From jgraybeal at stanford.edu  Wed Apr  1 13:35:43 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 1 Apr 2020 20:35:43 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Eoin Vaughan
In-Reply-To: <ca22465b7af44b0b91373dc907290c9b@ubc.ca>
References: <5e8372cbc1b50_305c1e682a456779@ncbo-prd-app-09.stanford.edu.mail>
 <C641A84F-96D4-4FB7-9F42-CD941665ED4B@stanford.edu>
 <ca22465b7af44b0b91373dc907290c9b@ubc.ca>
Message-ID: <A6769A86-0380-4383-B74E-D97BB4381CD9@stanford.edu>

For the list,

Rob Taylor from REDCap provided this information, and said I could relay it.

John

To answer the question, in REDCap v8.4.0 (released two years ago) and higher, REDCap should *always* make calls to data.bioontology.org<http://data.bioontology.org> over SSL. If your REDCap installation doesn?t do this (or if you?re not sure), have your REDCap database person execute the SQL below in the REDCap database to fix it. Note: This will not hurt anything at all either way. Also, if this is not working, then you may need to have your IT folks who manage your REDCap server ensure that the server can make outbound HTTP requests to https://data.bioontology.org, in case that is being prevented by a firewall or something. You shouldn?t have to worry about certificates or anything. Hope that helps.

update redcap_config set value = 'https://data.bioontology.org/' <https://data.bioontology.org/'%20where%20field_name%20=%20'bioportal_api_url'%20and%20value%20=%20'http://data.bioontology.org/> where <https://data.bioontology.org/'%20where%20field_name%20=%20'bioportal_api_url'%20and%20value%20=%20'http://data.bioontology.org/> field_name =<https://data.bioontology.org/'%20where%20field_name%20=%20'bioportal_api_url'%20and%20value%20=%20'http://data.bioontology.org/>'bioportal_api_url' <https://data.bioontology.org/'%20where%20field_name%20=%20'bioportal_api_url'%20and%20value%20=%20'http://data.bioontology.org/> and value <https://data.bioontology.org/'%20where%20field_name%20=%20'bioportal_api_url'%20and%20value%20=%20'http://data.bioontology.org/> = <https://data.bioontology.org/'%20where%20field_name%20=%20'bioportal_api_url'%20and%20value%20=%20'http://data.bioontology.org/> 'http://data.bioontology.org/<https://data.bioontology.org/'%20where%20field_name%20=%20'bioportal_api_url'%20and%20value%20=%20'http://data.bioontology.org/>';


Rob Taylor
REDCap Team Manager and Lead Developer (https://projectredcap.org<https://projectredcap.org/>)
Vanderbilt Institute for Clinical and Translational Research (VICTR)


On Apr 1, 2020, at 9:12 AM, Vaughan, Eoin <eoin.vaughan at ubc.ca<mailto:eoin.vaughan at ubc.ca>> wrote:

Hi John,

Yes that is exactly what I was trying to ask.

I believe that REDCap by default has the cert validation for HTTPS requests option turned off maybe to to prevent errors and loss of functionality, can happen easily from a certificate swap.

I have contacted our IT service and they're looking into it. Thanks again for this information I can at least tell them the actions from your side now.

Thanks,
Eoin.
________________________________
From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: March 31, 2020 10:43:21 PM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Vaughan, Eoin
Subject: Re: [bioontology-support] [BioPortal] Feedback from Eoin Vaughan

Eoin,

I'm going to restate your request a little bit to make sure we're talking about the same thing. You want to be sure that when REDCap is configured to get data from BioPortal, it is able to do so on a connection secured by SSL, so that the content going back and forth is not in plain text and not capable of being intercepted/rewritten. Correct?

The typical scenario for SSL encryption is that the client?your REDCap service?makes the request using https, and the HTTP server on our end provides a certificate to show it can securely manage the encrypted communication. BioPortal doesn't really know anything about that process, but the web server ensures your end-to-end encryption requirement is met, if your client uses the https protocol.

For this to work, however, I believe your IT service will have to ensure that REDCap makes it requests using the https protocol. You will need to contact the REDCap team if REDCap does not support this option.  I will provide some REDCap contacts offline to facilitate this for you.

(I should mention for the record that the service endpoint URLs provided by BioPortal in its API responses are prefixed with http, not https. This does not affect clients' ability to make the same requests using https, but I'm pretty sure it doesn't matter for the REDCap use case.)

John



On Mar 31, 2020, at 9:41 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Eoin Vaughan
Email: eoin.vaughan at ubc.ca<mailto:eoin.vaughan at ubc.ca>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2F

Feedback:
I'm just looking into utilising the "Bioportal Ontology Service" within our departments REDCap instance and I'm in the process of writing up the PIA for this request to our IT service, I was hoping to find out whether the Bioportal Service checks/verifies the SSL certificate like curl does in our API calls for R,Python scripts.
I know they will be wary of the 'man in middle' attack that we may be subject to if not, don't want to assume anything.
Thanks,
Eoin.

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

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

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



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From eoin.vaughan at ubc.ca  Wed Apr  1 09:12:04 2020
From: eoin.vaughan at ubc.ca (Vaughan, Eoin)
Date: Wed, 1 Apr 2020 16:12:04 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Eoin Vaughan
In-Reply-To: <C641A84F-96D4-4FB7-9F42-CD941665ED4B@stanford.edu>
References: <5e8372cbc1b50_305c1e682a456779@ncbo-prd-app-09.stanford.edu.mail>,
 <C641A84F-96D4-4FB7-9F42-CD941665ED4B@stanford.edu>
Message-ID: <ca22465b7af44b0b91373dc907290c9b@ubc.ca>

Hi John,

Yes that is exactly what I was trying to ask.

I believe that REDCap by default has the cert validation for HTTPS requests option turned off maybe to to prevent errors and loss of functionality, can happen easily from a certificate swap.

I have contacted our IT service and they're looking into it. Thanks again for this information I can at least tell them the actions from your side now.

Thanks,
Eoin.
________________________________
From: John Graybeal <jgraybeal at stanford.edu>
Sent: March 31, 2020 10:43:21 PM
To: support at bioontology.org
Cc: Vaughan, Eoin
Subject: Re: [bioontology-support] [BioPortal] Feedback from Eoin Vaughan

Eoin,

I'm going to restate your request a little bit to make sure we're talking about the same thing. You want to be sure that when REDCap is configured to get data from BioPortal, it is able to do so on a connection secured by SSL, so that the content going back and forth is not in plain text and not capable of being intercepted/rewritten. Correct?

The typical scenario for SSL encryption is that the client?your REDCap service?makes the request using https, and the HTTP server on our end provides a certificate to show it can securely manage the encrypted communication. BioPortal doesn't really know anything about that process, but the web server ensures your end-to-end encryption requirement is met, if your client uses the https protocol.

For this to work, however, I believe your IT service will have to ensure that REDCap makes it requests using the https protocol. You will need to contact the REDCap team if REDCap does not support this option.  I will provide some REDCap contacts offline to facilitate this for you.

(I should mention for the record that the service endpoint URLs provided by BioPortal in its API responses are prefixed with http, not https. This does not affect clients' ability to make the same requests using https, but I'm pretty sure it doesn't matter for the REDCap use case.)

John



On Mar 31, 2020, at 9:41 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Eoin Vaughan

Email: eoin.vaughan at ubc.ca<mailto:eoin.vaughan at ubc.ca>

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

Feedback:

I'm just looking into utilising the "Bioportal Ontology Service" within our departments REDCap instance and I'm in the process of writing up the PIA for this request to our IT service, I was hoping to find out whether the Bioportal Service checks/verifies the SSL certificate like curl does in our API calls for R,Python scripts.

I know they will be wary of the 'man in middle' attack that we may be subject to if not, don't want to assume anything.

Thanks,
Eoin.

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

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



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From support at bioontology.org  Wed Apr  1 10:06:12 2020
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 01 Apr 2020 10:06:12 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Joseph Greschner
Message-ID: <5e84ca047498b_1939295e30c5106e@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Wed Apr  1 14:51:51 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 1 Apr 2020 21:51:51 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Joseph Greschner
In-Reply-To: <5e84ca047498b_1939295e30c5106e@ncbo-prd-app-08.stanford.edu.mail>
References: <5e84ca047498b_1939295e30c5106e@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <97077F79-C862-41FD-8B91-315B809744EC@stanford.edu>

Joseph,

You would have to ask the contact person for that ontology. Unfortunately, you don't mention which ontology you found the term in, but the contact informationis provided on the summary page of each ontology. For the SNOMEDCT ontology, for example, the summary page is
   http://bioportal.bioontology.org/ontologies/SNOMEDCT

John

On Apr 1, 2020, at 10:06 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Joseph Greschner

Email: joseph.greschner at ohiohealth.com<mailto:joseph.greschner at ohiohealth.com>

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

Feedback:

In your ontology of trimalleolar fracture, what do the "specialty" percentages next to 'orthopedic surgery' and 'podiatry' indicate?

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

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



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From mrbarnes at uw.edu  Thu Apr  2 12:31:41 2020
From: mrbarnes at uw.edu (Megan R Barnes)
Date: Thu, 2 Apr 2020 19:31:41 +0000
Subject: [bioontology-support] NCBO Annotator VM Question
Message-ID: <A74EC4B7-3C87-40DE-A90D-6115F3BF7F74@uw.edu>

Hello BioPortal Support,

I?m writing with a question about the VMWare Virtual Appliance.  We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API.  I am aware that this is not the same version of the annotator that is running at http://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions.  This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/<https://bioportal.bioontology.org/>.  Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API?

Thanks for your help,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington


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From support at bioontology.org  Thu Apr  2 03:13:45 2020
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 02 Apr 2020 03:13:45 -0700
Subject: [bioontology-support] [BioPortal] Feedback from emicholt
Message-ID: <5e85bad981800_50362002f10276bb@ncbo-prd-app-09.stanford.edu.mail>

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From support at bioontology.org  Fri Apr  3 04:42:05 2020
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 03 Apr 2020 04:42:05 -0700
Subject: [bioontology-support] [BioPortal] Feedback from nrhardiker
Message-ID: <5e87210d109e6_70642545cd487023@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Fri Apr  3 09:31:30 2020
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 03 Apr 2020 09:31:30 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Jonathan Gardner
Message-ID: <5e8764e2d57cd_33712a629ec31562@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Fri Apr  3 11:31:36 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 3 Apr 2020 18:31:36 +0000
Subject: [bioontology-support] NCBO Annotator VM Question
In-Reply-To: <A74EC4B7-3C87-40DE-A90D-6115F3BF7F74@uw.edu>
References: <A74EC4B7-3C87-40DE-A90D-6115F3BF7F74@uw.edu>
Message-ID: <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu>

Megan,

Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame.

Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.)  It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies.

If you send us the example of your two responses, we can look closely at them and give you more specific feedback.

John

On Apr 2, 2020, at 12:31 PM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Hello BioPortal Support,

I?m writing with a question about the VMWare Virtual Appliance.  We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API.  I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions.  This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/<https://bioportal.bioontology.org/>.  Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API?

Thanks for your help,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington


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

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



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From jgraybeal at stanford.edu  Fri Apr  3 11:35:13 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 3 Apr 2020 18:35:13 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jonathan Gardner
In-Reply-To: <5e8764e2d57cd_33712a629ec31562@ncbo-prd-app-08.stanford.edu.mail>
References: <5e8764e2d57cd_33712a629ec31562@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <601F47B8-25F5-4E19-BF7B-1E5985BD3EC1@stanford.edu>

Jonathan,

Our apologies, you are correct that these scripts are not functioning. We have an outstanding ticket on this (https://github.com/ncbo/bioportal_web_ui/issues/79), and expected to fix it before now.

We'll prioritize the task to document/handle the issue on the site soon.

John

On Apr 3, 2020, at 9:31 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jonathan Gardner

Email: jgardner at qualityhealthnd.org<mailto:jgardner at qualityhealthnd.org>

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

Feedback:

The "Form Autocomplete" scripts do not appear to be functioning. I would really like to use this widget on our own web application, but even the demo page doesn't appear to work (nothing happens). Is there something I might be doing wrong? The page URL I'm trying to use is: http://bioportal.bioontology.org/ontologies/CPT/?p=widgets

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

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



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From jgraybeal at stanford.edu  Fri Apr  3 13:06:09 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 3 Apr 2020 20:06:09 +0000
Subject: [bioontology-support] Posting large amounts of text into
	Annotator
In-Reply-To: <CANeC7=ak+H1qEABKjpA-WhnvXOBQLdpRAPTAseKWtgrZVqtFhA@mail.gmail.com>
References: <CANeC7=ak+H1qEABKjpA-WhnvXOBQLdpRAPTAseKWtgrZVqtFhA@mail.gmail.com>
Message-ID: <59963F56-CC54-4366-9E28-120BCCB5A069@stanford.edu>

Vivian,

The Annotator API is what we mean when we say Annotator Web Service.

The HTTP 414 error is a function of HTTP limits on URL size enforced by various services. (See for example http://ncbo-support.2288202.n4.nabble.com/bioontology-support-JAVA-IOException-code-414-URL-too-long-with-get-call-td4652615.html.)

Try using a POST instead of a GET URI. (Reference this previous support message: http://ncbo-support.2288202.n4.nabble.com/bioontology-support-Annotating-large-texts-tp4652649p4652661.html). I'm sorry, I don't think we have explicit examples, but this is a common way of communicating over HTTP, so lots of web documentation.

You reach a practical limit of 60 seconds before a timeout occurs on your request, so especially during busy times you will haeve to keep your request sizes lower. (Limiting the number of ontologies that you request annotation against is another way to minimize the computation time.)

If you have a lot of large pieces of text, you will need to install the virtual appliance (free), or ask us to set up a dedicated server (contact us).

John




On Apr 3, 2020, at 12:05 PM, Vivian Zhu <vivianzhu88 at gmail.com<mailto:vivianzhu88 at gmail.com>> wrote:

Dear Mr. Graybeal,

I was wondering how I could annotate large amounts of text (500 words or more) with the Annotator.

The Annotator website tells me that I can use the Annotator Web Service to annotate large pieces of text. However, when I click the link to the web service, I am redirected to the Annotator API.

The API says that I can post text using "/annotator?text={input text}", but this only works if I input small pieces of text. When I input large pieces of text, I get an HTTP 414 error saying that my URI request is too large. How can I solve this issue?

Thank you!
Vivian

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



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From vivianzhu88 at gmail.com  Fri Apr  3 12:05:53 2020
From: vivianzhu88 at gmail.com (Vivian Zhu)
Date: Fri, 3 Apr 2020 12:05:53 -0700
Subject: [bioontology-support] Posting large amounts of text into Annotator
Message-ID: <CANeC7=ak+H1qEABKjpA-WhnvXOBQLdpRAPTAseKWtgrZVqtFhA@mail.gmail.com>

Dear Mr. Graybeal,

I was wondering how I could annotate large amounts of text (500 words or
more) with the Annotator.

The Annotator website tells me that I can use the Annotator Web Service to
annotate large pieces of text. However, when I click the link to the web
service, I am redirected to the Annotator API.

The API says that I can post text using "/annotator?text={input text}", but
this only works if I input small pieces of text. When I input large pieces
of text, I get an HTTP 414 error saying that my URI request is too large.
How can I solve this issue?

Thank you!
Vivian
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From rakesh at pieriandx.com  Tue Apr  7 13:26:15 2020
From: rakesh at pieriandx.com (Rakesh Nagarajan)
Date: Tue, 7 Apr 2020 15:26:15 -0500
Subject: [bioontology-support] Issue
Message-ID: <CAOaXRCfHP6b64u+mhzm9LgOjER6dSx0aNcfsdW4t9gKxB2+ruw@mail.gmail.com>

Hello,
     For the following URLs:

http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718

http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children

I get the following error:

{
-"errors": [
"Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in
ontology DOID submission 598"
],
"status": 404
}


Can you please fix this?

Thanks,
Rakesh
-- 

*Rakesh Nagarajan*

Founder and Executive Chairman

m: 314-504-5620
e: rakesh at pieriandx.com

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From jgraybeal at stanford.edu  Tue Apr  7 16:56:19 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 7 Apr 2020 23:56:19 +0000
Subject: [bioontology-support] Issue
In-Reply-To: <CAOaXRCfHP6b64u+mhzm9LgOjER6dSx0aNcfsdW4t9gKxB2+ruw@mail.gmail.com>
References: <CAOaXRCfHP6b64u+mhzm9LgOjER6dSx0aNcfsdW4t9gKxB2+ruw@mail.gmail.com>
Message-ID: <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu>

Rakesh,

I'm sorry, I'm unable to duplicate this problem.

When I click on the first URL I get the actual content I'd expect from the API. [1]

When I click on the second URL I get a simple response that suggests there are no children, which matches what BioPortal and OntoBee say.

My only thought is that perhaps there was a brief outage and your browser or application cached the results. Perhaps you can try another browser to see if it has the same behavior?

If you are still having this problem in another browser, please let us know with any additional details you can provide, and we can brainstorm ideas about what might be happening.

John



[1] Content from API for http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718<http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>

{
? "prefLabel": "Warburg micro syndrome 3",
? -"synonym": [
? "Micro Syndrome 3",
? "WARBM3"
],
? -"definition": [
? "A Warburg micro syndrome that has_material_basis_in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the RAB18 gene on chromosome 10p12."
],
? "cui": [ ],
? "semanticType": [ ],
? "obsolete": false,
? "@id": "http://purl.obolibrary.org/obo/DOID_0110718",
? "@type": "http://www.w3.org/2002/07/owl#Class",
? -"links": {
? "self": "http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718",
? "ontology": "http://data.bioontology.org/ontologies/DOID",
? "children": "http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children",

On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:

Hello,
     For the following URLs:

http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718<http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>

http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children

I get the following error:

{
-"errors": [
"Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in ontology DOID submission 598"
],
"status": 404
}


Can you please fix this?

Thanks,
Rakesh
--

Rakesh Nagarajan

Founder and Executive Chairman

m: 314-504-5620
e: rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>

[pierian-logo-trans-light-background]<http://www.pieriandx.com/>   [linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/>  [twitter_circle-512] <https://twitter.com/pieriandx>

Wisdom in Every Report?

CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email.


