of our AWS environments but can?t seem to login using the credentials:

Username: admin
Password: changemeNOW

Whenever I try I get the error:

?Errors On Form.
Invalid account name/password combination?

The default ssh user credentials worked and I can confirm ssh access.

I can also confirm that creating a new user and uploading an ontology works, so good news there ?

The process I followed to deploy this appliance is as follows:


  1.  Download OVA image from https://bioportal.bioontology.org/virtual_appliance
  2.  Copy OVA to s3 bucket
  3.  Use aws cli to convert image to AMI as detailed here<https://docs.aws.amazon.com/vm-import/latest/userguide/vmimport-image-import.html>
  4.  Launched virtual machine using the converted AMI
  5.  Navigate to portal
  6.  Try to login as admin
  7.  Get error

Can you please confirm that the credentials I?m trying to use are correct? And is there a way to reset the ?admin? user?s password?

Thanks,
Alex.
_______________________________________________
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



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200724/da092c07/attachment-0001.html>

From coss at cnb.csic.es  Thu Jul 23 22:43:48 2020
From: coss at cnb.csic.es (Carlos Oscar Sorzano)
Date: Fri, 24 Jul 2020 07:43:48 +0200
Subject: [bioontology-support] Problem retrieving classes
Message-ID: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es>

Dear colleagues,

I uploaded yesterday an ontology file for Cryo Electron Microscopy 
(http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). 
The OWL file was generated with Protege and it does not show any obvious 
error in Protege. However, when it is read at BioPortal there is some 
problem because we see the error message "Problem retrieving classes" 
(see previous link). The file is partly parsed because it shows some 
metrics, but we must have something wrong with the file. Could you help 
us with any hint?

Kind regards and thanks, Carlos Oscar

From vendetti at stanford.edu  Fri Jul 24 11:30:28 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 24 Jul 2020 18:30:28 +0000
Subject: [bioontology-support] Getting IDs to resolve correctly with the
 GSSO
In-Reply-To: <1595534280745-0.post@n4.nabble.com>
References: <1595534280745-0.post@n4.nabble.com>
Message-ID: <6D1EF297-EAD2-4D0A-AEB4-0DFCE7C41635@stanford.edu>

Hello,

I started looking into this yesterday evening, and I?m not sure I have a complete answer for you yet.

When end users submit ontologies to BioPortal, an ontology PURL is created using this format:

http://purl.bioontology.org/ontology/GSSO

? where your ontology acronym makes up the last fragment of the PURL. If you enter that PURL in a browser address bar, the BioPortal PURL server will resolve it to the following URL pattern:

http://bioportal.bioontology.org/ontologies/GSSO

This is the home page for your ontology in the BioPortal web application (developed in Ruby on Rails).

If you want a permanent link to any given class in your ontology that will resolve to the corresponding page in the BioPortal web application, you can use a URL pattern where you tack the URL encoded class ID onto the end of the ontology PURL using the ?conceptid=? parameter in the query string. For example, the permanent link to the ?transgender? class from your GSSO ontology would be the following:

http://purl.bioontology.org/ontology/GSSO?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FGSSO%2FGSSO_000096<http://purl.bioontology.org/ontology/GSSO?conceptid=http://purl.bioontology.org/ontology/GSSO/GSSO_000096>

I did find an exception to the above information that occurs with all of the UMLS format ontologies in BioPortal, e.g., SNOMEDCT, etc. These ontologies are bulk-imported into BioPortal twice per year using a custom process that writes the ontology data directly into the RDF store, bypassing the file upload process normally performed by end users. For these ontologies, several formats for permanent class links work, e.g., all of the following PURLS will resolve to the ?Body structure? class in the SNOMEDCT ontology:

http://purl.bioontology.org/ontology/SNOMEDCT/123037004
http://purl.bioontology.org/ontology/SNOMEDCT?conceptid=123037004
http://purl.bioontology.org/ontology/SNOMEDCT?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F123037004<http://purl.bioontology.org/ontology/SNOMEDCT?conceptid=http://purl.bioontology.org/ontology/SNOMEDCT/123037004>

 I?m not yet able to provide more details about why this only works for UMLS format ontologies.