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

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



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From rakesh at pieriandx.com  Wed Apr  8 06:17:45 2020
From: rakesh at pieriandx.com (Rakesh Nagarajan)
Date: Wed, 8 Apr 2020 08:17:45 -0500
Subject: [bioontology-support] Issue
In-Reply-To: <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu>
References: <CAOaXRCfHP6b64u+mhzm9LgOjER6dSx0aNcfsdW4t9gKxB2+ruw@mail.gmail.com>
 <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu>
Message-ID: <CAOaXRCfkUiOt1z6aa=WJ+Q0J5d1i3wKcp-HAA1Dv=dR2PWmy2A@mail.gmail.com>

Thanks John. I agree it is intermittent but somewhat frequent. I got errors
for the following overnight:

Error in
http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_5503/children
Error in
http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3185/children

When I get such an error I wait 60 seconds and then try again but then exit
when it fails 30 times. So these errors do occur for >30 minutes or so. I
also noticed that this specific ontology has long response times per call.
Any ideas how this can be more robust?

Thanks,
Rakesh



On Tue, Apr 7, 2020 at 6:56 PM John Graybeal <jgraybeal at stanford.edu> wrote:

> Rakesh,
>
> I'm sorry, I'm unable to duplicate this problem.
>
> When I click on the first URL I get the actual content I'd expect from the
> API. [1]
>
> When I click on the second URL I get a simple response that suggests there
> are no children, which matches what BioPortal and OntoBee say.
>
> My only thought is that perhaps there was a brief outage and your browser
> or application cached the results. Perhaps you can try another browser to
> see if it has the same behavior?
>
> If you are still having this problem in another browser, please let us
> know with any additional details you can provide, and we can brainstorm
> ideas about what might be happening.
>
> John
>
>
>
> [1] Content from API for
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
> <http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>
>
> {
> ? "prefLabel": "Warburg micro syndrome 3",
> ? -"synonym": [
> ? "Micro Syndrome 3",
> ? "WARBM3"
> ],
> ? -"definition": [
> ? "A Warburg micro syndrome that has_material_basis_in autosomal recessive
> inheritance of homozygous or compound heterozygous mutation in the RAB18
> gene on chromosome 10p12."
> ],
> ? "cui": [ ],
> ? "semanticType": [ ],
> ? "obsolete": false,
> ? "@id": "http://purl.obolibrary.org/obo/DOID_0110718",
> ? "@type": "http://www.w3.org/2002/07/owl#Class",
> ? -"links": {
> ? "self": "
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
> ",
> ? "ontology": "http://data.bioontology.org/ontologies/DOID",
> ? "children": "
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children
> ",
>
> On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan <rakesh at pieriandx.com> wrote:
>
> Hello,
>      For the following URLs:
>
>
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
> <http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>
>
>
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children
>
> I get the following error:
>
> {
> -"errors": [
> "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in
> ontology DOID submission 598"
> ],
> "status": 404
> }
>
>
> Can you please fix this?
>
> Thanks,
> Rakesh
> --
>
> *Rakesh Nagarajan*
>
> Founder and Executive Chairman
>
> m: 314-504-5620
> e: rakesh at pieriandx.com
>
> [image: pierian-logo-trans-light-background] <http://www.pieriandx.com/>
>  [image: linkedin_circle-512]
> <https://www.linkedin.com/in/rakeshnagarajan/> [image: twitter_circle-512]
> <https://twitter.com/pieriandx>
>
> Wisdom in Every Report?
>
> CONFIDENTIALITY NOTICE: This message and any attachments are solely for
> the use of the intended recipient and may contain privileged, confidential
> or other legally protected information. If you are not the intended
> recipient, please destroy all copies without reading or disclosing their
> contents and notify the sender of the error by reply email.
>
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632  | ORCID  0000-0001-6875-5360
>
>
>
>

-- 

*Rakesh Nagarajan*

Founder and Executive Chairman

m: 314-504-5620
e: rakesh at pieriandx.com

[image: pierian-logo-trans-light-background]
<http://www.pieriandx.com/>   [image:
linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/> [image:
twitter_circle-512] <https://twitter.com/pieriandx>

Wisdom in Every Report?

CONFIDENTIALITY NOTICE: This message and any attachments are solely for the
use of the intended recipient and may contain privileged, confidential or
other legally protected information. If you are not the intended recipient,
please destroy all copies without reading or disclosing their contents and
notify the sender of the error by reply email.
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From rakesh at pieriandx.com  Wed Apr  8 06:50:02 2020
From: rakesh at pieriandx.com (Rakesh Nagarajan)
Date: Wed, 8 Apr 2020 08:50:02 -0500
Subject: [bioontology-support] Issue
In-Reply-To: <CAOaXRCfkUiOt1z6aa=WJ+Q0J5d1i3wKcp-HAA1Dv=dR2PWmy2A@mail.gmail.com>
References: <CAOaXRCfHP6b64u+mhzm9LgOjER6dSx0aNcfsdW4t9gKxB2+ruw@mail.gmail.com>
 <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu>
 <CAOaXRCfkUiOt1z6aa=WJ+Q0J5d1i3wKcp-HAA1Dv=dR2PWmy2A@mail.gmail.com>
Message-ID: <CAOaXRCeCyNWOBBcu3utM+-Ko-1pr6sUDO5=V+qh8_4kxGSZ_Nw@mail.gmail.com>

John,
     May I also request access to the virtual appliance as I can cache some
ontologies (e.g. HPO, NCIT, SNOMED-CT, MeSH, and Disease Ontology) that we
frequently refresh and perhaps wouldn't run into these errors where we're
hitting your instance?

Thanks,
Rakesh

On Wed, Apr 8, 2020 at 8:17 AM Rakesh Nagarajan <rakesh at pieriandx.com>
wrote:

> Thanks John. I agree it is intermittent but somewhat frequent. I got
> errors for the following overnight:
>
> Error in
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_5503/children
> Error in
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3185/children
>
> When I get such an error I wait 60 seconds and then try again but then
> exit when it fails 30 times. So these errors do occur for >30 minutes or
> so. I also noticed that this specific ontology has long response times per
> call. Any ideas how this can be more robust?
>
> Thanks,
> Rakesh
>
>
>
> On Tue, Apr 7, 2020 at 6:56 PM John Graybeal <jgraybeal at stanford.edu>
> wrote:
>
>> Rakesh,
>>
>> I'm sorry, I'm unable to duplicate this problem.
>>
>> When I click on the first URL I get the actual content I'd expect from
>> the API. [1]
>>
>> When I click on the second URL I get a simple response that suggests
>> there are no children, which matches what BioPortal and OntoBee say.
>>
>> My only thought is that perhaps there was a brief outage and your browser
>> or application cached the results. Perhaps you can try another browser to
>> see if it has the same behavior?
>>
>> If you are still having this problem in another browser, please let us
>> know with any additional details you can provide, and we can brainstorm
>> ideas about what might be happening.
>>
>> John
>>
>>
>>
>> [1] Content from API for
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
>> <http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>
>>
>> {
>> ? "prefLabel": "Warburg micro syndrome 3",
>> ? -"synonym": [
>> ? "Micro Syndrome 3",
>> ? "WARBM3"
>> ],
>> ? -"definition": [
>> ? "A Warburg micro syndrome that has_material_basis_in autosomal
>> recessive inheritance of homozygous or compound heterozygous mutation in
>> the RAB18 gene on chromosome 10p12."
>> ],
>> ? "cui": [ ],
>> ? "semanticType": [ ],
>> ? "obsolete": false,
>> ? "@id": "http://purl.obolibrary.org/obo/DOID_0110718",
>> ? "@type": "http://www.w3.org/2002/07/owl#Class",
>> ? -"links": {
>> ? "self": "
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
>> ",
>> ? "ontology": "http://data.bioontology.org/ontologies/DOID",
>> ? "children": "
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children
>> ",
>>
>> On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan <rakesh at pieriandx.com>
>> wrote:
>>
>> Hello,
>>      For the following URLs:
>>
>>
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
>> <http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>
>>
>>
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children
>>
>> I get the following error:
>>
>> {
>> -"errors": [
>> "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in
>> ontology DOID submission 598"
>> ],
>> "status": 404
>> }
>>
>>
>> Can you please fix this?
>>
>> Thanks,
>> Rakesh
>> --
>>
>> *Rakesh Nagarajan*
>>
>> Founder and Executive Chairman
>>
>> m: 314-504-5620
>> e: rakesh at pieriandx.com
>>
>> [image: pierian-logo-trans-light-background] <http://www.pieriandx.com/>
>>    [image: linkedin_circle-512]
>> <https://www.linkedin.com/in/rakeshnagarajan/> [image:
>> twitter_circle-512] <https://twitter.com/pieriandx>
>>
>> Wisdom in Every Report?
>>
>> CONFIDENTIALITY NOTICE: This message and any attachments are solely for
>> the use of the intended recipient and may contain privileged, confidential
>> or other legally protected information. If you are not the intended
>> recipient, please destroy all copies without reading or disclosing their
>> contents and notify the sender of the error by reply email.
>>
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>> 650-736-1632  | ORCID  0000-0001-6875-5360
>>
>>
>>
>>
>
> --
>
> *Rakesh Nagarajan*
>
> Founder and Executive Chairman
>
> m: 314-504-5620
> e: rakesh at pieriandx.com
>
> [image: pierian-logo-trans-light-background] <http://www.pieriandx.com/>
>  [image: linkedin_circle-512]
> <https://www.linkedin.com/in/rakeshnagarajan/> [image: twitter_circle-512]
> <https://twitter.com/pieriandx>
>
> Wisdom in Every Report?
>
> CONFIDENTIALITY NOTICE: This message and any attachments are solely for
> the use of the intended recipient and may contain privileged, confidential
> or other legally protected information. If you are not the intended
> recipient, please destroy all copies without reading or disclosing their
> contents and notify the sender of the error by reply email.
>
>
>
>

-- 

*Rakesh Nagarajan*

Founder and Executive Chairman

m: 314-504-5620
e: rakesh at pieriandx.com

[image: pierian-logo-trans-light-background]
<http://www.pieriandx.com/>   [image:
linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/> [image:
twitter_circle-512] <https://twitter.com/pieriandx>

Wisdom in Every Report?

CONFIDENTIALITY NOTICE: This message and any attachments are solely for the
use of the intended recipient and may contain privileged, confidential or
other legally protected information. If you are not the intended recipient,
please destroy all copies without reading or disclosing their contents and
notify the sender of the error by reply email.
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From mrbarnes at uw.edu  Wed Apr  8 07:16:45 2020
From: mrbarnes at uw.edu (Megan R Barnes)
Date: Wed, 8 Apr 2020 14:16:45 +0000
Subject: [bioontology-support] FW:  NCBO Annotator VM Question
In-Reply-To: <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu>
References: <A74EC4B7-3C87-40DE-A90D-6115F3BF7F74@uw.edu>
 <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu>
 <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu>
Message-ID: <81156C25-4423-401A-A712-0B3E2D773404@uw.edu>

Forwarding this message to the support channel, as I realize I forgot to include it in my reply.

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: Megan R Barnes <mrbarnes at uw.edu>
Date: Friday, April 3, 2020 at 2:04 PM
To: John Graybeal <jgraybeal at stanford.edu>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Hi John,

Thanks for your help.  As an example, we are looking to reproduce the NCIT annotations that we get from BioPortal, in the API request:

http://data.bioontology.org/annotator?text=surrounding+end+of+life+care

with params: {"longest_only": "false", "exclude_numbers": "true", "exclude_synonyms": "false", "whole_word_only": "true"}

The annotations we get back that come from NCIT are:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 28, 'matchType': 'SYN', 'text': 'END OF LIFE CARE'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'SYN', 'text': 'LIFE'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

However, when we run the same request on our VM, using the newest version of NCIT (released 3/31/2020 on BioPortal), we get:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

I will attach full responses from each, as well.  Let me know if there?s more info I can provide.

Thanks,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: John Graybeal <jgraybeal at stanford.edu>
Date: Friday, April 3, 2020 at 11:32 AM
To: Megan R Barnes <mrbarnes at uw.edu>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Megan,

Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame.

Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.)  It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies.

If you send us the example of your two responses, we can look closely at them and give you more specific feedback.

John



On Apr 2, 2020, at 12:31 PM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Hello BioPortal Support,

I?m writing with a question about the VMWare Virtual Appliance.  We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API.  I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions.  This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/<https://bioportal.bioontology.org/>.  Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API?

Thanks for your help,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington


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

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



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From Philip.Whalen at RoswellPark.org  Wed Apr  8 08:52:13 2020
From: Philip.Whalen at RoswellPark.org (Whalen, Philip)
Date: Wed, 8 Apr 2020 15:52:13 +0000
Subject: [bioontology-support] NCIT API key
Message-ID: <C2586D5F-9C79-4374-935D-96382AD01EEC@roswellpark.org>

Hello,

I?ve been working with the NCIT for some time now and was just looking into utilizing the API that is provided. However, I don?t see anywhere to request an API key for this service. Would you be able to point me to where I may request one?

Thank you!

Philip Whalen, MA
Business Systems Analyst, Biomedical Data Science Shared Resource
Roswell Park Cancer Institute
Elm and Carlton Streets
Buffalo, NY 14263
Ext. 7197


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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From jgraybeal at stanford.edu  Wed Apr  8 10:55:49 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 8 Apr 2020 17:55:49 +0000
Subject: [bioontology-support] NCIT API key
In-Reply-To: <C2586D5F-9C79-4374-935D-96382AD01EEC@roswellpark.org>
References: <C2586D5F-9C79-4374-935D-96382AD01EEC@roswellpark.org>
Message-ID: <942A2A88-1D50-4A0A-8468-E18AB7ABABDA@stanford.edu>

Philip,

Information on how to get and see your API key is at https://bioportal.bioontology.org/help#Getting_an_API_key.

John

On Apr 8, 2020, at 8:52 AM, Whalen, Philip <Philip.Whalen at RoswellPark.org<mailto:Philip.Whalen at RoswellPark.org>> wrote:

Hello,

I?ve been working with the NCIT for some time now and was just looking into utilizing the API that is provided. However, I don?t see anywhere to request an API key for this service. Would you be able to point me to where I may request one?

Thank you!

Philip Whalen, MA
Business Systems Analyst, Biomedical Data Science Shared Resource
Roswell Park Cancer Institute
Elm and Carlton Streets
Buffalo, NY 14263
Ext. 7197

This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. _______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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



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From jgraybeal at stanford.edu  Wed Apr  8 11:13:01 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 8 Apr 2020 18:13:01 +0000
Subject: [bioontology-support] NCBO Annotator VM Question
In-Reply-To: <81156C25-4423-401A-A712-0B3E2D773404@uw.edu>
References: <A74EC4B7-3C87-40DE-A90D-6115F3BF7F74@uw.edu>
 <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu>
 <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu>
 <81156C25-4423-401A-A712-0B3E2D773404@uw.edu>
Message-ID: <95363F1A-9718-46CF-A3C3-E169F04AFC9D@stanford.edu>

Thanks Megan.

I saw your earlier email and started to work on it before getting pulled away, so this reminder is a good thing.

The only difference between the two responses is that the first, from BioPortal, includes the synonyms, which should be excluded according to the fragment you sent.

When I add "&exclude_synonyms=true" to the API string you sent, I find that BioPortal in fact excludes synonyms from the mappings.

If you can send us the actual API request string that you use, we can troubleshoot this further to see what could be causing synonyms to be incorrectly included.

John



On Apr 8, 2020, at 7:16 AM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Forwarding this message to the support channel, as I realize I forgot to include it in my reply.

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Date: Friday, April 3, 2020 at 2:04 PM
To: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Hi John,

Thanks for your help.  As an example, we are looking to reproduce the NCIT annotations that we get from BioPortal, in the API request:

http://data.bioontology.org/annotator?text=surrounding+end+of+life+care

with params: {"longest_only": "false", "exclude_numbers": "true", "exclude_synonyms": "false", "whole_word_only": "true"}

The annotations we get back that come from NCIT are:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 28, 'matchType': 'SYN', 'text': 'END OF LIFE CARE'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'SYN', 'text': 'LIFE'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

However, when we run the same request on our VM, using the newest version of NCIT (released 3/31/2020 on BioPortal), we get:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

I will attach full responses from each, as well.  Let me know if there?s more info I can provide.

Thanks,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Friday, April 3, 2020 at 11:32 AM
To: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Megan,

Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame.

Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.)  It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies.

If you send us the example of your two responses, we can look closely at them and give you more specific feedback.

John



On Apr 2, 2020, at 12:31 PM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Hello BioPortal Support,

I?m writing with a question about the VMWare Virtual Appliance.  We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API.  I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions.  This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/<https://bioportal.bioontology.org/>.  Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API?

Thanks for your help,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington


_______________________________________________
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



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

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



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From p.vandamme at amsterdamumc.nl  Thu Apr  9 02:35:46 2020
From: p.vandamme at amsterdamumc.nl (Damme, P. van (Philip))
Date: Thu, 9 Apr 2020 09:35:46 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Philip van Damme
In-Reply-To: <EB6F0FDE-488C-40F5-B9BE-DF308CD14DCE@stanford.edu>
References: <5e6910a5ebd82_2b0221a26cc130b6@ncbo-prd-app-09.stanford.edu.mail>
 <EB6F0FDE-488C-40F5-B9BE-DF308CD14DCE@stanford.edu>
Message-ID: <09AFCD82-DF5A-495D-94AD-6A3C05D856EF@amsterdamumc.nl>

Dear Michael, others,

Thank you for your quick response back on the 12th of March, I appreciate it. First and foremost I hope you?re all doing well under the current circumstances.

I stumbled upon something what seems like a discrepancy between the mappings returned by the API calling "/ontologies/:ontology/classes/:cls/mappings? and "/mappings?ontologies=ONT1,ONT2?. When I try to get mappings between a pair of ontologies involving SNOMED CT, I get different results.

For example, I want to check if this mappings exists in BioPortal: http://www.orpha.net/ORDO/Orphanet_3389 = http://purl.bioontology.org/ontology/SNOMEDCT/56717001. I can use the API calling
http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings<http://data.bioontology.org/ontologies/ORDO/classes/http://www.orpha.net/ORDO/Orphanet_3389/mappings>
or http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT and check if the mapping exists. However, when I compare the returned set from the API calls above with https://bioportal.bioontology.org/ontologies/ORDO?p=classes&conceptid=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389#mappings<https://bioportal.bioontology.org/ontologies/ORDO?p=classes&conceptid=http://www.orpha.net/ORDO/Orphanet_3389#mappings> I noticed the following:

  *   The mapping exists according to the class mappings on the webpage, referring to URI http://purl.bioontology.org/ontology/SNOMEDCT/56717001 and SNOMEDCT.
  *   The mapping exists according to http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings<http://data.bioontology.org/ontologies/ORDO/classes/http://www.orpha.net/ORDO/Orphanet_3389/mappings>, however, using different URI (http://snomed.info/id/56717001) and referring to ontology SNO_COPY which is not accessible.
  *   The mappings doesn?t exist according to http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT.

I decided to only use mappings from http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT, but that still makes me wonder why the webpage shows SNOMED CT mappings that are not returned by the API in the same way (point 1 vs. point 2). Am I missing something? I checked http://data.bioontology.org/mappings?ontologies=ORDO,SNO_COPY, which is returning an empty set.

I was hoping that you could help me to clarify this. Thank you in advance! Please know that you have my full understanding if it?s not possible to answer my email due to the coronavirus.

Best, Philip


On 12 Mar 2020, at 20:17, Michael Vladimir Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Philip,

Thank you for alerting us to this issue. We?ve had an operational outage yesterday that triggered a full rebuild of our Annotator/Recommender database. The services have now been fully restored. Please try your API calls again and let us know if you run into any further issues.

Thank you so much for your patience.

Sincerely,


----------------------------------------------------
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 Mar 11, 2020, at 9:24 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Philip van Damme

Email: p.vandamme at amsterdamumc.nl<mailto:p.vandamme at amsterdamumc.nl>

Location: https%3A%2F%2Fbioportal.bioontology.org<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C2977fdfb8a004034522f08d7c6ba13ad%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637196374813659646&sdata=0dqxew7XxnNSxfvcIMBVzEnuDYKKjuhJfGo85dwOGrc%3D&reserved=0>%2F

Feedback:

Both the annotator and the recommender don't return any results. A few hours ago the website had some brief downtime and did not accept API-calls.

_______________________________________________
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


______________________________________________________
VUmc disclaimer : www.vumc.nl/disclaimer
AMC disclaimer : www.amc.nl/disclaimer
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From support at bioontology.org  Fri Apr 10 08:53:12 2020
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 10 Apr 2020 08:53:12 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Jean
Message-ID: <5e9096681c90e_34362a24868954d@ncbo-prd-app-09.stanford.edu.mail>

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From jgraybeal at stanford.edu  Fri Apr 10 16:00:08 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 10 Apr 2020 23:00:08 +0000
Subject: [bioontology-support] BioPortal maintenance this weekend;
	minimal impact planned
Message-ID: <1450E9EE-141B-4334-AA3E-41EE3EE31A3D@stanford.edu>

Hello everyone,

This Saturday evening at 21:00 (GMT-7), we'll begin a maintenance upgrade activity on BioPortal which we hope will be almost transparent, with perhaps a brief interrupt in service.

If there are problems, which we think highly unlikely, we need to reserve the next day for possible corrections.

On Tuesday evening we'll be performing another maintenance upgrade, which is not expected to require any downtime or service interruptions.

For more about why we're performing these barely-visible upgrades, visit https://www.bioontology.org/non-breaking-news-changes-coming-to-bioportal/.

Some interesting things are coming to BioPortal. We look forward to sharing more about those soon.

John

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



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From jgraybeal at stanford.edu  Fri Apr 10 16:08:48 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 10 Apr 2020 23:08:48 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jean
In-Reply-To: <5e9096681c90e_34362a24868954d@ncbo-prd-app-09.stanford.edu.mail>
References: <5e9096681c90e_34362a24868954d@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <5B2E23F3-61C1-465C-BE99-3BAEE1D63D2C@stanford.edu>

Jean,

I confess I am uncertain about what might is causing this, but I can ask some useful questions that will help our team troubleshoot more next week.

The clearest picture would be to see the logs corresponding to those requests, ideally from the Apache or similar logs. The requests from your NiFi flow almost certainly will look different in some way.

Is it possible there are two ontologies that look almost the same, and the flow is asking for the second ontology which only has one submission?  Or alternatively, there are two Bioportal instances and the Apache flow is accessing an instance with only one submission for that ontology?

The more concrete details you can provide, the better our chance of coming up with useful suggestions.

John

On Apr 10, 2020, at 8:53 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jean

Email: jean.travassos-ext at glpg.com<mailto:jean.travassos-ext at glpg.com>

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

Feedback:

Hello, I'm facing a problem while using BioPortal API and was wondering if you can get me some clarification.

I have BP installed in one server for dev purposes and while I use the URL to GET all children of the master node of our Ontology, it works well (testing in Postman or Firefox or curl).

However, our Ontology has 3 submissions. When another application (an Apache NiFi flow) makes the http GET request with exactly the same URL, in returns only data from the FIRST submission. It should return the data of the latest submission, of course.

Can you get any direction? Is there any parameter or something like that I should configure to prevent this to happen?

Thank you for your attention.
Best regards

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

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



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From jgraybeal at stanford.edu  Fri Apr 10 16:10:35 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 10 Apr 2020 23:10:35 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Philip van Damme
In-Reply-To: <09AFCD82-DF5A-495D-94AD-6A3C05D856EF@amsterdamumc.nl>
References: <5e6910a5ebd82_2b0221a26cc130b6@ncbo-prd-app-09.stanford.edu.mail>
 <EB6F0FDE-488C-40F5-B9BE-DF308CD14DCE@stanford.edu>
 <09AFCD82-DF5A-495D-94AD-6A3C05D856EF@amsterdamumc.nl>
Message-ID: <8F031C33-78D2-4849-92F9-567D04E752D7@stanford.edu>

Philip,

Thanks for your understanding, and your detailed query! I know we will not be able to dig into it this week, as it is not a trivial situation. We should have a chance to revisit this next week?please ping me if you haven't heard anything by late in the week.

John

On Apr 9, 2020, at 2:35 AM, Damme, P. van (Philip) <p.vandamme at amsterdamumc.nl<mailto:p.vandamme at amsterdamumc.nl>> wrote:

Dear Michael, others,

Thank you for your quick response back on the 12th of March, I appreciate it. First and foremost I hope you?re all doing well under the current circumstances.

I stumbled upon something what seems like a discrepancy between the mappings returned by the API calling "/ontologies/:ontology/classes/:cls/mappings? and "/mappings?ontologies=ONT1,ONT2?. When I try to get mappings between a pair of ontologies involving SNOMED CT, I get different results.

For example, I want to check if this mappings exists in BioPortal: http://www.orpha.net/ORDO/Orphanet_3389 = http://purl.bioontology.org/ontology/SNOMEDCT/56717001. I can use the API calling
http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings<http://data.bioontology.org/ontologies/ORDO/classes/http://www.orpha.net/ORDO/Orphanet_3389/mappings>
or http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT and check if the mapping exists. However, when I compare the returned set from the API calls above with https://bioportal.bioontology.org/ontologies/ORDO?p=classes&conceptid=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389#mappings<https://bioportal.bioontology.org/ontologies/ORDO?p=classes&conceptid=http://www.orpha.net/ORDO/Orphanet_3389#mappings> I noticed the following:

  *   The mapping exists according to the class mappings on the webpage, referring to URI http://purl.bioontology.org/ontology/SNOMEDCT/56717001 and SNOMEDCT.
  *   The mapping exists according to http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings<http://data.bioontology.org/ontologies/ORDO/classes/http://www.orpha.net/ORDO/Orphanet_3389/mappings>, however, using different URI (http://snomed.info/id/56717001) and referring to ontology SNO_COPY which is not accessible.
  *   The mappings doesn?t exist according to http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT.

I decided to only use mappings from http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT, but that still makes me wonder why the webpage shows SNOMED CT mappings that are not returned by the API in the same way (point 1 vs. point 2). Am I missing something? I checked http://data.bioontology.org/mappings?ontologies=ORDO,SNO_COPY, which is returning an empty set.

I was hoping that you could help me to clarify this. Thank you in advance! Please know that you have my full understanding if it?s not possible to answer my email due to the coronavirus.

Best, Philip


On 12 Mar 2020, at 20:17, Michael Vladimir Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Philip,

Thank you for alerting us to this issue. We?ve had an operational outage yesterday that triggered a full rebuild of our Annotator/Recommender database. The services have now been fully restored. Please try your API calls again and let us know if you run into any further issues.

Thank you so much for your patience.

Sincerely,


----------------------------------------------------
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 Mar 11, 2020, at 9:24 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Philip van Damme

Email: p.vandamme at amsterdamumc.nl<mailto:p.vandamme at amsterdamumc.nl>

Location: https%3A%2F%2Fbioportal.bioontology.org<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C2977fdfb8a004034522f08d7c6ba13ad%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637196374813659646&sdata=0dqxew7XxnNSxfvcIMBVzEnuDYKKjuhJfGo85dwOGrc%3D&reserved=0>%2F

Feedback:

Both the annotator and the recommender don't return any results. A few hours ago the website had some brief downtime and did not accept API-calls.

_______________________________________________
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


______________________________________________________
VUmc disclaimer : www.vumc.nl/disclaimer<http://www.vumc.nl/disclaimer>
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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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From jgraybeal at stanford.edu  Fri Apr 10 16:17:20 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 10 Apr 2020 23:17:20 +0000
Subject: [bioontology-support] Issue
In-Reply-To: <CAOaXRCfkUiOt1z6aa=WJ+Q0J5d1i3wKcp-HAA1Dv=dR2PWmy2A@mail.gmail.com>
References: <CAOaXRCfHP6b64u+mhzm9LgOjER6dSx0aNcfsdW4t9gKxB2+ruw@mail.gmail.com>
 <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu>
 <CAOaXRCfkUiOt1z6aa=WJ+Q0J5d1i3wKcp-HAA1Dv=dR2PWmy2A@mail.gmail.com>
Message-ID: <345E1AFC-3525-4DEA-8C69-585D7876BBC6@stanford.edu>

Rakesh,

Belatedly, we've thought about these behaviors and none of us could put our finger on what is causing your problem.

It is the case that there is a timeout on API requests, I believe it is 60 seconds. So if a request is making a complex query, it might be taking too long during period of heavy use.  The longer response times for this ontology suggest complexity that might be slowing things down.

Sometimes when BioPortal gets a bad response from the backend store, it can get cached for an extended period. If you're able to check in real time when an error occurs, you could see if the browser gets the same error; and if other calls are getting the same error. Unfortunately our browser caches for as long as 2 hours, so that is not totally satisfying to know that. (Perhaps you could try making a different query that asks for more than just children, so that any cached results wouldn't affect the variant query.)

We would be happy to take this offline if it remains a significant issue for you.

John

On Apr 8, 2020, at 6:17 AM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:

Thanks John. I agree it is intermittent but somewhat frequent. I got errors for the following overnight:

Error in http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_5503/children
Error in http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3185/children

When I get such an error I wait 60 seconds and then try again but then exit when it fails 30 times. So these errors do occur for >30 minutes or so. I also noticed that this specific ontology has long response times per call. Any ideas how this can be more robust?

Thanks,
Rakesh



On Tue, Apr 7, 2020 at 6:56 PM John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:
Rakesh,

I'm sorry, I'm unable to duplicate this problem.

When I click on the first URL I get the actual content I'd expect from the API. [1]

When I click on the second URL I get a simple response that suggests there are no children, which matches what BioPortal and OntoBee say.

My only thought is that perhaps there was a brief outage and your browser or application cached the results. Perhaps you can try another browser to see if it has the same behavior?

If you are still having this problem in another browser, please let us know with any additional details you can provide, and we can brainstorm ideas about what might be happening.

John



[1] Content from API for http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718<http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>

{
? "prefLabel": "Warburg micro syndrome 3",
? -"synonym": [
? "Micro Syndrome 3",
? "WARBM3"
],
? -"definition": [
? "A Warburg micro syndrome that has_material_basis_in autosomal recessive inheritance of homozygous or compound heterozygous mutation in the RAB18 gene on chromosome 10p12."
],
? "cui": [ ],
? "semanticType": [ ],
? "obsolete": false,
? "@id": "http://purl.obolibrary.org/obo/DOID_0110718",
? "@type": "http://www.w3.org/2002/07/owl#Class",
? -"links": {
? "self": "http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718",
? "ontology": "http://data.bioontology.org/ontologies/DOID",
? "children": "http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children",

On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan <rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>> wrote:

Hello,
     For the following URLs:

http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718<http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>

http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children

I get the following error:

{
-"errors": [
"Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in ontology DOID submission 598"
],
"status": 404
}


Can you please fix this?

Thanks,
Rakesh
--

Rakesh Nagarajan

Founder and Executive Chairman

m: 314-504-5620
e: rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>

[pierian-logo-trans-light-background]<http://www.pieriandx.com/>   [linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/>  [twitter_circle-512] <https://twitter.com/pieriandx>

Wisdom in Every Report?

CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email.


_______________________________________________
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





--

Rakesh Nagarajan

Founder and Executive Chairman

m: 314-504-5620
e: rakesh at pieriandx.com<mailto:rakesh at pieriandx.com>

[pierian-logo-trans-light-background]<http://www.pieriandx.com/>   [linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/>  [twitter_circle-512] <https://twitter.com/pieriandx>

Wisdom in Every Report?

CONFIDENTIALITY NOTICE: This message and any attachments are solely for the use of the intended recipient and may contain privileged, confidential or other legally protected information. If you are not the intended recipient, please destroy all copies without reading or disclosing their contents and notify the sender of the error by reply email.



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



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From chinghua at us.ibm.com  Sun Apr 12 13:41:08 2020
From: chinghua at us.ibm.com (Ching-Hua Chen)
Date: Sun, 12 Apr 2020 20:41:08 +0000
Subject: [bioontology-support] API key on Virtual Appliance
Message-ID: <OFBF162ECC.87DC94AD-ON00258548.0071470F-00258548.0071A12C@notes.na.collabserv.com>

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From jgraybeal at stanford.edu  Sun Apr 12 18:43:46 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 13 Apr 2020 01:43:46 +0000
Subject: [bioontology-support] API key on Virtual Appliance
In-Reply-To: <OFBF162ECC.87DC94AD-ON00258548.0071470F-00258548.0071A12C@notes.na.collabserv.com>
References: <OFBF162ECC.87DC94AD-ON00258548.0071470F-00258548.0071A12C@notes.na.collabserv.com>
Message-ID: <FC0897AC-31DE-4D00-B40E-C3DB65B1EBDB@stanford.edu>

Ching-Hua Chen,

Thanks for this question. No, your APIkey for your Virtual Appliance installation is not supposed to be the same one you use to access the BIoPortal.

To access your Virtual Appliance via the API, you will need to get an account on *that* Virtual Appliance. This will create a unique API key for you for that Appliance.

Whoever installed the Virtual Appliance for you should be able to give you the address at which you can access the Virtual Appliance. Once logged in, you can visit the Drop-down menu with your user name on it to see Account Settings, or visit the URL https://{ip_address_of_application/account.  You will see your API key on that page.

John

On Apr 12, 2020, at 1:41 PM, Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> wrote:

Hi,

Is the APIkey on the virtual appliance supposed to be the same one used in the bioportal?

One of my admins installed the virtual appliance for me, and didn't give me a key... Wondering if I should be asking my admin for it?

I tried going to http://{ip_address_of_appliance}<http://{ip_address_of_appliance}/>/account in my browser but this doesn't seem to work.


Thanks,

Ching-Hua Chen

Computational Health Behavior & Decision Science
IBM, T.J. Watson Research Center
1101 Kitchawan Road, Yorktown Heights, NY 10598

chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>
(914) 945-2061 (o); (845) 519-7582 (m)

"Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson

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

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



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From rakesh at pieriandx.com  Mon Apr 13 14:03:31 2020
From: rakesh at pieriandx.com (Rakesh Nagarajan)
Date: Mon, 13 Apr 2020 16:03:31 -0500
Subject: [bioontology-support] Issue
In-Reply-To: <345E1AFC-3525-4DEA-8C69-585D7876BBC6@stanford.edu>
References: <CAOaXRCfHP6b64u+mhzm9LgOjER6dSx0aNcfsdW4t9gKxB2+ruw@mail.gmail.com>
 <3CC75D34-13BB-4050-B739-A18DF1CB022B@stanford.edu>
 <CAOaXRCfkUiOt1z6aa=WJ+Q0J5d1i3wKcp-HAA1Dv=dR2PWmy2A@mail.gmail.com>
 <345E1AFC-3525-4DEA-8C69-585D7876BBC6@stanford.edu>
Message-ID: <CAOaXRCdK+e+mpD29uW17gijK7o0OKDy97NSX8aGz6KpWMYJYiw@mail.gmail.com>

John,
     Let's discuss offline if you can, say by phone. I am simply trying to
get information about a node and then recursing through children to leaf to
get their information. To determine children for a part (one root node
only- e.g. "Drug, Food, Chemical, or Biomedical Material") of an ontology
like NCIT using the API is now taking more than 5 days when it used to
complete in about 1 day. Did something materially change to reduce the
performance of the API?