You mentioned that you?re editing a large number of entries in Protege. I?m not sure if you?re aware that we provide a REST API for programmatic retrieval of ontology data, documented here: http://data.bioontology.org/documentation. For example, you could retrieve data about the ?transgender? class using the following REST call:

http://data.bioontology.org/ontologies/GSSO/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FGSSO%2FGSSO_000096<http://data.bioontology.org/ontologies/GSSO/classes/http://purl.bioontology.org/ontology/GSSO/GSSO_000096>

It?s a hypermedia API, and one of the links returned is a ?ui? link with a URL that navigates to the page for said class in the BioPortal web application (http://bioportal.bioontology.org/ontologies/GSSO?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FGSSO%2FGSSO_000096).

We provide examples of using the API in several languages in one of our GitHub repositories: https://github.com/ncbo/ncbo_rest_sample_code.

Hope this information is helpful.

Kind regards,
Jennifer


[cid:385A57B1-A516-4F52-A9F3-C0422509D101 at stanford.edu]


On Jul 23, 2020, at 12:58 PM, superraptor2 <clair.kronk at gmail.com<mailto:clair.kronk at gmail.com>> wrote:

Hi! I'm attempting to log the GSSO with a prefix at identifiers.org<http://identifiers.org> and part
of that process requires agnostic identifiers.

Basically, when I applied, the GSSO resolved individual identifiers with
URLs such as
http://purl.bioontology.org/ontology/GSSO?p=classes&conceptid=http://purl.bioontology.org/ontology/GSSO/000096
instead of http://purl.bioontology.org/ontology/GSSO/GSSO:000096.

I attempted to update this from 2.0.0 to 2.0.1, changing the IDs from
http://purl.bioontology.org/ontology/GSSO/000096 to
http://purl.bioontology.org/ontology/GSSO/GSSO_006778, in order to mimic
those at the Gene Ontology, but it still requires something like
http://bioportal.bioontology.org/ontologies/GSSO/?p=classes&conceptid=http://purl.bioontology.org/ontology/GSSO/GSSO_006778
instead of http://bioportal.bioontology.org/ontologies/GSSO/GSSO:006778 or
http://bioportal.bioontology.org/ontologies/GSSO/GSSO_006778.

What's the best/fastest way to resolve these URLs? i.e. what do I need to
change within the annotations themselves for this to work? I'm editing
~12,000 entries via Protege, so anything I can do non-manually and in bulk
would be incredibly useful!

Thanks so much!



--
Sent from: http://ncbo-support.2288202.n4.nabble.com/
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200724/329dc648/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-07-24 11.23.10.png
Type: image/png
Size: 242536 bytes
Desc: Screenshot 2020-07-24 11.23.10.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200724/329dc648/attachment-0001.png>

From vendetti at stanford.edu  Fri Jul 24 11:53:48 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 24 Jul 2020 18:53:48 +0000
Subject: [bioontology-support] Problem retrieving classes
In-Reply-To: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es>
References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es>
Message-ID: <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu>

Hello Carlos Oscar,

I looked at the contents of your ontology source file. You mentioned that it?s an OWL file, but the contents appear to be in OBO format, i.e., see the following snippet from the top of your ontology showing OBO-style term stanzas:

format-version: 1.2
ontology: http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))\n\n\nAnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2#ProtMovies> \"ProtProcessMovies\"^^xsd:string)\n)

[Term]
id: Acquisition
comment: Contains acquisition parameters such as magnification, voltage, spherical aberration, amplitude contrast, dose per frame and inital dose, optics group, and beam tilt
is_a: EMObject

[Term]
id: AtomStruct
comment: File representing an atomic structure (PDB, mmCIF, ...)
is_a: EMObject
property_value: hasVolume "Volume"

The first line indicates that the ontology file is written in OBO format version 1.2, however the rest of the header tags aren?t valid according to OBO file format documentation here:

https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1

Could you provide more detail about how this ontology was generated? Do you have an OBO source file that you attempted to convert to a different format using the Protege desktop application? Also, I do see an error message in the Protege log when opening your ontology in the desktop version (Window -> Show log?).

[cid:810EFD70-59D3-4894-8185-3BC4CF96DC3E at stanford.edu]

Kind regards,
Jennifer


On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano <coss at cnb.csic.es<mailto:coss at cnb.csic.es>> wrote:

Dear colleagues,

I uploaded yesterday an ontology file for Cryo Electron Microscopy (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). The OWL file was generated with Protege and it does not show any obvious error in Protege. However, when it is read at BioPortal there is some problem because we see the error message "Problem retrieving classes" (see previous link). The file is partly parsed because it shows some metrics, but we must have something wrong with the file. Could you help us with any hint?

Kind regards and thanks, Carlos Oscar
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200724/4bc97966/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-07-24 11.52.33.png
Type: image/png
Size: 448373 bytes
Desc: Screenshot 2020-07-24 11.52.33.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200724/4bc97966/attachment-0001.png>

From support at bioontology.org  Sun Jul 26 22:47:27 2020
From: support at bioontology.org (support at bioontology.org)
Date: Sun, 26 Jul 2020 22:47:27 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Farid
Message-ID: <5f1e6a6f9d191_65e120eb0bc70533@ncbo-prd-app-09.stanford.edu.mail>

An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200726/3394bf65/attachment.html>

From coss at cnb.csic.es  Sat Jul 25 01:13:41 2020
From: coss at cnb.csic.es (Carlos Oscar Sorzano)
Date: Sat, 25 Jul 2020 10:13:41 +0200
Subject: [bioontology-support] Problem retrieving classes
In-Reply-To: <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu>
References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es>
 <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu>
Message-ID: <e0538883-6f3c-391e-3d9d-6821341fb1e7@cnb.csic.es>

Thank you, Jennifer. I will check the configuration of Protege and see 
if I can save a truly OWL file. At least I have now something to look at.

Kind regards, Carlos Oscar

El 24/07/2020 a las 20:53, Jennifer Leigh Vendetti escribi?:
> Hello Carlos Oscar,
>
> I looked at the contents of your ontology source file. You mentioned 
> that it?s an OWL file, but the contents appear to be in OBO format, 
> i.e., see the following snippet from the top of your ontology showing 
> OBO-style term stanzas:
>
> format-version: 1.2
> ontology: 
> http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2
> owl-axioms: 
> Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))\n\n\nAnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> 
> <http://purl.obolibrary.org/obo/http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2#ProtMovies> 
> \"ProtProcessMovies\"^^xsd:string)\n)
>
> [Term]
> id: Acquisition
> comment: Contains acquisition parameters such as magnification, 
> voltage, spherical aberration, amplitude contrast, dose per frame and 
> inital dose, optics group, and beam tilt
> is_a: EMObject
>
> [Term]
> id: AtomStruct
> comment: File representing an atomic structure (PDB, mmCIF, ...)
> is_a: EMObject
> property_value: hasVolume "Volume"
>
> The first line indicates that the ontology file is written in OBO 
> format version 1.2, however the rest of the header tags aren?t valid 
> according to OBO file format documentation here:
>
> https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1
>
> Could you provide more detail about how this ontology was generated? 
> Do you have an OBO source file that you attempted to convert to a 
> different format using the Protege desktop application? Also, I do see 
> an error message in the Protege log when opening your ontology in the 
> desktop version (Window -> Show log?).
>
>
> Kind regards,
> Jennifer
>
>
>> On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano <coss at cnb.csic.es 
>> <mailto:coss at cnb.csic.es>> wrote:
>>
>> Dear colleagues,
>>
>> I uploaded yesterday an ontology file for Cryo Electron Microscopy 
>> (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). 
>> The OWL file was generated with Protege and it does not show any 
>> obvious error in Protege. However, when it is read at BioPortal there 
>> is some problem because we see the error message "Problem retrieving 
>> classes" (see previous link). The file is partly parsed because it 
>> shows some metrics, but we must have something wrong with the file. 
>> Could you help us with any hint?
>>
>> Kind regards and thanks, Carlos Oscar
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu 
>> <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200725/25a4cb29/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-07-24 11.52.33.png
Type: image/png
Size: 448373 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200725/25a4cb29/attachment-0001.png>