Thanks,
Rakesh

On Fri, Apr 10, 2020 at 6:17 PM John Graybeal <jgraybeal at stanford.edu>
wrote:

> Rakesh,
>
> Belatedly, we've thought about these behaviors and none of us could put
> our finger on what is causing your problem.
>
> It is the case that there is a timeout on API requests, I believe it is 60
> seconds. So if a request is making a complex query, it might be taking too
> long during period of heavy use.  The longer response times for this
> ontology suggest complexity that might be slowing things down.
>
> Sometimes when BioPortal gets a bad response from the backend store, it
> can get cached for an extended period. If you're able to check in real time
> when an error occurs, you could see if the browser gets the same error; and
> if other calls are getting the same error. Unfortunately our browser caches
> for as long as 2 hours, so that is not totally satisfying to know that.
> (Perhaps you could try making a different query that asks for more than
> just children, so that any cached results wouldn't affect the variant
> query.)
>
> We would be happy to take this offline if it remains a significant issue
> for you.
>
> John
>
> On Apr 8, 2020, at 6:17 AM, Rakesh Nagarajan <rakesh at pieriandx.com> wrote:
>
> Thanks John. I agree it is intermittent but somewhat frequent. I got
> errors for the following overnight:
>
> Error in
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_5503/children
> Error in
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3185/children
>
> When I get such an error I wait 60 seconds and then try again but then
> exit when it fails 30 times. So these errors do occur for >30 minutes or
> so. I also noticed that this specific ontology has long response times per
> call. Any ideas how this can be more robust?
>
> Thanks,
> Rakesh
>
>
>
> On Tue, Apr 7, 2020 at 6:56 PM John Graybeal <jgraybeal at stanford.edu>
> wrote:
>
>> Rakesh,
>>
>> I'm sorry, I'm unable to duplicate this problem.
>>
>> When I click on the first URL I get the actual content I'd expect from
>> the API. [1]
>>
>> When I click on the second URL I get a simple response that suggests
>> there are no children, which matches what BioPortal and OntoBee say.
>>
>> My only thought is that perhaps there was a brief outage and your browser
>> or application cached the results. Perhaps you can try another browser to
>> see if it has the same behavior?
>>
>> If you are still having this problem in another browser, please let us
>> know with any additional details you can provide, and we can brainstorm
>> ideas about what might be happening.
>>
>> John
>>
>>
>>
>> [1] Content from API for
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
>> <http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>
>>
>> {
>> ? "prefLabel": "Warburg micro syndrome 3",
>> ? -"synonym": [
>> ? "Micro Syndrome 3",
>> ? "WARBM3"
>> ],
>> ? -"definition": [
>> ? "A Warburg micro syndrome that has_material_basis_in autosomal
>> recessive inheritance of homozygous or compound heterozygous mutation in
>> the RAB18 gene on chromosome 10p12."
>> ],
>> ? "cui": [ ],
>> ? "semanticType": [ ],
>> ? "obsolete": false,
>> ? "@id": "http://purl.obolibrary.org/obo/DOID_0110718",
>> ? "@type": "http://www.w3.org/2002/07/owl#Class",
>> ? -"links": {
>> ? "self": "
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
>> ",
>> ? "ontology": "http://data.bioontology.org/ontologies/DOID",
>> ? "children": "
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children
>> ",
>>
>> On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan <rakesh at pieriandx.com>
>> wrote:
>>
>> Hello,
>>      For the following URLs:
>>
>>
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
>> <http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>
>>
>>
>> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children
>>
>> I get the following error:
>>
>> {
>> -"errors": [
>> "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in
>> ontology DOID submission 598"
>> ],
>> "status": 404
>> }
>>
>>
>> Can you please fix this?
>>
>> Thanks,
>> Rakesh
>> --
>>
>> *Rakesh Nagarajan*
>>
>> Founder and Executive Chairman
>>
>> m: 314-504-5620
>> e: rakesh at pieriandx.com
>>
>> [image: pierian-logo-trans-light-background] <http://www.pieriandx.com/>
>>    [image: linkedin_circle-512]
>> <https://www.linkedin.com/in/rakeshnagarajan/> [image:
>> twitter_circle-512] <https://twitter.com/pieriandx>
>>
>> Wisdom in Every Report?
>>
>> CONFIDENTIALITY NOTICE: This message and any attachments are solely for
>> the use of the intended recipient and may contain privileged, confidential
>> or other legally protected information. If you are not the intended
>> recipient, please destroy all copies without reading or disclosing their
>> contents and notify the sender of the error by reply email.
>>
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>> 650-736-1632  | ORCID  0000-0001-6875-5360
>>
>>
>>
>>
>
> --
>
> *Rakesh Nagarajan*
>
> Founder and Executive Chairman
>
> m: 314-504-5620
> e: rakesh at pieriandx.com
>
> [image: pierian-logo-trans-light-background] <http://www.pieriandx.com/>
>  [image: linkedin_circle-512]
> <https://www.linkedin.com/in/rakeshnagarajan/> [image: twitter_circle-512]
> <https://twitter.com/pieriandx>
>
> Wisdom in Every Report?
>
> CONFIDENTIALITY NOTICE: This message and any attachments are solely for
> the use of the intended recipient and may contain privileged, confidential
> or other legally protected information. If you are not the intended
> recipient, please destroy all copies without reading or disclosing their
> contents and notify the sender of the error by reply email.
>
>
>
>
> ========================
> 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
>
>
>
>

-- 

*Rakesh Nagarajan*

Founder and Executive Chairman

m: 314-504-5620
e: rakesh at pieriandx.com

[image: pierian-logo-trans-light-background]
<http://www.pieriandx.com/>   [image:
linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/> [image:
twitter_circle-512] <https://twitter.com/pieriandx>

Wisdom in Every Report?

CONFIDENTIALITY NOTICE: This message and any attachments are solely for the
use of the intended recipient and may contain privileged, confidential or
other legally protected information. If you are not the intended recipient,
please destroy all copies without reading or disclosing their contents and
notify the sender of the error by reply email.
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From mrbarnes at uw.edu  Tue Apr 14 14:28:05 2020
From: mrbarnes at uw.edu (Megan R Barnes)
Date: Tue, 14 Apr 2020 21:28:05 +0000
Subject: [bioontology-support] NCBO Annotator VM Question
In-Reply-To: <95363F1A-9718-46CF-A3C3-E169F04AFC9D@stanford.edu>
References: <A74EC4B7-3C87-40DE-A90D-6115F3BF7F74@uw.edu>
 <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu>
 <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu>
 <81156C25-4423-401A-A712-0B3E2D773404@uw.edu>
 <95363F1A-9718-46CF-A3C3-E169F04AFC9D@stanford.edu>
Message-ID: <EF7616E4-5BE2-4FC6-9CB9-3A51FB6CD658@uw.edu>

Thanks John,

It?s true that adding ?&exclude_synonyms=true" to the API string removes synonyms from the BioPortal mappings (despite the curious fact that I had been including that parameter setting in the data POSTed already).  We would actually like for the synonyms to be included in the response from our VM, however.  I tried adding ?&exclude_synonyms=false" to the API string we send to our VM and synonyms are still not included.

Best,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: John Graybeal <jgraybeal at stanford.edu>
Date: Wednesday, April 8, 2020 at 11:17 AM
To: Megan R Barnes <mrbarnes at uw.edu>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Thanks Megan.

I saw your earlier email and started to work on it before getting pulled away, so this reminder is a good thing.

The only difference between the two responses is that the first, from BioPortal, includes the synonyms, which should be excluded according to the fragment you sent.

When I add "&exclude_synonyms=true" to the API string you sent, I find that BioPortal in fact excludes synonyms from the mappings.

If you can send us the actual API request string that you use, we can troubleshoot this further to see what could be causing synonyms to be incorrectly included.

John




On Apr 8, 2020, at 7:16 AM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Forwarding this message to the support channel, as I realize I forgot to include it in my reply.

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Date: Friday, April 3, 2020 at 2:04 PM
To: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Hi John,

Thanks for your help.  As an example, we are looking to reproduce the NCIT annotations that we get from BioPortal, in the API request:

http://data.bioontology.org/annotator?text=surrounding+end+of+life+care

with params: {"longest_only": "false", "exclude_numbers": "true", "exclude_synonyms": "false", "whole_word_only": "true"}

The annotations we get back that come from NCIT are:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 28, 'matchType': 'SYN', 'text': 'END OF LIFE CARE'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'SYN', 'text': 'LIFE'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

However, when we run the same request on our VM, using the newest version of NCIT (released 3/31/2020 on BioPortal), we get:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

I will attach full responses from each, as well.  Let me know if there?s more info I can provide.

Thanks,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Friday, April 3, 2020 at 11:32 AM
To: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Megan,

Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame.

Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.)  It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies.

If you send us the example of your two responses, we can look closely at them and give you more specific feedback.

John




On Apr 2, 2020, at 12:31 PM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Hello BioPortal Support,

I?m writing with a question about the VMWare Virtual Appliance.  We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API.  I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions.  This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/<https://bioportal.bioontology.org/>.  Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API?

Thanks for your help,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington


_______________________________________________
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



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

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



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From jgraybeal at stanford.edu  Tue Apr 14 17:03:12 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 15 Apr 2020 00:03:12 +0000
Subject: [bioontology-support] NCBO Annotator VM Question
In-Reply-To: <EF7616E4-5BE2-4FC6-9CB9-3A51FB6CD658@uw.edu>
References: <A74EC4B7-3C87-40DE-A90D-6115F3BF7F74@uw.edu>
 <2F9C36BA-4FBD-4B5C-9288-F890C42A2D00@stanford.edu>
 <9C37445E-5FAB-40F7-B682-6C46E62C8554@uw.edu>
 <81156C25-4423-401A-A712-0B3E2D773404@uw.edu>
 <95363F1A-9718-46CF-A3C3-E169F04AFC9D@stanford.edu>
 <EF7616E4-5BE2-4FC6-9CB9-3A51FB6CD658@uw.edu>
Message-ID: <D0ECF5FC-DED7-474C-A8A0-8F5888443021@stanford.edu>

Megan,

Please send me your exact API request that you are sending, so we can attempt to duplicate the issue here. Thank you.

John

On Apr 14, 2020, at 2:28 PM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Thanks John,

It?s true that adding ?&exclude_synonyms=true" to the API string removes synonyms from the BioPortal mappings (despite the curious fact that I had been including that parameter setting in the data POSTed already).  We would actually like for the synonyms to be included in the response from our VM, however.  I tried adding ?&exclude_synonyms=false" to the API string we send to our VM and synonyms are still not included.

Best,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Wednesday, April 8, 2020 at 11:17 AM
To: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Thanks Megan.

I saw your earlier email and started to work on it before getting pulled away, so this reminder is a good thing.

The only difference between the two responses is that the first, from BioPortal, includes the synonyms, which should be excluded according to the fragment you sent.

When I add "&exclude_synonyms=true" to the API string you sent, I find that BioPortal in fact excludes synonyms from the mappings.

If you can send us the actual API request string that you use, we can troubleshoot this further to see what could be causing synonyms to be incorrectly included.

John




On Apr 8, 2020, at 7:16 AM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Forwarding this message to the support channel, as I realize I forgot to include it in my reply.

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Date: Friday, April 3, 2020 at 2:04 PM
To: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Hi John,

Thanks for your help.  As an example, we are looking to reproduce the NCIT annotations that we get from BioPortal, in the API request:

http://data.bioontology.org/annotator?text=surrounding+end+of+life+care

with params: {"longest_only": "false", "exclude_numbers": "true", "exclude_synonyms": "false", "whole_word_only": "true"}

The annotations we get back that come from NCIT are:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 28, 'matchType': 'SYN', 'text': 'END OF LIFE CARE'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'SYN', 'text': 'END'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'SYN', 'text': 'LIFE'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

However, when we run the same request on our VM, using the newest version of NCIT (released 3/31/2020 on BioPortal), we get:

[
[{'from': 1, 'to': 11, 'matchType': 'PREF', 'text': 'SURROUNDING'}],
[{'from': 13, 'to': 15, 'matchType': 'PREF', 'text': 'END'}],
[{'from': 20, 'to': 23, 'matchType': 'PREF', 'text': 'LIFE'}],
[{'from': 25, 'to': 28, 'matchType': 'PREF', 'text': 'CARE'}]
]

I will attach full responses from each, as well.  Let me know if there?s more info I can provide.

Thanks,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Date: Friday, April 3, 2020 at 11:32 AM
To: Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] NCBO Annotator VM Question

Megan,

Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal?nothing mentioned Annotator since 2.5 release of the Virtual Appliance?and tickets, which showed nothing in that time frame.

Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.)  It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies.

If you send us the example of your two responses, we can look closely at them and give you more specific feedback.

John




On Apr 2, 2020, at 12:31 PM, Megan R Barnes <mrbarnes at uw.edu<mailto:mrbarnes at uw.edu>> wrote:

Hello BioPortal Support,

I?m writing with a question about the VMWare Virtual Appliance.  We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API.  I am aware that this is not the same version of the annotator that is running athttp://data.bioontology.org/annotator , and have noticed that the shape of the API response is different between the two versions.  This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from bioportal.bioontology.org/<https://bioportal.bioontology.org/>.  Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API?

Thanks for your help,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington


_______________________________________________
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



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

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

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



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From jgraybeal at stanford.edu  Wed Apr 15 09:53:25 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 15 Apr 2020 16:53:25 +0000
Subject: [bioontology-support] Fwd:  [BioPortal] Feedback from Jean
References: <3d94eb1b28004a6ebc26ac521102dea1@glpg.com>
Message-ID: <C1DAC3BF-722D-4AB8-BA9E-DF9324726FB0@stanford.edu>

Reforwarding to list after deleting API key information...

Begin forwarded message:

From: Jean Travassos-EXT <Jean.Travassos-EXT at glpg.com<mailto:Jean.Travassos-EXT at glpg.com>>
Subject: RE: [bioontology-support] [BioPortal] Feedback from Jean
Date: April 15, 2020 at 6:11:46 AM PDT
To: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>, "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>

Hello John,

Thank you for replying me.
I don?t actually know why but I could get this working in NiFi by passing parameters twice:

http://10.10.3.79:8080/ontologies/GAAT38/classes/http%3A%2F%2Fwebprotege.stanford.edu%2FR8T0KZCbVZAr6ly04QxKhXU?apikey=<DELETED>&include=all&include=all&display_context=false&display_context=false<http://10.10.3.79:8080/ontologies/GAAT38/classes/http://webprotege.stanford.edu/R8T0KZCbVZAr6ly04QxKhXU?apikey=%3CDELETED%3E&include=all&include=all&display_context=false&display_context=false>

Params include=all and display_context=false was only read after duplicate them. But it is working.

I checked with our infrastructure team and we only have one instance of BP.

Another strange behaviour is exclusive of BP:
We have this Ontology with 3 submissions. When we open the Ontology, its tree is outdated.
After we click in any node, the tree updates itself for the latest and correct version.
Do you know if this may be caused by the lack of any property when submitting a new version?
There?s nothing to do with we trying to consume data, it?s something exclusive from BioPortal?

In attachment there?s examples:
-          AAT38 is our Ontology, contains 3 submissions.
-          Submission3-WhenEnters is the tree in the moment when we first see the Ontology. There?s ?Reference Compound UoM? node, which is outdated.
-          Submission3-AfterSelection show the reloaded tree after we select any valid node.
-          Submission3-SelectingUnexisting is the error page if we select the node that shouldn?t be shown anymore, since it existed only in the first submission.

Thank you very much for your attention and time.

If you prefer, I can arrange a quick call.

Best Regards,
Jean Travassos



From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: 11 April 2020 01:09
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Jean Travassos-EXT <Jean.Travassos-EXT at glpg.com<mailto:Jean.Travassos-EXT at glpg.com>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Jean

*** CAUTION : External e-mail ***

Jean,

I confess I am uncertain about what might is causing this, but I can ask some useful questions that will help our team troubleshoot more next week.

The clearest picture would be to see the logs corresponding to those requests, ideally from the Apache or similar logs. The requests from your NiFi flow almost certainly will look different in some way.

Is it possible there are two ontologies that look almost the same, and the flow is asking for the second ontology which only has one submission?  Or alternatively, there are two Bioportal instances and the Apache flow is accessing an instance with only one submission for that ontology?

The more concrete details you can provide, the better our chance of coming up with useful suggestions.

John


On Apr 10, 2020, at 8:53 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Jean
Email: jean.travassos-ext at glpg.com<mailto:jean.travassos-ext at glpg.com>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2F

Feedback:
Hello, I'm facing a problem while using BioPortal API and was wondering if you can get me some clarification.
I have BP installed in one server for dev purposes and while I use the URL to GET all children of the master node of our Ontology, it works well (testing in Postman or Firefox or curl).
However, our Ontology has 3 submissions. When another application (an Apache NiFi flow) makes the http GET request with exactly the same URL, in returns only data from the FIRST submission. It should return the data of the latest submission, of course.
Can you get any direction? Is there any parameter or something like that I should configure to prevent this to happen?
Thank you for your attention.
Best regards

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

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




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



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From chinghua at us.ibm.com  Thu Apr 16 03:58:02 2020
From: chinghua at us.ibm.com (Ching-Hua Chen)
Date: Thu, 16 Apr 2020 10:58:02 +0000
Subject: [bioontology-support] API key on Virtual Appliance
In-Reply-To: <FC0897AC-31DE-4D00-B40E-C3DB65B1EBDB@stanford.edu>
References: <FC0897AC-31DE-4D00-B40E-C3DB65B1EBDB@stanford.edu>,
 <OFBF162ECC.87DC94AD-ON00258548.0071470F-00258548.0071A12C@notes.na.collabserv.com>
Message-ID: <OF72E01AC4.3D29E679-ON0025854C.003C3E3F-0025854C.003C3EEF@notes.na.collabserv.com>

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From chinghua at us.ibm.com  Thu Apr 16 04:06:25 2020
From: chinghua at us.ibm.com (Ching-Hua Chen)
Date: Thu, 16 Apr 2020 11:06:25 +0000
Subject: [bioontology-support] Trying to troubleshoot annotate_text output
Message-ID: <OF90D5C0E5.2005C0FE-ON0025854C.003C4E3A-0025854C.003D036A@notes.na.collabserv.com>

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From chinghua at us.ibm.com  Thu Apr 16 07:48:13 2020
From: chinghua at us.ibm.com (Ching-Hua Chen)
Date: Thu, 16 Apr 2020 14:48:13 +0000
Subject: [bioontology-support] Trying to troubleshoot annotate_text
	output
In-Reply-To: <OF90D5C0E5.2005C0FE-ON0025854C.003C4E3A-0025854C.003D036A@LocalDomain>
References: <OF90D5C0E5.2005C0FE-ON0025854C.003C4E3A-0025854C.003D036A@LocalDomain>
Message-ID: <OF218385B7.40791561-ON0025854C.00514B6B-0025854C.00515194@notes.na.collabserv.com>

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From jgraybeal at stanford.edu  Thu Apr 16 09:06:01 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 16 Apr 2020 16:06:01 +0000
Subject: [bioontology-support] Trying to troubleshoot
	annotate_text	output
In-Reply-To: <OF218385B7.40791561-ON0025854C.00514B6B-0025854C.00515194@notes.na.collabserv.com>
References: <OF90D5C0E5.2005C0FE-ON0025854C.003C4E3A-0025854C.003D036A@LocalDomain>
 <OF218385B7.40791561-ON0025854C.00514B6B-0025854C.00515194@notes.na.collabserv.com>
Message-ID: <6878BDA4-B9E1-435E-A8B0-4C626A7B4854@stanford.edu>

I'm glad the issue is resolved.

One thing you can check if it comes back is whether the same annotation request from the UI works. If it does, then the delay may be coming from your application. (You can also try running the request from a browser, or from curl, to see how fast it comes back, and to make sure your API command is working as you expect.)