From support at bioontology.org  Mon Jul 27 03:50:49 2020
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 27 Jul 2020 03:50:49 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Marwa
Message-ID: <5f1eb189b7697_6a51274577850840@ncbo-prd-app-09.stanford.edu.mail>

An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200727/41384c15/attachment-0001.html>

From mdorf at stanford.edu  Mon Jul 27 13:25:28 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Mon, 27 Jul 2020 20:25:28 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Marwa
In-Reply-To: <5f1eb189b7697_6a51274577850840@ncbo-prd-app-09.stanford.edu.mail>
References: <5f1eb189b7697_6a51274577850840@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <EB7CE6DD-89C7-49BC-8CE4-1D090623DE22@stanford.edu>

Hi Marwa,

Thank you for your questions. In BioPortal there are optional categories that one can assign to his/her ontology during the creation phase. An ontology can belong to multiple categories, but they are not hierarchical. You can obtain the list of available categories by using this API service endpoint:

http://data.bioontology.org/categories

To determine which group an ontology belongs to, you can make this call:

http://data.bioontology.org/ontologies/SNOMEDCT?display=all

The ?hasDomain? field contains the list of the categories for a given ontology.

To your second question, our current data store is an RDF database called ?4store?:

https://github.com/4store/4store

We do, however, have short-term plans to migrate to AllegroGraph:

https://allegrograph.com/products/allegrograph/

Our Virtual Appliance v3.0, which you can download and install in your own environment, already includes compatibility with AllegroGraph.

As far the direct access to the database, we have a SPARQL endpoint that you can use:

http://sparql.bioontology.org/

Unfortunately, the data contained in that endpoint isn?t regularly synced with our production data, so it will not contain all the ontologies that exist in BioPortal. As part of the near future migration to AllegroGraph, we plan to implement a SPARQL endpoint that mirrors our production data.

Please let me know if I omitted anything or if you have further questions.

Michael


----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Jul 27, 2020, at 3:50 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Marwa

Email: marwa.abdelrehem at fci.au.edu.eg<mailto:marwa.abdelrehem at fci.au.edu.eg>

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

Feedback:

I am a researcher interested in ontology reuse and especially in bio-ontologies. In a part of my research, I am interested to determine the ontology domain (Category). My question is does bioportal has a hierarchy for those categories? and if so, can I have access to it?
The second question is what is the type of database that you store the ontologies information in? and also can I have access to it?
Thanks in advance.

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200727/cb8c6514/attachment.html>

From mdorf at stanford.edu  Mon Jul 27 16:17:03 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Mon, 27 Jul 2020 23:17:03 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Farid
In-Reply-To: <5f1e6a6f9d191_65e120eb0bc70533@ncbo-prd-app-09.stanford.edu.mail>
References: <5f1e6a6f9d191_65e120eb0bc70533@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <0CA80811-B45C-49EE-B908-A07B8DF036D7@stanford.edu>

Hi Farid,

Thank you for your inquiry. I am not an ontology expert, but you can look at a few ontologies, such as:

Human Disease Ontology (DOID)
https://bioportal.bioontology.org/ontologies/DOID

Foundational Model of Anatomy (FMA)
https://bioportal.bioontology.org/ontologies/FMA

The Clinical Terms Ontology (SNOMEDCT)
https://bioportal.bioontology.org/ontologies/SNOMEDCT

Medical Dictionary for Regulatory Activities Terminology (MedDRA)
https://bioportal.bioontology.org/ontologies/MEDDRA

If you have a specific text that you need to match against the most relevant ontologies, you can use our Ontology Recommender service:

https://bioportal.bioontology.org/recommender

Based on your text, the Recommender finds ontologies that are best suited for the terms found in that text.

You can also use the Category filter on the Ontologies page to narrow the list down to ontologies you deem the most relevant:

https://bioportal.bioontology.org/ontologies

You can access any of these ontologies or tools using our REST API services. The usage instructions can be found here: http://data.bioontology.org/documentation

Thanks,

Michael


----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Jul 26, 2020, at 10:47 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Farid

Email: ismayilzadeh.farid at gmail.com<mailto:ismayilzadeh.farid at gmail.com>

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

Feedback:

Hi. I am looking for a dataset that include list of all diseases, categories, body types, causes and symptoms. Can i get these data from you ?