If the UI request doesn't work, then there may be a problem with processing the ontology. If the UI works but the API doesn't, there is likely a problem with the API request format, and you could send it to the support list (along with the behaviors that result) if you can't figure out what it should be.

John

On Apr 16, 2020, at 7:48 AM, Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> wrote:

This issue is resolved. Not sure why... but I am getting outputs. I think there was a really long lag in print to screen for some reason. Thanks.

Ching-Hua Chen

Computational Health Behavior & Decision Science
IBM, T.J. Watson Research Center
1101 Kitchawan Road, Yorktown Heights, NY 10598

chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>
(914) 945-2061 (o); (845) 519-7582 (m)

"Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson


----- Original message -----
From: Ching-Hua Chen/Watson/IBM
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc:
Subject: Trying to troubleshoot annotate_text output
Date: Thu, Apr 16, 2020 7:06 AM

Hi,

I have used the ruby script (bioportal_ontologies_import.rb) provided to import the OCHV ontology to my virtual appliance. When I run "list_ontologies.py" I see that it is listed, after the ontology "STY". I only have these two ontologies on my appliance at the moment.

When I ran "annotate_text.py", as is, using the data.bioontology.org<http://data.bioontology.org> URL, the script returned results from OCHV (I only have OCHV in my bioportal account).

However, when I edited "annotate_text.py" to reference my virtual appliance URL (I didn't not edit anything else in the script), the script returned nothing. It ran to completion without error.

I'm wondering why I'm not getting any results when I run "annotate_text" on my virtual appliance, compared to when I ran the same thing on the bioontology.org<http://bioontology.org>.

Best,

Ching-Hua Chen

Computational Health Behavior & Decision Science
IBM, T.J. Watson Research Center
1101 Kitchawan Road, Yorktown Heights, NY 10598

chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>
(914) 945-2061 (o); (845) 519-7582 (m)

"Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson


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

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



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From s1anbenn at uni-bayreuth.de  Thu Apr 16 10:41:21 2020
From: s1anbenn at uni-bayreuth.de (Andreas Benndorf)
Date: Thu, 16 Apr 2020 19:41:21 +0200
Subject: [bioontology-support] Usage of Semantic Types via BioPortal REST-API
Message-ID: <003101d61416$3e7c2e10$bb748a30$@uni-bayreuth.de>

Dear Sir or Madam,

 

in my master's thesis I am developing a Named Entity Recognition system that
can retrieve, inter alia, health care activities and diseases in text
documents.

For the recognition I will use the BioPortal REST-API as follows:

1.	Send the document text to the annotator endpoint using the MEDDRA
ontology.
2.	For every found term in the text, look up the semantic type in the
returned JSON file and distinguish with the aid of several semantic types
whether the term is a health care activity or a disease. For this, some
constants are used in my program for several semantic types like "Sign or
Symptom (T184)".
3.	Then the term is saved as an annotation without the semantic type
information.

 

I don't have a UMLS license and I live in a non-member territory. Is the
described procedure compliant to the Terms of Use of BioPortal?

In particular, I am referring to the following passage of the Terms of Use:

 

"The sub-licensee is only permitted to access SNOMED CTR using this software
(or service) for the purpose of exploring and evaluating the terminology. 2,
The sub-licensee is not permitted the use of this software as part of a
system that constitutes a SNOMED CT "Data Creation System" or "Data Analysis
System", as defined in the IHTSDO Affiliate License. This means that the
sub-licensee must not use NCBO BioPortal to add or copy SNOMED CT
identifiers into any type of record system, database or document."

 

MEDDRA allows the usage without a license for a research project. So, this
shouldn't be a problem.

But is the extraction and the distinction of the semantic type from the
response of MEDDRA adding or copying "SNOMED CT identifiers into any type of
record system, database or document" - especially regarding the fact that I
am not saving the semantic type anywhere permanently?

 

Thank you very much in advance for your response.

 

Kind regards,

Andreas Benndorf

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From jgraybeal at stanford.edu  Fri Apr 17 09:57:14 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 17 Apr 2020 16:57:14 +0000
Subject: [bioontology-support] Usage of Semantic Types via BioPortal
 REST-API
In-Reply-To: <003101d61416$3e7c2e10$bb748a30$@uni-bayreuth.de>
References: <003101d61416$3e7c2e10$bb748a30$@uni-bayreuth.de>
Message-ID: <2D52FB1F-7A91-4165-B8F1-FC6BDB1A589A@stanford.edu>

Hello Andreas,

I think this question is ideally asked of the SNOMED CT organization. We are not lawyers, and our users need to resolve legal and licensing questions directly with the providers who have specified the license. (Also, we have no idea what the legal system says in your non-member territory.)

I would just note, as a lay person, that a literal reading of the cited language would mean that Google could never put up a web page (which relies on record systems, databases, *and* documents) that contain a SNOMED CT identifier. So, no public resource could ever put up a web page with such an identifier. So, there could never be any posted discussion of SNOMED CT identifiers. Which would fairly clearly violate fair use legal standards in the United States, but your situation in a non-member territory would be different.

That may or may not have any implications for your application. As a practical matter, it would inform how I would interpret this kind of narrow use of a secondary provision of the identifier. (If I had to. Which I don't, because, see first paragraph.)

Hope this helps your process. Best wishes for your thesis.

John



On Apr 16, 2020, at 10:41 AM, Andreas Benndorf <s1anbenn at uni-bayreuth.de<mailto:s1anbenn at uni-bayreuth.de>> wrote:

Dear Sir or Madam,

in my master?s thesis I am developing a Named Entity Recognition system that can retrieve, inter alia, health care activities and diseases in text documents.
For the recognition I will use the BioPortal REST-API as follows:

  1.  Send the document text to the annotator endpoint using the MEDDRA ontology.
  2.  For every found term in the text, look up the semantic type in the returned JSON file and distinguish with the aid of several semantic types whether the term is a health care activity or a disease. For this, some constants are used in my program for several semantic types like ?Sign or Symptom (T184)?.
  3.  Then the term is saved as an annotation without the semantic type information.


I don?t have a UMLS license and I live in a non-member territory. Is the described procedure compliant to the Terms of Use of BioPortal?
In particular, I am referring to the following passage of the Terms of Use:

?The sub-licensee is only permitted to access SNOMED CT? using this software (or service) for the purpose of exploring and evaluating the terminology. 2, The sub-licensee is not permitted the use of this software as part of a system that constitutes a SNOMED CT ?Data Creation System? or ?Data Analysis System?, as defined in the IHTSDO Affiliate License. This means that the sub-licensee must not use NCBO BioPortal to add or copy SNOMED CT identifiers into any type of record system, database or document.?

MEDDRA allows the usage without a license for a research project. So, this shouldn?t be a problem.
But is the extraction and the distinction of the semantic type from the response of MEDDRA adding or copying ?SNOMED CT identifiers into any type of record system, database or document? ? especially regarding the fact that I am not saving the semantic type anywhere permanently?

Thank you very much in advance for your response.

Kind regards,
Andreas Benndorf
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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



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From support at bioontology.org  Sat Apr 18 06:25:36 2020
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 18 Apr 2020 06:25:36 -0700
Subject: [bioontology-support] [BioPortal] Feedback from VJHenry
Message-ID: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail>

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From jgraybeal at stanford.edu  Sun Apr 19 13:41:56 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Sun, 19 Apr 2020 20:41:56 +0000
Subject: [bioontology-support] [BioPortal] Feedback from VJHenry
In-Reply-To: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail>
References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu>

Hi Vincent,

Here are some quick replies for now, please respond with whatever issues remain.

- the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST)

If you are asking to have this deleted, we can do that. Please confirm that is what you want.

- the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following

Descriptions can be modified by you; click on the pencil icon to edit the ontology metadata (at upper right) or the submission metadata (above the submission list).

- the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.

Acronyms can not be changed they are the index for everything in the system. To make this happen, you will need to re-submit your ontology(ies) under the new acronym you want to use, then tell us to delete the original ontology(ies). Unfortunately the history will be lost.

Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?

I don't have time to look at the details at this moment, but the best way to figure this out is to try loading the ontology in Protege. If it is not parseable in BioPortal (which is what this indicates), it is almost always not parseable in Protege, for the same reasons because they use the same parser. And Protege actually shows you the errors, which makes it a much better tool for finding and fixing issues.

Hope this helps!

John


On Apr 18, 2020, at 6:25 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: VJHenry

Email: vincent643 at gmail.com<mailto:vincent643 at gmail.com>

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

Feedback:

Hi,
I'm wondering if its possible to change some mistakes I made:
- the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST)
- the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following
- the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.

Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?

Thank you very much for all,
Best regards,
Vincent (VJHenry; vincent643 at gmail.com<mailto:vincent643 at gmail.com>)

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

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



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From alexgarciac at gmail.com  Mon Apr 20 05:59:27 2020
From: alexgarciac at gmail.com (Alexander Garcia Castro)
Date: Mon, 20 Apr 2020 14:59:27 +0200
Subject: [bioontology-support] icd10
Message-ID: <CALAe=OKiJG65rXEdg6NQa8qS9mOWhbO4dC3tcSW4S2GijEPZWQ@mail.gmail.com>

hi, I need the latest version of ICD10 in a format that is not a pdf. a
CSV, or XLS, or JSON, or a DB dump but not PDF. do anyone here know where
can I get it? I have only been able to find pdfs for the latest version of
ICD10.

Who on earth publishes a vocabulary like ICD10 as a book in PDF.... in what
world is the WHO living? am I missing something, I hope so.


Best.

-- 
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac
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From support at bioontology.org  Sun Apr 19 21:50:21 2020
From: support at bioontology.org (support at bioontology.org)
Date: Sun, 19 Apr 2020 21:50:21 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Chai
Message-ID: <5e9d2a0d9c355_1c827ca2e865015@ncbo-prd-app-08.stanford.edu.mail>

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From mdorf at stanford.edu  Mon Apr 20 10:33:10 2020
From: mdorf at stanford.edu (Michael Vladimir Dorf)
Date: Mon, 20 Apr 2020 17:33:10 +0000
Subject: [bioontology-support] icd10
In-Reply-To: <CALAe=OKiJG65rXEdg6NQa8qS9mOWhbO4dC3tcSW4S2GijEPZWQ@mail.gmail.com>
References: <CALAe=OKiJG65rXEdg6NQa8qS9mOWhbO4dC3tcSW4S2GijEPZWQ@mail.gmail.com>
Message-ID: <05377287-56C5-438D-AFD0-2A221F3A7D8E@stanford.edu>

Hi Alexander,

Thanks for contacting us. Our version of ICD10 comes from  the UMLS distribution that we import into BioPortal roughly twice per year.  Due to licensing restrictions, we can?t post a download link on our site. If you have a UMLS license, please send us the license number (exclude the NCBO support list when replying) and we can provide you with a TTL file privately. If you don?t already have a license, they are free and you can sign up for one here:

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

Thanks,

Michael




On Apr 20, 2020, at 5:59 AM, Alexander Garcia Castro <alexgarciac at gmail.com<mailto:alexgarciac at gmail.com>> wrote:

hi, I need the latest version of ICD10 in a format that is not a pdf. a CSV, or XLS, or JSON, or a DB dump but not PDF. do anyone here know where can I get it? I have only been able to find pdfs for the latest version of ICD10.

Who on earth publishes a vocabulary like ICD10 as a book in PDF.... in what world is the WHO living? am I missing something, I hope so.


Best.

--
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac

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

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From alexgarciac at gmail.com  Mon Apr 20 12:50:03 2020
From: alexgarciac at gmail.com (Alexander Garcia Castro)
Date: Mon, 20 Apr 2020 21:50:03 +0200
Subject: [bioontology-support] icd10
In-Reply-To: <05377287-56C5-438D-AFD0-2A221F3A7D8E@stanford.edu>
References: <CALAe=OKiJG65rXEdg6NQa8qS9mOWhbO4dC3tcSW4S2GijEPZWQ@mail.gmail.com>
 <05377287-56C5-438D-AFD0-2A221F3A7D8E@stanford.edu>
Message-ID: <CALAe=O+yDQBHq68w9sXwoREjYNFxUd6XG2E+Uj17FLSbRMoyeA@mail.gmail.com>

thanks for the quick response. does it mean that if I want to use the 2020
OWL version of ICD10 then I have to have a umls licence? doesnt icd
releases something that is not a PDF?

thanks a lot in advance.

On Mon, Apr 20, 2020 at 7:33 PM Michael Vladimir Dorf <mdorf at stanford.edu>
wrote:

> Hi Alexander,
>
> Thanks for contacting us. Our version of ICD10 comes from  the UMLS
> distribution that we import into BioPortal roughly twice per year.  Due to
> licensing restrictions, we can?t post a download link on our site. If you
> have a UMLS license, please send us the license number (exclude the NCBO
> support list when replying) and we can provide you with a TTL file
> privately. If you don?t already have a license, they are free and you can
> sign up for one here:
>
> https://www.nlm.nih.gov/databases/umls.html#license_request
>
> Thanks,
>
> Michael
>
>
>
>
> On Apr 20, 2020, at 5:59 AM, Alexander Garcia Castro <
> alexgarciac at gmail.com> wrote:
>
> hi, I need the latest version of ICD10 in a format that is not a pdf. a
> CSV, or XLS, or JSON, or a DB dump but not PDF. do anyone here know where
> can I get it? I have only been able to find pdfs for the latest version of
> ICD10.
>
> Who on earth publishes a vocabulary like ICD10 as a book in PDF.... in
> what world is the WHO living? am I missing something, I hope so.
>
>
> Best.
>
> --
> Alexander Garcia
> https://www.researchgate.net/profile/Alexander_Garcia
> http://www.usefilm.com/photographer/75943.html
> http://www.linkedin.com/in/alexgarciac
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>

-- 
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac
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From jgraybeal at stanford.edu  Mon Apr 20 13:21:31 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 20 Apr 2020 20:21:31 +0000
Subject: [bioontology-support] icd10
In-Reply-To: <CALAe=O+yDQBHq68w9sXwoREjYNFxUd6XG2E+Uj17FLSbRMoyeA@mail.gmail.com>
References: <CALAe=OKiJG65rXEdg6NQa8qS9mOWhbO4dC3tcSW4S2GijEPZWQ@mail.gmail.com>
 <05377287-56C5-438D-AFD0-2A221F3A7D8E@stanford.edu>
 <CALAe=O+yDQBHq68w9sXwoREjYNFxUd6XG2E+Uj17FLSbRMoyeA@mail.gmail.com>
Message-ID: <EE733315-C2B0-427C-82D7-A0A3FF5D6D8E@stanford.edu>

I would have said "yes", although a quick Google search found https://dkm.fbk.eu/technologies/icd-10-ontology.

John

On Apr 20, 2020, at 12:50 PM, Alexander Garcia Castro <alexgarciac at gmail.com<mailto:alexgarciac at gmail.com>> wrote:

thanks for the quick response. does it mean that if I want to use the 2020 OWL version of ICD10 then I have to have a umls licence? doesnt icd releases something that is not a PDF?

thanks a lot in advance.

On Mon, Apr 20, 2020 at 7:33 PM Michael Vladimir Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Alexander,

Thanks for contacting us. Our version of ICD10 comes from  the UMLS distribution that we import into BioPortal roughly twice per year.  Due to licensing restrictions, we can?t post a download link on our site. If you have a UMLS license, please send us the license number (exclude the NCBO support list when replying) and we can provide you with a TTL file privately. If you don?t already have a license, they are free and you can sign up for one here:

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

Thanks,

Michael




On Apr 20, 2020, at 5:59 AM, Alexander Garcia Castro <alexgarciac at gmail.com<mailto:alexgarciac at gmail.com>> wrote:

hi, I need the latest version of ICD10 in a format that is not a pdf. a CSV, or XLS, or JSON, or a DB dump but not PDF. do anyone here know where can I get it? I have only been able to find pdfs for the latest version of ICD10.

Who on earth publishes a vocabulary like ICD10 as a book in PDF.... in what world is the WHO living? am I missing something, I hope so.


Best.

--
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac

_______________________________________________
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



--
Alexander Garcia
https://www.researchgate.net/profile/Alexander_Garcia
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac

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



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From mdorf at stanford.edu  Mon Apr 20 16:31:44 2020
From: mdorf at stanford.edu (Michael Vladimir Dorf)
Date: Mon, 20 Apr 2020 23:31:44 +0000
Subject: [bioontology-support] [BioPortal] Feedback from VJHenry
In-Reply-To: <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu>
References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail>
 <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu>
Message-ID: <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu>

Hi Vincent,

I?ve done some further troubleshooting of your ontologies, and some flags were raised by our tools in regards to their source:

Although we can load the ontologies without errors (including in Protege), the second step in the parsing process fails when we attempt to serialize the data to ntriples format to load it into our RDF store:

? repository/BIPOM-CC-INF/1 ? rapper -i ntriples -c data.triples
rapper: Parsing URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples with parser ntriples
rapper: Error - URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:2 column 2531 - Junk after terminating "."
rapper: Error - URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:9647 column 2561 - Junk after terminating ?."

Both of these errors refer to a comment that appears inside ALL of your ontology source files. The NTriples file refers to this section of code:

<http://purl.obolibrary.org/obo/<http://purl.obolibrary.org/obo/>BiPOm> <http://www.w3.org/2000/01/rdf-schema#comment> "BiPOm\n\n1. Copyright of ontology\n\nThe ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science  \nfrom genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit\u00E9 Paris-Sud/CNRS, France  and by the D\u00E9partement MMIP AgroParisTech of the INRA, France.\nINRA, Agroparistech and  Universit\u00E9 Paris-Sud own the copyright of the ontology BiPOm. \n\n2. License terms\n\nThe ontology BiPOm is licensed under the Creative Commons\nAttribution 4.0 Unported (CC BY 4.0) license. To view a\ncopy of this license, visit http://creativecommons.org/licenses/by/4.0/\nor send a letter to Creative Commons, 444 Castro Street, Suite 900,\nMountain View, California, 94041, USA.   \n\n\n3. Notice\nThis product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, \nlicensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/).\n\nThis product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. \n\nThis product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. \n\nThis product contains references to classes of the Systems Biology Ontology (SBO)  (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, \nlicensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php).\n\nThis product contains references to properties of the Relation Ontology (RO)  (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, \nlicensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\nThis product contains references to properties of the Basic Formal Ontology (BFO)  (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium,\n licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\n4. Contact\nFor questions and remarks concerning BiPOm:\nAnne Goelzer\nAnne.Goelzer"@inra.fr .