Best regards
Farid Ismayilzada

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200727/9742fd3a/attachment-0001.html>

From coss at cnb.csic.es  Tue Jul 28 04:25:29 2020
From: coss at cnb.csic.es (Carlos Oscar Sorzano)
Date: Tue, 28 Jul 2020 13:25:29 +0200
Subject: [bioontology-support] Problem retrieving classes
In-Reply-To: <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu>
References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es>
 <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu>
Message-ID: <5bfb1388-7c1b-0848-87db-d063c8a72909@cnb.csic.es>

Dear Jennifer,

presumably I have uploaded now a true OWL file, but BioPortal cannot 
show yet the classes. Would you mind having a look? And thank you very much.

Kind regards, Carlos Oscar

On 7/24/20 8:53 PM, Jennifer Leigh Vendetti wrote:
> Hello Carlos Oscar,
>
> I looked at the contents of your ontology source file. You mentioned 
> that it?s an OWL file, but the contents appear to be in OBO format, 
> i.e., see the following snippet from the top of your ontology showing 
> OBO-style term stanzas:
>
> format-version: 1.2
> ontology: 
> http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2
> owl-axioms: 
> Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))\n\n\nAnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> 
> <http://purl.obolibrary.org/obo/http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2#ProtMovies> 
> \"ProtProcessMovies\"^^xsd:string)\n)
>
> [Term]
> id: Acquisition
> comment: Contains acquisition parameters such as magnification, 
> voltage, spherical aberration, amplitude contrast, dose per frame and 
> inital dose, optics group, and beam tilt
> is_a: EMObject
>
> [Term]
> id: AtomStruct
> comment: File representing an atomic structure (PDB, mmCIF, ...)
> is_a: EMObject
> property_value: hasVolume "Volume"
>
> The first line indicates that the ontology file is written in OBO 
> format version 1.2, however the rest of the header tags aren?t valid 
> according to OBO file format documentation here:
>
> https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1
>
> Could you provide more detail about how this ontology was generated? 
> Do you have an OBO source file that you attempted to convert to a 
> different format using the Protege desktop application? Also, I do see 
> an error message in the Protege log when opening your ontology in the 
> desktop version (Window -> Show log?).
>
>
> Kind regards,
> Jennifer
>
>
>> On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano <coss at cnb.csic.es 
>> <mailto:coss at cnb.csic.es>> wrote:
>>
>> Dear colleagues,
>>
>> I uploaded yesterday an ontology file for Cryo Electron Microscopy 
>> (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). 
>> The OWL file was generated with Protege and it does not show any 
>> obvious error in Protege. However, when it is read at BioPortal there 
>> is some problem because we see the error message "Problem retrieving 
>> classes" (see previous link). The file is partly parsed because it 
>> shows some metrics, but we must have something wrong with the file. 
>> Could you help us with any hint?
>>
>> Kind regards and thanks, Carlos Oscar
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu 
>> <mailto:bioontology-support at lists.stanford.edu>
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200728/944618a0/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2020-07-24 11.52.33.png
Type: image/png
Size: 448373 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200728/944618a0/attachment-0001.png>

From support at bioontology.org  Tue Jul 28 04:52:07 2020
From: support at bioontology.org (support at bioontology.org)
Date: Tue, 28 Jul 2020 04:52:07 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Emma Vos
Message-ID: <5f201167d183c_1d3c1b2da1c8797@ncbo-prd-app-09.stanford.edu.mail>

An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200728/63566ba8/attachment.html>

From mdorf at stanford.edu  Tue Jul 28 09:13:09 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 28 Jul 2020 16:13:09 +0000
Subject: [bioontology-support] Problem retrieving classes
In-Reply-To: <5bfb1388-7c1b-0848-87db-d063c8a72909@cnb.csic.es>
References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es>
 <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu>
 <5bfb1388-7c1b-0848-87db-d063c8a72909@cnb.csic.es>
Message-ID: <8615803C-0030-42E0-B6AA-8B2CEF22060A@stanford.edu>

Hi Carlos,

It looks like the ontology has loaded correctly, but it hasn?t had a chance to propagate through our caching layers. I?ve cleared the system caches manually, and the ontology now appears and functions correctly.