Below is the original source code corresponding to this triple:

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BiPOm">
<rdfs:comment xml:lang="inra.fr<http://inra.fr>">BiPOm

1. Copyright of ontology

The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science
from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit? Paris-Sud/CNRS, France  and by the D?partement MMIP AgroParisTech of the INRA, France.

***************** SNIP *****************

    4. Contact
For questions and remarks concerning BiPOm:
                                         Anne Goelzer
Anne.Goelzer</rdfs:comment>
    </rdf:Description>

I am not an ontology development expert to point to the exact issue with this code, but both my colleague and I think that the language definition is incorrect:


<rdfs:comment xml:lang="inra.fr<http://inra.fr/>">

The expectation is to see something like xml:lang="en" or xml:lang=?fr"

I?d recommend correcting this entry and adding a new submission of your ontology(ies). Also, please let us know which ontologies need to be deleted so as to address the incorrect acronym issue.

Thank you,

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 Apr 19, 2020, at 1:41 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Hi Vincent,

Here are some quick replies for now, please respond with whatever issues remain.

- the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST)

If you are asking to have this deleted, we can do that. Please confirm that is what you want.

- the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following

Descriptions can be modified by you; click on the pencil icon to edit the ontology metadata (at upper right) or the submission metadata (above the submission list).

- the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.

Acronyms can not be changed they are the index for everything in the system. To make this happen, you will need to re-submit your ontology(ies) under the new acronym you want to use, then tell us to delete the original ontology(ies). Unfortunately the history will be lost.

Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?

I don't have time to look at the details at this moment, but the best way to figure this out is to try loading the ontology in Protege. If it is not parseable in BioPortal (which is what this indicates), it is almost always not parseable in Protege, for the same reasons because they use the same parser. And Protege actually shows you the errors, which makes it a much better tool for finding and fixing issues.

Hope this helps!

John


On Apr 18, 2020, at 6:25 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: VJHenry

Email: vincent643 at gmail.com<mailto:vincent643 at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FBIPOM-CC-INF

Feedback:

Hi,
I'm wondering if its possible to change some mistakes I made:
- the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST)
- the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following
- the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.

Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?

Thank you very much for all,
Best regards,
Vincent (VJHenry; vincent643 at gmail.com<mailto:vincent643 at gmail.com>)

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

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



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

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From mdorf at stanford.edu  Mon Apr 20 18:21:43 2020
From: mdorf at stanford.edu (Michael Vladimir Dorf)
Date: Tue, 21 Apr 2020 01:21:43 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Chai
In-Reply-To: <5e9d2a0d9c355_1c827ca2e865015@ncbo-prd-app-08.stanford.edu.mail>
References: <5e9d2a0d9c355_1c827ca2e865015@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <35C902F9-2F7C-4B43-BF7D-161AED7FF399@stanford.edu>

Hi Chai,

Thank you for contacting us. I am not exactly sure how I can help except to point out that we display the hierarchy of the classes based on the subClassOf relationship. The details of each class presented in our user interface display ALL available properties of the class. You can view the same data using our REST API, and you can see, the two views are identical. For example:

https://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma293882<https://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http://purl.org/sig/ont/fma/fma293882>

AND

http://data.bioontology.org/ontologies/FMA/classes/http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma293882?no_links=true&no_context=true&display=prefLabel,synonym,definition,properties,submission<http://data.bioontology.org/ontologies/FMA/classes/http://purl.org/sig/ont/fma/fma293882?no_links=true&no_context=true&display=prefLabel,synonym,definition,properties,submission>

You?ll need to append your BioPortal API key to the latter example for it to display properly.

You can also try using the FMA Visualization tool to see if that presentation gives you a better idea of the relationships between FMA classes:

http://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fsig%2Font%2Ffma%2Ffma293882#visualization<http://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http://purl.org/sig/ont/fma/fma293882#visualization>

Just note that there?s currently a known issue in BioPortal where the visualizations don?t work over HTTPS, so please make sure to use ?http://? instead of ?https://? when viewing that tab.

Do you have specific examples of classes in FMA, whose relationships are missing from BioPortal?

Thanks,

Michael


On Apr 19, 2020, at 9:50 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Chai

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

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

Feedback:

Dear Person-in-Charge

My question pertains to the Foundational Model of Anatomy. As from the original website for the FMA, there are (1) spatial (2) part-of/contains relationship data available between classes in the FMA. However, I cannot seem to find these on your website. Can you advise where I can access such data?

Regards,
Chai

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

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From mdorf at stanford.edu  Tue Apr 21 12:56:49 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Tue, 21 Apr 2020 19:56:49 +0000
Subject: [bioontology-support] [BioPortal] Feedback from VJHenry
In-Reply-To: <CAE681gryqt22a1_DXk63QeOeOcxJmKYqb7k7p4m=rY+4dLfxEA@mail.gmail.com>
References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail>
 <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu>
 <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu>
 <CAE681gryqt22a1_DXk63QeOeOcxJmKYqb7k7p4m=rY+4dLfxEA@mail.gmail.com>
Message-ID: <7E4F9CF6-A52D-46B0-8DD4-D4E819855B2E@stanford.edu>

Hi Vincent,

I?ve deleted BIPOM-INST ontology from our system. As far the error, I think the culprit is the language designation, not the contact email. That last fragment should end with:


nAnne Goelzer\nAnne.Goelzer?@en

instead of:

nAnne Goelzer\nAnne.Goelzer"@inra.fr

The @en indicates the language from this field:


<rdfs:comment xml:lang="inra.fr<http://inra.fr/>">

This should instead read:


<rdfs:comment xml:lang="en">

Hope this clarifies it.

Michael


On Apr 21, 2020, at 9:26 AM, Vincent Henry <vincent643 at gmail.com<mailto:vincent643 at gmail.com>> wrote:

Hi Michael,

Thank you very much for your return.
You're right, it is a contact email address with "@" that was misinterpreted.
I'll never find it by myself. I'll upload new files.

Best regards,
Vincent

On Tue, Apr 21, 2020 at 1:31 AM Michael Vladimir Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Vincent,

I?ve done some further troubleshooting of your ontologies, and some flags were raised by our tools in regards to their source:

Although we can load the ontologies without errors (including in Protege), the second step in the parsing process fails when we attempt to serialize the data to ntriples format to load it into our RDF store:

? repository/BIPOM-CC-INF/1 ? rapper -i ntriples -c data.triples
rapper: Parsing URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples with parser ntriples
rapper: Error - URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:2 column 2531 - Junk after terminating "."
rapper: Error - URI file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:9647 column 2561 - Junk after terminating ?."

Both of these errors refer to a comment that appears inside ALL of your ontology source files. The NTriples file refers to this section of code:

<http://purl.obolibrary.org/obo/<http://purl.obolibrary.org/obo/>BiPOm> <http://www.w3.org/<http://www.w3.org/>2000/01/rdf-schema#comment> "BiPOm\n\n1. Copyright of ontology\n\nThe ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science  \nfrom genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit\u00E9 Paris-Sud/CNRS, France  and by the D\u00E9partement MMIP AgroParisTech of the INRA, France.\nINRA, Agroparistech and  Universit\u00E9 Paris-Sud own the copyright of the ontology BiPOm. \n\n2. License terms\n\nThe ontology BiPOm is licensed under the Creative Commons\nAttribution 4.0 Unported (CC BY 4.0) license. To view a\ncopy of this license, visit http://creativecommons.org/licenses/by/4.0/\nor<http://creativecommons.org/licenses/by/4.0/%5Cnor> send a letter to Creative Commons, 444 Castro Street, Suite 900,\nMountain View, California, 94041, USA.   \n\n\n3. Notice\nThis product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, \nlicensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/).\n\nThis product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. \n\nThis product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. \n\nThis product contains references to classes of the Systems Biology Ontology (SBO)  (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, \nlicensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php).\n\nThis product contains references to properties of the Relation Ontology (RO)  (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, \nlicensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\nThis product contains references to properties of the Basic Formal Ontology (BFO)  (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium,\n licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\n4. Contact\nFor questions and remarks concerning BiPOm:\nAnne Goelzer\nAnne.Goelzer"@inra.fr .

Below is the original source code corresponding to this triple:

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BiPOm">
<rdfs:comment xml:lang="inra.fr<http://inra.fr/>">BiPOm

1. Copyright of ontology

The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science
from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit? Paris-Sud/CNRS, France  and by the D?partement MMIP AgroParisTech of the INRA, France.

***************** SNIP *****************

    4. Contact
For questions and remarks concerning BiPOm:
                                         Anne Goelzer
Anne.Goelzer</rdfs:comment>
    </rdf:Description>

I am not an ontology development expert to point to the exact issue with this code, but both my colleague and I think that the language definition is incorrect:


<rdfs:comment xml:lang="inra.fr<http://inra.fr/>">

The expectation is to see something like xml:lang="en" or xml:lang=?fr"

I?d recommend correcting this entry and adding a new submission of your ontology(ies). Also, please let us know which ontologies need to be deleted so as to address the incorrect acronym issue.

Thank you,

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 Apr 19, 2020, at 1:41 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Hi Vincent,

Here are some quick replies for now, please respond with whatever issues remain.

- the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST)

If you are asking to have this deleted, we can do that. Please confirm that is what you want.

- the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following

Descriptions can be modified by you; click on the pencil icon to edit the ontology metadata (at upper right) or the submission metadata (above the submission list).

- the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.

Acronyms can not be changed they are the index for everything in the system. To make this happen, you will need to re-submit your ontology(ies) under the new acronym you want to use, then tell us to delete the original ontology(ies). Unfortunately the history will be lost.

Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?

I don't have time to look at the details at this moment, but the best way to figure this out is to try loading the ontology in Protege. If it is not parseable in BioPortal (which is what this indicates), it is almost always not parseable in Protege, for the same reasons because they use the same parser. And Protege actually shows you the errors, which makes it a much better tool for finding and fixing issues.

Hope this helps!

John


On Apr 18, 2020, at 6:25 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: VJHenry

Email: vincent643 at gmail.com<mailto:vincent643 at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FBIPOM-CC-INF

Feedback:

Hi,
I'm wondering if its possible to change some mistakes I made:
- the creation of "BiPOm-RPCC-instanciated" (https://bioportal.bioontology.org/ontologies/BIPOM-INST)
- the description of "BiPOm inferences for Calvin cycle" (https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed instead of following
- the acronym of "BiPOm E-Coli metabolism instantiation" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF) BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
and the the acronym of "BiPOm inferences for E-Coli metabolism" (https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF) BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.

Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?

Thank you very much for all,
Best regards,
Vincent (VJHenry; vincent643 at gmail.com<mailto:vincent643 at gmail.com>)

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

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



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


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From vincent643 at gmail.com  Tue Apr 21 09:26:31 2020
From: vincent643 at gmail.com (Vincent Henry)
Date: Tue, 21 Apr 2020 18:26:31 +0200
Subject: [bioontology-support] [BioPortal] Feedback from VJHenry
In-Reply-To: <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu>
References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail>
 <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu>
 <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu>
Message-ID: <CAE681gryqt22a1_DXk63QeOeOcxJmKYqb7k7p4m=rY+4dLfxEA@mail.gmail.com>

Hi Michael,

Thank you very much for your return.
You're right, it is a contact email address with "@" that was
misinterpreted.
I'll never find it by myself. I'll upload new files.

Best regards,
Vincent

On Tue, Apr 21, 2020 at 1:31 AM Michael Vladimir Dorf <mdorf at stanford.edu>
wrote:

> Hi Vincent,
>
> I?ve done some further troubleshooting of your ontologies, and some flags
> were raised by our tools in regards to their source:
>
> Although we can load the ontologies without errors (including in Protege),
> the second step in the parsing process fails when we attempt to serialize
> the data to ntriples format to load it into our RDF store:
>
> ? repository/BIPOM-CC-INF/1 ? rapper -i ntriples -c data.triples
> rapper: Parsing URI
> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples with parser
> ntriples
> rapper: Error - URI
> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:2 column
> 2531 - Junk after terminating "."
> rapper: Error - URI
> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:9647 column
> 2561 - Junk after terminating ?."
>
> Both of these errors refer to a comment that appears inside ALL of your
> ontology source files. The NTriples file refers to this section of code:
>
> <http://purl.obolibrary.org/obo/BiPOm> <http://www.w3.org/2000/01/rdf-schema#comment> "BiPOm\n\n1. Copyright of ontology\n\nThe ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science  \nfrom genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit\u00E9 Paris-Sud/CNRS, France  and by the D\u00E9partement MMIP AgroParisTech of the INRA, France.\nINRA, Agroparistech and  Universit\u00E9 Paris-Sud own the copyright of the ontology BiPOm. \n\n2. License terms\n\nThe ontology BiPOm is licensed under the Creative Commons\nAttribution 4.0 Unported (CC BY 4.0) license. To view a\ncopy of this license, visit http://creativecommons.org/licenses/by/4.0/\nor send a letter to Creative Commons, 444 Castro Street, Suite 900,\nMountain View, California, 94041, USA.   \n\n\n3. Notice\nThis product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, \nlicensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/).\n\nThis product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. \n\nThis product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. \n\nThis product contains references to classes of the Systems Biology Ontology (SBO)  (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, \nlicensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php).\n\nThis product contains references to properties of the Relation Ontology (RO)  (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, \nlicensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\nThis product contains references to properties of the Basic Formal Ontology (BFO)  (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium,\n licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\n4. Contact\nFor questions and remarks concerning BiPOm:\nAnne Goelzer\nAnne.Goelzer"@inra.fr .
>
> Below is the original source code corresponding to this triple:
>
> <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BiPOm">
> <rdfs:comment xml:lang="inra.fr">BiPOm
>
> 1. Copyright of ontology
>
> The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science
> from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit? Paris-Sud/CNRS, France  and by the D?partement MMIP AgroParisTech of the INRA, France.
>
> ***************** SNIP *****************
>
>     4. Contact
> For questions and remarks concerning BiPOm:
>                                          Anne Goelzer
> Anne.Goelzer</rdfs:comment>
>     </rdf:Description>
>
> I am not an ontology development expert to point to the exact issue with
> this code, but both my colleague and I think that the language definition
> is incorrect:
>
> <rdfs:comment xml:lang="inra.fr">
>
>
> The expectation is to see something like xml:lang="en" or xml:lang=?fr"
>
> I?d recommend correcting this entry and adding a new submission of your
> ontology(ies). Also, please let us know which ontologies need to be deleted
> so as to address the incorrect acronym issue.
>
> Thank you,
>
> Michael
>
>
> ----------------------------------------------------
> Michael Dorf
> Chief Software Architect
> The National Center for Biomedical Ontology
> Stanford Biomedical Informatics Research
> mdorf at stanford.edu
> O: 650-723-0357
> M: 650-995-4374
> ----------------------------------------------------
>
> On Apr 19, 2020, at 1:41 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
>
> Hi Vincent,
>
> Here are some quick replies for now, please respond with whatever issues
> remain.
>
> - the creation of "BiPOm-RPCC-instanciated" (
> https://bioportal.bioontology.org/ontologies/BIPOM-INST)
>
> If you are asking to have this deleted, we can do that. Please confirm
> that is what you want.
>
> - the description of "BiPOm inferences for Calvin cycle" (
> https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed
> instead of following
>
> Descriptions can be modified by you; click on the pencil icon to edit the
> ontology metadata (at upper right) or the submission metadata (above the
> submission list).
>
> - the acronym of "BiPOm E-Coli metabolism instantiation" (
> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF)
> BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
> and the the acronym of "BiPOm inferences for E-Coli metabolism" (
> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF)
> BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.
>
> Acronyms can not be changed they are the index for everything in the
> system. To make this happen, you will need to re-submit your ontology(ies)
> under the new acronym you want to use, then tell us to delete the original
> ontology(ies). Unfortunately the history will be lost.
>
> Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?
>
> I don't have time to look at the details at this moment, but the best way
> to figure this out is to try loading the ontology in Protege. If it is not
> parseable in BioPortal (which is what this indicates), it is almost always
> not parseable in Protege, for the same reasons because they use the same
> parser. And Protege actually shows you the errors, which makes it a much
> better tool for finding and fixing issues.
>
> Hope this helps!
>
> John
>
>
> On Apr 18, 2020, at 6:25 AM, support at bioontology.org wrote:
>
> Name: VJHenry
>
> Email: vincent643 at gmail.com <vincent643 at gmail.com>
>
> Location: https%3A%2F%2Fbioportal.bioontology.org
> <http://2fbioportal.bioontology.org/>%2Fontologies%2FBIPOM-CC-INF
>
>
> *Feedback:*
>
> Hi,
> I'm wondering if its possible to change some mistakes I made:
> - the creation of "BiPOm-RPCC-instanciated" (
> https://bioportal.bioontology.org/ontologies/BIPOM-INST)
> - the description of "BiPOm inferences for Calvin cycle" (
> https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed
> instead of following
> - the acronym of "BiPOm E-Coli metabolism instantiation" (
> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF)
> BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
> and the the acronym of "BiPOm inferences for E-Coli metabolism" (
> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF)
> BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.
>
> Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?
>
> Thank you very much for all,
> Best regards,
> Vincent (VJHenry; vincent643 at gmail.com)
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632  | ORCID  0000-0001-6875-5360
>
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
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From support at bioontology.org  Mon Apr 20 23:56:41 2020
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 20 Apr 2020 23:56:41 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Serenella Ferro
	Rojas
Message-ID: <5e9e9929eb6c0_6d24292ade0910cc@ncbo-prd-app-09.stanford.edu.mail>

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From vincent643 at gmail.com  Wed Apr 22 01:00:08 2020
From: vincent643 at gmail.com (Vincent Henry)
Date: Wed, 22 Apr 2020 10:00:08 +0200
Subject: [bioontology-support] [BioPortal] Feedback from VJHenry
In-Reply-To: <7E4F9CF6-A52D-46B0-8DD4-D4E819855B2E@stanford.edu>
References: <5e9affd09c4c_46e31f6ed7491039@ncbo-prd-app-09.stanford.edu.mail>
 <70FD3E82-3BE3-477A-8BF7-6BC634D646D3@stanford.edu>
 <6722A1B6-7671-4B54-A6BE-3C3144A80937@stanford.edu>
 <CAE681gryqt22a1_DXk63QeOeOcxJmKYqb7k7p4m=rY+4dLfxEA@mail.gmail.com>
 <7E4F9CF6-A52D-46B0-8DD4-D4E819855B2E@stanford.edu>
Message-ID: <CAE681gr1TO50t7t7LTpJG9fsXwALSY0VPTsxfCGZNoNx94epuQ@mail.gmail.com>

Hi Micheal,

Thank you very much for your the deletion (all my apologies for my mistake)
and for your help.
I modified the files and it were well integrate in BioPortal.

Thanks again,
Best regards,

Vincent

On Tue, Apr 21, 2020 at 9:57 PM Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Vincent,
>
> I?ve deleted BIPOM-INST ontology from our system. As far the error, I
> think the culprit is the language designation, not the contact email. That
> last fragment should end with:
>
> nAnne Goelzer\nAnne.Goelzer?@en
>>
>> instead of:
>
> nAnne Goelzer\nAnne.Goelzer"@inra.fr
>>
>>
> The @en indicates the language from this field:
>
> <rdfs:comment xml:lang="inra.fr">
>>
>>
> This should instead read:
>
> <rdfs:comment xml:lang="en">
>>
>>
> Hope this clarifies it.
>
> Michael
>
>
> On Apr 21, 2020, at 9:26 AM, Vincent Henry <vincent643 at gmail.com> wrote:
>
> Hi Michael,
>
> Thank you very much for your return.
> You're right, it is a contact email address with "@" that was
> misinterpreted.
> I'll never find it by myself. I'll upload new files.
>
> Best regards,
> Vincent
>
> On Tue, Apr 21, 2020 at 1:31 AM Michael Vladimir Dorf <mdorf at stanford.edu>
> wrote:
>
>> Hi Vincent,
>>
>> I?ve done some further troubleshooting of your ontologies, and some flags
>> were raised by our tools in regards to their source:
>>
>> Although we can load the ontologies without errors (including in
>> Protege), the second step in the parsing process fails when we attempt to
>> serialize the data to ntriples format to load it into our RDF store:
>>
>> ? repository/BIPOM-CC-INF/1 ? rapper -i ntriples -c data.triples
>> rapper: Parsing URI
>> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples with parser
>> ntriples
>> rapper: Error - URI
>> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:2 column
>> 2531 - Junk after terminating "."
>> rapper: Error - URI
>> file:///dev/ncbo/test/repository/BIPOM-CC-INF/1/data.triples:9647 column
>> 2561 - Junk after terminating ?."
>>
>> Both of these errors refer to a comment that appears inside ALL of your
>> ontology source files. The NTriples file refers to this section of code:
>>
>> <http://purl.obolibrary.org/obo/BiPOm> <http://www.w3.org/2000/01/rdf-schema#comment> "BiPOm\n\n1. Copyright of ontology\n\nThe ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science  \nfrom genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit\u00E9 Paris-Sud/CNRS, France  and by the D\u00E9partement MMIP AgroParisTech of the INRA, France.\nINRA, Agroparistech and  Universit\u00E9 Paris-Sud own the copyright of the ontology BiPOm. \n\n2. License terms\n\nThe ontology BiPOm is licensed under the Creative Commons\nAttribution 4.0 Unported (CC BY 4.0) license. To view a\ncopy of this license, visit http://creativecommons.org/licenses/by/4.0/\nor send a letter to Creative Commons, 444 Castro Street, Suite 900,\nMountain View, California, 94041, USA.   \n\n\n3. Notice\nThis product contains references to classes of the Gene Ontology (GO) (http://geneontology.org/) developed by the Gene Ontology consortium, \nlicensed under the terms Creative Commons Attribution 4.0 Unported license (https://creativecommons.org/licenses/by/4.0/).\n\nThis product contains references to classes of the Chemical Entities of Biological Interest (ChEBI) (https://www.ebi.ac.uk/chebi/init.do) developed by the ChEBI consortium. \n\nThis product contains references to classes of the Sequence Ontology (SO) (http://www.sequenceontology.org/) developed by the SO consortium and are freely reusable. \n\nThis product contains references to classes of the Systems Biology Ontology (SBO)  (http://www.ebi.ac.uk/sbo/main/) developed by the SBO consortium, \nlicensed under the terms of Artistic License 2.0 (https://opensource.org/licenses/artistic-license-2.0.php).\n\nThis product contains references to properties of the Relation Ontology (RO)  (http://www.obofoundry.org/ontology/ro.html) developed by the OBO foundry, \nlicensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\nThis product contains references to properties of the Basic Formal Ontology (BFO)  (http://ifomis.uni-saarland.de/bfo/) developed by the BFO consortium,\n licensed under the terms Creative Commons Attribution 3.0 Unported License (https://creativecommons.org/licenses/by/3.0/).\n\n4. Contact\nFor questions and remarks concerning BiPOm:\nAnne Goelzer\nAnne.Goelzer"@inra.fr .
>>
>> Below is the original source code corresponding to this triple:
>>
>> <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BiPOm">
>> <rdfs:comment xml:lang="inra.fr">BiPOm
>>
>> 1. Copyright of ontology
>>
>> The ontology was created jointly by the BioSys group at the research unit of Applied mathematics and computer science
>> from genomes to the environment (MaIAGE) of the Institut National de la Recherche Agronomique (INRA) France, by the group the Large-scale Heterogeneous DAta and Knowledge (LaHDAK team) of the Laboratoire de recherche en informatique (LRI) of the Universit? Paris-Sud/CNRS, France  and by the D?partement MMIP AgroParisTech of the INRA, France.
>>
>> ***************** SNIP *****************
>>
>>     4. Contact
>> For questions and remarks concerning BiPOm:
>>                                          Anne Goelzer
>> Anne.Goelzer</rdfs:comment>
>>     </rdf:Description>
>>
>> I am not an ontology development expert to point to the exact issue with
>> this code, but both my colleague and I think that the language definition
>> is incorrect:
>>
>> <rdfs:comment xml:lang="inra.fr">
>>
>>
>> The expectation is to see something like xml:lang="en" or xml:lang=?fr"
>>
>> I?d recommend correcting this entry and adding a new submission of your
>> ontology(ies). Also, please let us know which ontologies need to be deleted
>> so as to address the incorrect acronym issue.
>>
>> Thank you,
>>
>> Michael
>>
>>
>> ----------------------------------------------------
>> Michael Dorf
>> Chief Software Architect
>> The National Center for Biomedical Ontology
>> Stanford Biomedical Informatics Research
>> mdorf at stanford.edu
>> O: 650-723-0357
>> M: 650-995-4374
>> ----------------------------------------------------
>>
>> On Apr 19, 2020, at 1:41 PM, John Graybeal <jgraybeal at stanford.edu>
>> wrote:
>>
>> Hi Vincent,
>>
>> Here are some quick replies for now, please respond with whatever issues
>> remain.
>>
>> - the creation of "BiPOm-RPCC-instanciated" (
>> https://bioportal.bioontology.org/ontologies/BIPOM-INST)
>>
>> If you are asking to have this deleted, we can do that. Please confirm
>> that is what you want.
>>
>> - the description of "BiPOm inferences for Calvin cycle" (
>> https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed
>> instead of following
>>
>> Descriptions can be modified by you; click on the pencil icon to edit the
>> ontology metadata (at upper right) or the submission metadata (above the
>> submission list).
>>
>> - the acronym of "BiPOm E-Coli metabolism instantiation" (
>> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF)
>> BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
>> and the the acronym of "BiPOm inferences for E-Coli metabolism" (
>> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF)
>> BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.
>>
>> Acronyms can not be changed they are the index for everything in the
>> system. To make this happen, you will need to re-submit your ontology(ies)
>> under the new acronym you want to use, then tell us to delete the original
>> ontology(ies). Unfortunately the history will be lost.
>>
>> Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?
>>
>> I don't have time to look at the details at this moment, but the best way
>> to figure this out is to try loading the ontology in Protege. If it is not
>> parseable in BioPortal (which is what this indicates), it is almost always
>> not parseable in Protege, for the same reasons because they use the same
>> parser. And Protege actually shows you the errors, which makes it a much
>> better tool for finding and fixing issues.
>>
>> Hope this helps!
>>
>> John
>>
>>
>> On Apr 18, 2020, at 6:25 AM, support at bioontology.org wrote:
>>
>> Name: VJHenry
>>
>> Email: vincent643 at gmail.com <vincent643 at gmail.com>
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org
>> <http://2fbioportal.bioontology.org/>%2Fontologies%2FBIPOM-CC-INF
>>
>>
>> *Feedback:*
>>
>> Hi,
>> I'm wondering if its possible to change some mistakes I made:
>> - the creation of "BiPOm-RPCC-instanciated" (
>> https://bioportal.bioontology.org/ontologies/BIPOM-INST)
>> - the description of "BiPOm inferences for Calvin cycle" (
>> https://bioportal.bioontology.org/ontologies/BIPOM-CC-INF) followed
>> instead of following
>> - the acronym of "BiPOm E-Coli metabolism instantiation" (
>> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INF)
>> BIPOM-ECMET-INST instead of BIPOM-ECMET-INF
>> and the the acronym of "BiPOm inferences for E-Coli metabolism" (
>> https://bioportal.bioontology.org/ontologies/BIPOM-ECMET-INFF)
>> BIPOM-ECMET-INF instead of BIPOM-ECMET-INFF.
>>
>> Finally I'm wondering why my recent uploads are mentioned as "Error Rdf" ?
>>
>> Thank you very much for all,
>> Best regards,
>> Vincent (VJHenry; vincent643 at gmail.com)
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>> 650-736-1632  | ORCID  0000-0001-6875-5360
>>
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>>
>
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From support at bioontology.org  Wed Apr 22 05:26:11 2020
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 22 Apr 2020 05:26:11 -0700
Subject: [bioontology-support] [BioPortal] Feedback from chen.yang@ugent.be
Message-ID: <5ea037e3b7038_7062820c889693a@ncbo-prd-app-09.stanford.edu.mail>

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From mdorf at stanford.edu  Wed Apr 22 12:13:33 2020
From: mdorf at stanford.edu (Michael Dorf)
Date: Wed, 22 Apr 2020 19:13:33 +0000
Subject: [bioontology-support] [BioPortal] Feedback from
 chen.yang@ugent.be
In-Reply-To: <5ea037e3b7038_7062820c889693a@ncbo-prd-app-09.stanford.edu.mail>
References: <5ea037e3b7038_7062820c889693a@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <D117FBAE-22A2-423E-9532-64DEA2103B18@stanford.edu>

Hi Chen,

Thank you for contacting us. The description for ontology is attached to the submission record, meaning if you submit a new version of the ontology (new submission), its description may be different from the previous one. To modify the description, click on the blue edit icon next to Submissions header (see image below).

Hope this helps!

Michael

[cid:66072A4E-44BA-417B-8B18-B75665EA0D44 at stanford.edu]

On Apr 22, 2020, at 5:26 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.bioontology.org<http://252Fpurl.bioontology.org>%252Fontology%252FONE%252Fstandards%2523caseStudies

Feedback:

Dear,
I am the developer of the ontology for nutritional epidemiology (https://bioportal.bioontology.org/ontologies/ONE). I was going to edit the "Description" of the ontology on the page. However, I did not find where I can do the change. Could you please help me?
Thanks in advance, Chen

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

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From support at bioontology.org  Fri Apr 24 12:47:36 2020
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 24 Apr 2020 12:47:36 -0700
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
Message-ID: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>

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From jgraybeal at stanford.edu  Fri Apr 24 15:09:25 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 24 Apr 2020 22:09:25 +0000
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>

Hi Shruthi,

I am happy to help you, and just want to clarify the situation.

I can see a public ontology called SCO that fits your description, with you as the contact, and it seems to be publicly visible. So if you are still having trouble seeing this ontology, can you please provide further details about what you are doing?

It appears the owner of the ontology may have been mis-assigned (possibly an operator error on our side); I have re-assigned you as the owner.

My apologies for this issue. Please try to access it and let me know if you have any difficulty.

john

On Apr 24, 2020, at 12:47 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: shruthichari

Email: charis at rpi.edu<mailto:charis at rpi.edu>

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

Feedback:

Hi Sir/Madam,

I had an ontology on Bioportal under the name, Study Cohort Ontology and acronym, SCO. Not only can I not find it anymore but I can't resubmit as somebody else has made a submission. I attest that I am the author of this ontology and we even have a paper in the International Semantic Web Conference (ISWC) last year: https://arxiv.org/abs/1907.04358. Can you please help me resubmit my ontology?

Feel free to reach out to me at charis at rpi.edu<mailto:charis at rpi.edu>

-Thanks,
Shruthi

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

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



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From jgraybeal at stanford.edu  Fri Apr 24 16:06:34 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 24 Apr 2020 23:06:34 +0000
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
 <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
 <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>
Message-ID: <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu>

Ah, that explains it, thank you.

I have changed the setting to not be View, and saved that. (It would have showed up previously, if you enabled the Views checkbox. But if it isn't a view that isn't what you want!)

There may be some additional processing required as a result; I'll ask our expert on such things when she is back on Monday.

I notice there are no classes being displayed, due to an RDF parsing error; do you understand why that is? Let us know if you need help figuring that out?my basic rule of thumb is to try opening it in Protege to see if that reports any errors, and fix all those first. If it works there but not in BioPortal, let us know and we'll try to hep.

John

On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu<mailto:charis at rpi.edu>> wrote:

Hi John,

Thanks so much for reassigning ownership to me, with this, I am able to upload a new version. I have a problem in that my ontology doesn't show up on Bioportal's main page as an ontology page as I accidentally made it an ontology view. Can you help revert this option and instead set it as an ontology?

-Thanks,
Shruthi

On 2020-04-24 18:09, John Graybeal wrote:
Hi Shruthi,
I am happy to help you, and just want to clarify the situation.
I can see a public ontology called SCO that fits your description,
with you as the contact, and it seems to be publicly visible. So if
you are still having trouble seeing this ontology, can you please
provide further details about what you are doing?
It appears the owner of the ontology may have been mis-assigned
(possibly an operator error on our side); I have re-assigned you as
the owner.
My apologies for this issue. Please try to access it and let me know
if you have any difficulty.
john
On Apr 24, 2020, at 12:47 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:
Name: shruthichari
Email: charis at rpi.edu<mailto:charis at rpi.edu>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/> [1]%2Fontologies
FEEDBACK:
Hi Sir/Madam,
I had an ontology on Bioportal under the name, Study Cohort Ontology
and acronym, SCO. Not only can I not find it anymore but I can't
resubmit as somebody else has made a submission. I attest that I am
the author of this ontology and we even have a paper in the
International Semantic Web Conference (ISWC) last year:
https://arxiv.org/abs/1907.04358 [2]. Can you please help me
resubmit my ontology?
Feel free to reach out to me at charis at rpi.edu
-Thanks,
Shruthi
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632 | ORCID 0000-0001-6875-5360
Links:
------
[1] http://2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>
[2] https://arxiv.org/abs/1907.04358

========================
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 --------------
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From jgraybeal at stanford.edu  Fri Apr 24 16:48:35 2020
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 24 Apr 2020 23:48:35 +0000
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <30a7355d5a089c13602f7139326bb4eb@rpi.edu>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
 <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
 <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>
 <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu>
 <30a7355d5a089c13602f7139326bb4eb@rpi.edu>
Message-ID: <AF01D482-E80D-4D26-9A96-C05BE383ADE4@stanford.edu>

Hi Shruthi,

I had a look at the logs.  There appear to be two locations in the file that say "rdf:resoure" (instead of rdf:resource). Just a warning in the OWLAPI parser, but our Rapper software (http://librdf.org/raptor/rapper.html) didn't like it.  See if fixing those makes it better, yes?

John



On Apr 24, 2020, at 4:23 PM, Shruthi Chari <charis at rpi.edu<mailto:charis at rpi.edu>> wrote:

Hi John,

I don't want it to be a view yes. Thanks for making the change.

As for the RDF parsing error, I am not sure what is happening. Can you send me the log as I don't see to it on my end. I don't see errors on Protege per se it opens there. I am attaching a screenshot for your reference.

However, I want to make some import clean up changes so I will work on that and hopefully it should render better?

Not sure why it doesn't render on Bioportal though.

-Thanks,
Shruthi

On 2020-04-24 19:06, John Graybeal wrote:
Ah, that explains it, thank you.
I have changed the setting to not be View, and saved that. (It would
have showed up previously, if you enabled the Views checkbox. But if
it isn't a view that isn't what you want!)
There may be some additional processing required as a result; I'll ask
our expert on such things when she is back on Monday.
I notice there are no classes being displayed, due to an RDF parsing
error; do you understand why that is? Let us know if you need help
figuring that out?my basic rule of thumb is to try opening it in
Protege to see if that reports any errors, and fix all those first. If
it works there but not in BioPortal, let us know and we'll try to hep.
John
On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu<mailto:charis at rpi.edu>> wrote:
Hi John,
Thanks so much for reassigning ownership to me, with this, I am
able to upload a new version. I have a problem in that my ontology
doesn't show up on Bioportal's main page as an ontology page as I
accidentally made it an ontology view. Can you help revert this
option and instead set it as an ontology?
-Thanks,
Shruthi
On 2020-04-24 18:09, John Graybeal wrote:
Hi Shruthi,
I am happy to help you, and just want to clarify the situation.
I can see a public ontology called SCO that fits your description,
with you as the contact, and it seems to be publicly visible. So if
you are still having trouble seeing this ontology, can you please
provide further details about what you are doing?
It appears the owner of the ontology may have been mis-assigned
(possibly an operator error on our side); I have re-assigned you as
the owner.
My apologies for this issue. Please try to access it and let me
know
if you have any difficulty.
john
On Apr 24, 2020, at 12:47 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:
Name: shruthichari
Email: charis at rpi.edu<mailto:charis at rpi.edu>
Location: https%3A%2F%2Fbioportal.bioontology.org [1]
[1]%2Fontologies
FEEDBACK:
Hi Sir/Madam,
I had an ontology on Bioportal under the name, Study Cohort
Ontology
and acronym, SCO. Not only can I not find it anymore but I can't
resubmit as somebody else has made a submission. I attest that I am
the author of this ontology and we even have a paper in the
International Semantic Web Conference (ISWC) last year:
https://arxiv.org/abs/1907.04358 [2] [2]. Can you please help me
resubmit my ontology?
Feel free to reach out to me at charis at rpi.edu<mailto:charis at rpi.edu>
-Thanks,
Shruthi
_______________________________________________
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
Links:
------
[1] http://2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/> [1]
[2] https://arxiv.org/abs/1907.04358 [2]
========================
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
Links:
------
[1] http://2fbioportal.bioontology.org/
[2] https://arxiv.org/abs/1907.04358
<Screenshot 2020-04-24 at 7.15.07 PM.png>

========================
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 --------------
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From charis at rpi.edu  Fri Apr 24 15:50:10 2020
From: charis at rpi.edu (Shruthi Chari)
Date: Fri, 24 Apr 2020 18:50:10 -0400
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
 <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
Message-ID: <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>

Hi John,

Thanks so much for reassigning ownership to me, with this, I am able to 
upload a new version. I have a problem in that my ontology doesn't show 
up on Bioportal's main page as an ontology page as I accidentally made 
it an ontology view. Can you help revert this option and instead set it 
as an ontology?