Let me know if you are still seeing any issues.

Thank you,

Michael




On Jul 28, 2020, at 4:25 AM, Carlos Oscar Sorzano <coss at cnb.csic.es<mailto:coss at cnb.csic.es>> wrote:


Dear Jennifer,

presumably I have uploaded now a true OWL file, but BioPortal cannot show yet the classes. Would you mind having a look? And thank you very much.

Kind regards, Carlos Oscar

On 7/24/20 8:53 PM, Jennifer Leigh Vendetti wrote:
Hello Carlos Oscar,

I looked at the contents of your ontology source file. You mentioned that it?s an OWL file, but the contents appear to be in OBO format, i.e., see the following snippet from the top of your ontology showing OBO-style term stanzas:

format-version: 1.2
ontology: http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))\n\n\nAnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2#ProtMovies> \"ProtProcessMovies\"^^xsd:string)\n)

[Term]
id: Acquisition
comment: Contains acquisition parameters such as magnification, voltage, spherical aberration, amplitude contrast, dose per frame and inital dose, optics group, and beam tilt
is_a: EMObject

[Term]
id: AtomStruct
comment: File representing an atomic structure (PDB, mmCIF, ...)
is_a: EMObject
property_value: hasVolume "Volume"

The first line indicates that the ontology file is written in OBO format version 1.2, however the rest of the header tags aren?t valid according to OBO file format documentation here:

https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1

Could you provide more detail about how this ontology was generated? Do you have an OBO source file that you attempted to convert to a different format using the Protege desktop application? Also, I do see an error message in the Protege log when opening your ontology in the desktop version (Window -> Show log?).

<Screenshot 2020-07-24 11.52.33.png>

Kind regards,
Jennifer


On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano <coss at cnb.csic.es<mailto:coss at cnb.csic.es>> wrote:

Dear colleagues,

I uploaded yesterday an ontology file for Cryo Electron Microscopy (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). The OWL file was generated with Protege and it does not show any obvious error in Protege. However, when it is read at BioPortal there is some problem because we see the error message "Problem retrieving classes" (see previous link). The file is partly parsed because it shows some metrics, but we must have something wrong with the file. Could you help us with any hint?

Kind regards and thanks, Carlos Oscar
_______________________________________________
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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200728/c8930a6c/attachment-0001.html>

From mdorf at stanford.edu  Tue Jul 28 13:24:46 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 28 Jul 2020 20:24:46 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Emma Vos
In-Reply-To: <5f201167d183c_1d3c1b2da1c8797@ncbo-prd-app-09.stanford.edu.mail>
References: <5f201167d183c_1d3c1b2da1c8797@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <2690D207-8E73-409D-96F5-1584823EC6C9@stanford.edu>

Hi Emma,

Thank you for your question. The "display=all? query parameter will give you the info you need:

http://data.bioontology.org/ontologies/CL/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000576?display=all<http://data.bioontology.org/ontologies/CL/classes/http://purl.obolibrary.org/obo/CL_0000576?display=all>

Let me know if you require further assistance.

Michael

On Jul 28, 2020, at 4:52 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Emma Vos

Email: emma at thehyve.nl<mailto:emma at thehyve.nl>

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

Feedback:

Dear BioPortal support,

I have a question about the API.
I would like to get the prefixIRI of a term, like CL:000576 in https://bioportal.bioontology.org/ontologies/CL?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000576.

But when accessing the data through the API (http://data.bioontology.org/ontologies/CL/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000576), I see some of the attributes of this term (like prefLabel and definition), but prefixIRI is missing from the attributes. I have read the API documentation, but it is not completely clear to me how I can get other attributes like prefixIRI. Could you potentially help me out with this?

Kind regards,
Emma Vos

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200728/388e7172/attachment.html>

From coss at cnb.csic.es  Tue Jul 28 08:04:53 2020
From: coss at cnb.csic.es (Carlos Oscar Sorzano)
Date: Tue, 28 Jul 2020 17:04:53 +0200
Subject: [bioontology-support] Problem retrieving classes
In-Reply-To: <8615803C-0030-42E0-B6AA-8B2CEF22060A@stanford.edu>
References: <65350038-9387-d5f9-269a-0e8c74c2e7ba@cnb.csic.es>
 <15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu>
 <5bfb1388-7c1b-0848-87db-d063c8a72909@cnb.csic.es>
 <8615803C-0030-42E0-B6AA-8B2CEF22060A@stanford.edu>
Message-ID: <ced80370-668b-edf8-7ed4-749c36bb28da@cnb.csic.es>

Thank you very much, it really worked.

Kind regards, Carlos Oscar

El 28/07/2020 a las 18:13, Michael Dorf escribi?:
> Hi Carlos,
>
> It looks like the ontology has loaded correctly, but it hasn?t had a 
> chance to propagate through our caching layers. I?ve cleared the 
> system caches manually, and the ontology now appears and functions 
> correctly.
>
> Let me know if you are still seeing any issues.
>
> Thank you,
>
> Michael
>
>
>
>
>> On Jul 28, 2020, at 4:25 AM, Carlos Oscar Sorzano <coss at cnb.csic.es 
>> <mailto:coss at cnb.csic.es>> wrote:
>>
>> Dear Jennifer,
>>
>> presumably I have uploaded now a true OWL file, but BioPortal cannot 
>> show yet the classes. Would you mind having a look? And thank you 
>> very much.
>>
>> Kind regards, Carlos Oscar
>>
>> On 7/24/20 8:53 PM, Jennifer Leigh Vendetti wrote:
>>> Hello Carlos Oscar,
>>>
>>> I looked at the contents of your ontology source file. You mentioned 
>>> that it?s an OWL file, but the contents appear to be in OBO format, 
>>> i.e., see the following snippet from the top of your ontology 
>>> showing OBO-style term stanzas:
>>>
>>> format-version: 1.2
>>> ontology: 
>>> http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2
>>> owl-axioms: 
>>> Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#id>))\n\n\nAnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> 
>>> <http://purl.obolibrary.org/obo/http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2#ProtMovies> 
>>> \"ProtProcessMovies\"^^xsd:string)\n)
>>>
>>> [Term]
>>> id: Acquisition
>>> comment: Contains acquisition parameters such as magnification, 
>>> voltage, spherical aberration, amplitude contrast, dose per frame 
>>> and inital dose, optics group, and beam tilt
>>> is_a: EMObject
>>>
>>> [Term]
>>> id: AtomStruct
>>> comment: File representing an atomic structure (PDB, mmCIF, ...)
>>> is_a: EMObject
>>> property_value: hasVolume "Volume"
>>>
>>> The first line indicates that the ontology file is written in OBO 
>>> format version 1.2, however the rest of the header tags aren?t valid 
>>> according to OBO file format documentation here:
>>>
>>> https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1
>>>
>>> Could you provide more detail about how this ontology was generated? 
>>> Do you have an OBO source file that you attempted to convert to a 
>>> different format using the Protege desktop application? Also, I do 
>>> see an error message in the Protege log when opening your ontology 
>>> in the desktop version (Window -> Show log?).
>>>
>>> <Screenshot 2020-07-24 11.52.33.png>
>>>
>>> Kind regards,
>>> Jennifer
>>>
>>>
>>>> On Jul 23, 2020, at 10:43 PM, Carlos Oscar Sorzano 
>>>> <coss at cnb.csic.es <mailto:coss at cnb.csic.es>> wrote:
>>>>
>>>> Dear colleagues,
>>>>
>>>> I uploaded yesterday an ontology file for Cryo Electron Microscopy 
>>>> (http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root). 
>>>> The OWL file was generated with Protege and it does not show any 
>>>> obvious error in Protege. However, when it is read at BioPortal 
>>>> there is some problem because we see the error message "Problem 
>>>> retrieving classes" (see previous link). The file is partly parsed 
>>>> because it shows some metrics, but we must have something wrong 
>>>> with the file. Could you help us with any hint?
>>>>
>>>> Kind regards and thanks, Carlos Oscar
>>>> _______________________________________________
>>>> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200728/15f24a92/attachment.html>