-Thanks,
Shruthi

On 2020-04-24 18:09, John Graybeal wrote:
> Hi Shruthi,
> 
> I am happy to help you, and just want to clarify the situation.
> 
> I can see a public ontology called SCO that fits your description,
> with you as the contact, and it seems to be publicly visible. So if
> you are still having trouble seeing this ontology, can you please
> provide further details about what you are doing?
> 
> It appears the owner of the ontology may have been mis-assigned
> (possibly an operator error on our side); I have re-assigned you as
> the owner.
> 
> My apologies for this issue. Please try to access it and let me know
> if you have any difficulty.
> 
> john
> 
>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote:
>> 
>> Name: shruthichari
>> 
>> Email: charis at rpi.edu
>> 
>> Location: https%3A%2F%2Fbioportal.bioontology.org [1]%2Fontologies
>> 
>> FEEDBACK:
>> 
>> Hi Sir/Madam,
>> 
>> I had an ontology on Bioportal under the name, Study Cohort Ontology
>> and acronym, SCO. Not only can I not find it anymore but I can't
>> resubmit as somebody else has made a submission. I attest that I am
>> the author of this ontology and we even have a paper in the
>> International Semantic Web Conference (ISWC) last year:
>> https://arxiv.org/abs/1907.04358 [2]. Can you please help me
>> resubmit my ontology?
>> 
>> Feel free to reach out to me at charis at rpi.edu
>> 
>> -Thanks,
>> Shruthi
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
>  ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
>  650-736-1632 | ORCID 0000-0001-6875-5360
> 
> 
> 
> Links:
> ------
> [1] http://2Fbioportal.bioontology.org
> [2] https://arxiv.org/abs/1907.04358

From support at bioontology.org  Mon Apr 27 00:13:55 2020
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 27 Apr 2020 00:13:55 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Thomas Lemberger
Message-ID: <5ea68633fb1e_56be2b660c88145e@ncbo-prd-app-08.stanford.edu.mail>

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From charis at rpi.edu  Fri Apr 24 16:23:03 2020
From: charis at rpi.edu (Shruthi Chari)
Date: Fri, 24 Apr 2020 19:23:03 -0400
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
 <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
 <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>
 <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu>
Message-ID: <30a7355d5a089c13602f7139326bb4eb@rpi.edu>

Hi John,

I don't want it to be a view yes. Thanks for making the change.

As for the RDF parsing error, I am not sure what is happening. Can you 
send me the log as I don't see to it on my end. I don't see errors on 
Protege per se it opens there. I am attaching a screenshot for your 
reference.

However, I want to make some import clean up changes so I will work on 
that and hopefully it should render better?

Not sure why it doesn't render on Bioportal though.

-Thanks,
Shruthi

On 2020-04-24 19:06, John Graybeal wrote:
> Ah, that explains it, thank you.
> 
> I have changed the setting to not be View, and saved that. (It would
> have showed up previously, if you enabled the Views checkbox. But if
> it isn't a view that isn't what you want!)
> 
> There may be some additional processing required as a result; I'll ask
> our expert on such things when she is back on Monday.
> 
> I notice there are no classes being displayed, due to an RDF parsing
> error; do you understand why that is? Let us know if you need help
> figuring that out?my basic rule of thumb is to try opening it in
> Protege to see if that reports any errors, and fix all those first. If
> it works there but not in BioPortal, let us know and we'll try to hep.
> 
> 
> John
> 
>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu> wrote:
>> 
>> Hi John,
>> 
>> Thanks so much for reassigning ownership to me, with this, I am
>> able to upload a new version. I have a problem in that my ontology
>> doesn't show up on Bioportal's main page as an ontology page as I
>> accidentally made it an ontology view. Can you help revert this
>> option and instead set it as an ontology?
>> 
>> -Thanks,
>> Shruthi
>> 
>> On 2020-04-24 18:09, John Graybeal wrote:
>> Hi Shruthi,
>> I am happy to help you, and just want to clarify the situation.
>> I can see a public ontology called SCO that fits your description,
>> with you as the contact, and it seems to be publicly visible. So if
>> you are still having trouble seeing this ontology, can you please
>> provide further details about what you are doing?
>> It appears the owner of the ontology may have been mis-assigned
>> (possibly an operator error on our side); I have re-assigned you as
>> the owner.
>> My apologies for this issue. Please try to access it and let me
>> know
>> if you have any difficulty.
>> john
>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote:
>> Name: shruthichari
>> Email: charis at rpi.edu
>> Location: https%3A%2F%2Fbioportal.bioontology.org [1]
>> [1]%2Fontologies
>> FEEDBACK:
>> Hi Sir/Madam,
>> I had an ontology on Bioportal under the name, Study Cohort
>> Ontology
>> and acronym, SCO. Not only can I not find it anymore but I can't
>> resubmit as somebody else has made a submission. I attest that I am
>> the author of this ontology and we even have a paper in the
>> International Semantic Web Conference (ISWC) last year:
>> https://arxiv.org/abs/1907.04358 [2] [2]. Can you please help me
>> resubmit my ontology?
>> Feel free to reach out to me at charis at rpi.edu
>> -Thanks,
>> Shruthi
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO
>> BioPortal
>> Stanford Center for Biomedical Informatics Research
>> 650-736-1632 | ORCID 0000-0001-6875-5360
>> Links:
>> ------
>> [1] http://2Fbioportal.bioontology.org [1]
>> [2] https://arxiv.org/abs/1907.04358 [2]
> 
>  ========================
> 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
> 
> 
> 
> Links:
> ------
> [1] http://2fbioportal.bioontology.org/
> [2] https://arxiv.org/abs/1907.04358
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From charis at rpi.edu  Fri Apr 24 19:02:23 2020
From: charis at rpi.edu (Shruthi Chari)
Date: Fri, 24 Apr 2020 22:02:23 -0400
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <AF01D482-E80D-4D26-9A96-C05BE383ADE4@stanford.edu>
References: <AF01D482-E80D-4D26-9A96-C05BE383ADE4@stanford.edu>
Message-ID: <9BC3F099-3A8C-4426-BE69-8A85D158C38E@rpi.edu>

Hi John,

Great thanks I will fix those issues. Thanks for the tool reference I will use it to test.

So just to confirm if I run my ontology through this tool, is Bioportal guaranteed to render it?

-Thanks,
Shruthi 

Sent from my iPhone

> On Apr 24, 2020, at 7:48 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
> 
> ? Hi Shruthi,
> 
> I had a look at the logs.  There appear to be two locations in the file that say "rdf:resoure" (instead of rdf:resource). Just a warning in the OWLAPI parser, but our Rapper software (http://librdf.org/raptor/rapper.html) didn't like it.  See if fixing those makes it better, yes?
> 
> John
> 
> 
> 
>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari <charis at rpi.edu> wrote:
>> 
>> Hi John,
>> 
>> I don't want it to be a view yes. Thanks for making the change.
>> 
>> As for the RDF parsing error, I am not sure what is happening. Can you send me the log as I don't see to it on my end. I don't see errors on Protege per se it opens there. I am attaching a screenshot for your reference.
>> 
>> However, I want to make some import clean up changes so I will work on that and hopefully it should render better?
>> 
>> Not sure why it doesn't render on Bioportal though.
>> 
>> -Thanks,
>> Shruthi
>> 
>>> On 2020-04-24 19:06, John Graybeal wrote:
>>> Ah, that explains it, thank you.
>>> I have changed the setting to not be View, and saved that. (It would
>>> have showed up previously, if you enabled the Views checkbox. But if
>>> it isn't a view that isn't what you want!)
>>> There may be some additional processing required as a result; I'll ask
>>> our expert on such things when she is back on Monday.
>>> I notice there are no classes being displayed, due to an RDF parsing
>>> error; do you understand why that is? Let us know if you need help
>>> figuring that out?my basic rule of thumb is to try opening it in
>>> Protege to see if that reports any errors, and fix all those first. If
>>> it works there but not in BioPortal, let us know and we'll try to hep.
>>> John
>>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>>> Hi John,
>>>> Thanks so much for reassigning ownership to me, with this, I am
>>>> able to upload a new version. I have a problem in that my ontology
>>>> doesn't show up on Bioportal's main page as an ontology page as I
>>>> accidentally made it an ontology view. Can you help revert this
>>>> option and instead set it as an ontology?
>>>> -Thanks,
>>>> Shruthi
>>>> On 2020-04-24 18:09, John Graybeal wrote:
>>>> Hi Shruthi,
>>>> I am happy to help you, and just want to clarify the situation.
>>>> I can see a public ontology called SCO that fits your description,
>>>> with you as the contact, and it seems to be publicly visible. So if
>>>> you are still having trouble seeing this ontology, can you please
>>>> provide further details about what you are doing?
>>>> It appears the owner of the ontology may have been mis-assigned
>>>> (possibly an operator error on our side); I have re-assigned you as
>>>> the owner.
>>>> My apologies for this issue. Please try to access it and let me
>>>> know
>>>> if you have any difficulty.
>>>> john
>>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote:
>>>> Name: shruthichari
>>>> Email: charis at rpi.edu
>>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1]
>>>> [1]%2Fontologies
>>>> FEEDBACK:
>>>> Hi Sir/Madam,
>>>> I had an ontology on Bioportal under the name, Study Cohort
>>>> Ontology
>>>> and acronym, SCO. Not only can I not find it anymore but I can't
>>>> resubmit as somebody else has made a submission. I attest that I am
>>>> the author of this ontology and we even have a paper in the
>>>> International Semantic Web Conference (ISWC) last year:
>>>> https://arxiv.org/abs/1907.04358 [2] [2]. Can you please help me
>>>> resubmit my ontology?
>>>> Feel free to reach out to me at charis at rpi.edu
>>>> -Thanks,
>>>> Shruthi
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>> ========================
>>>> John Graybeal
>>>> Technical Program Manager
>>>> Center for Expanded Data Annotation and Retrieval /+/ NCBO
>>>> BioPortal
>>>> Stanford Center for Biomedical Informatics Research
>>>> 650-736-1632 | ORCID 0000-0001-6875-5360
>>>> Links:
>>>> ------
>>>> [1] http://2Fbioportal.bioontology.org [1]
>>>> [2] https://arxiv.org/abs/1907.04358 [2]
>>> ========================
>>> 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
>>> Links:
>>> ------
>>> [1] http://2fbioportal.bioontology.org/
>>> [2] https://arxiv.org/abs/1907.04358
>> <Screenshot 2020-04-24 at 7.15.07 PM.png>
> 
> ========================
> 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 --------------
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From charis at rpi.edu  Sat Apr 25 13:38:44 2020
From: charis at rpi.edu (Shruthi Chari)
Date: Sat, 25 Apr 2020 16:38:44 -0400
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <AF01D482-E80D-4D26-9A96-C05BE383ADE4@stanford.edu>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
 <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
 <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>
 <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu>
 <30a7355d5a089c13602f7139326bb4eb@rpi.edu>
 <AF01D482-E80D-4D26-9A96-C05BE383ADE4@stanford.edu>
Message-ID: <92d937d82850397ea6d36aab9f7bc85a@rpi.edu>

Hi John,

Thanks a bunch the logs you sent me were a lifesaver. I was able to 
reupload our ontology and now the classes show up. I should have reached 
out to support a year earlier, but never too late.

I am still waiting on the ontology view fix as in to revert this to be a 
stand-alone ontology and not a view. This would then allow our ontology 
to be queryable by the BioAnnotator.

Thanks for your assistance and looking forward to getting this last 
issue resolved.

-Thanks,
Shruthi

  On 2020-04-24 19:48, John Graybeal wrote:
> Hi Shruthi,
> 
> I had a look at the logs. There appear to be two locations in the file
> that say "rdf:resoure" (instead of rdf:resource). Just a warning in
> the OWLAPI parser, but our Rapper software
> (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if
> fixing those makes it better, yes?
> 
> John
> 
>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari <charis at rpi.edu> wrote:
>> 
>> Hi John,
>> 
>> I don't want it to be a view yes. Thanks for making the change.
>> 
>> As for the RDF parsing error, I am not sure what is happening. Can
>> you send me the log as I don't see to it on my end. I don't see
>> errors on Protege per se it opens there. I am attaching a screenshot
>> for your reference.
>> 
>> However, I want to make some import clean up changes so I will work
>> on that and hopefully it should render better?
>> 
>> Not sure why it doesn't render on Bioportal though.
>> 
>> -Thanks,
>> Shruthi
>> 
>> On 2020-04-24 19:06, John Graybeal wrote:
>> Ah, that explains it, thank you.
>> I have changed the setting to not be View, and saved that. (It
>> would
>> have showed up previously, if you enabled the Views checkbox. But
>> if
>> it isn't a view that isn't what you want!)
>> There may be some additional processing required as a result; I'll
>> ask
>> our expert on such things when she is back on Monday.
>> I notice there are no classes being displayed, due to an RDF
>> parsing
>> error; do you understand why that is? Let us know if you need help
>> figuring that out?my basic rule of thumb is to try opening it in
>> Protege to see if that reports any errors, and fix all those first.
>> If
>> it works there but not in BioPortal, let us know and we'll try to
>> hep.
>> John
>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu> wrote:
>> Hi John,
>> Thanks so much for reassigning ownership to me, with this, I am
>> able to upload a new version. I have a problem in that my ontology
>> doesn't show up on Bioportal's main page as an ontology page as I
>> accidentally made it an ontology view. Can you help revert this
>> option and instead set it as an ontology?
>> -Thanks,
>> Shruthi
>> On 2020-04-24 18:09, John Graybeal wrote:
>> Hi Shruthi,
>> I am happy to help you, and just want to clarify the situation.
>> I can see a public ontology called SCO that fits your description,
>> with you as the contact, and it seems to be publicly visible. So if
>> you are still having trouble seeing this ontology, can you please
>> provide further details about what you are doing?
>> It appears the owner of the ontology may have been mis-assigned
>> (possibly an operator error on our side); I have re-assigned you as
>> the owner.
>> My apologies for this issue. Please try to access it and let me
>> know
>> if you have any difficulty.
>> john
>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote:
>> Name: shruthichari
>> Email: charis at rpi.edu
>> Location: https%3A%2F%2Fbioportal.bioontology.org [1]
>> [1]%2Fontologies
>> FEEDBACK:
>> Hi Sir/Madam,
>> I had an ontology on Bioportal under the name, Study Cohort
>> Ontology
>> and acronym, SCO. Not only can I not find it anymore but I can't
>> resubmit as somebody else has made a submission. I attest that I am
>> the author of this ontology and we even have a paper in the
>> International Semantic Web Conference (ISWC) last year:
>> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help
>> me
>> resubmit my ontology?
>> Feel free to reach out to me at charis at rpi.edu
>> -Thanks,
>> Shruthi
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> [2]
>> ========================
>> 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
>> Links:
>> ------
>> [1] http://2Fbioportal.bioontology.org [3] [1]
>> [2] https://arxiv.org/abs/1907.04358 [1] [2]
>> ========================
>> 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
>> Links:
>> ------
>> [1] http://2fbioportal.bioontology.org/ [3]
>> [2] https://arxiv.org/abs/1907.04358 [1]
>  <Screenshot 2020-04-24 at 7.15.07 PM.png>
> 
>  ========================
> 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
> 
> 
> 
> Links:
> ------
> [1] https://arxiv.org/abs/1907.04358
> [2] https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> [3] http://2fbioportal.bioontology.org/
> [4] http://librdf.org/raptor/rapper.html

From support at bioontology.org  Sat Apr 25 14:19:32 2020
From: support at bioontology.org (support at bioontology.org)
Date: Sat, 25 Apr 2020 14:19:32 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Jay Franklin
Message-ID: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail>

An HTML attachment was scrubbed...
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From vendetti at stanford.edu  Mon Apr 27 10:10:46 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 27 Apr 2020 17:10:46 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Thomas Lemberger
In-Reply-To: <5ea68633fb1e_56be2b660c88145e@ncbo-prd-app-08.stanford.edu.mail>
References: <5ea68633fb1e_56be2b660c88145e@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <0CFC2970-5C49-49C2-B2E4-E87922E982ED@stanford.edu>

Hi Thomas,

Apologies that I?m not following your question. When end users upload an ontology to BioPortal, we generate the CSV from the original ontology source file. Could you give me an example of a term from the ontology where you feel there is a discrepancy between the OWL file content and the CSV? It would be helpful if I could have a starting point to look into this in more detail.

Kind regards,
Jennifer



On Apr 27, 2020, at 12:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Thomas Lemberger

Email: thomas.lemberger at embo.org<mailto:thomas.lemberger at embo.org>

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

Feedback:

Dear Helpdesk,

I am trying to download the BAO ontology http://bioportal.bioontology.org/ontologies/BAO as an .owl file from http://data.bioontology.org/ontologies/BAO/submissions/36/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb
Unfortunately, this owl file seems incomplete and does not include any description of the terms, definitions etc. This information is present in the .csv file http://data.bioontology.org/ontologies/BAO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=csv but not in the owl.

Is there a way to regenerate the .owl files so that they contain the complete ontology?

Man thanks!

Thomas

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

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From vendetti at stanford.edu  Mon Apr 27 10:26:24 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 27 Apr 2020 17:26:24 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jay Franklin
In-Reply-To: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail>
References: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <BB18EE09-65F3-4F62-9CFB-4EB645339953@stanford.edu>

Hi Jay,

I looked at CMO in our system and it appears that the latest version (uploaded on January 7th) failed to parse. The status is showing as "Error Rdf?. This is the underlying reason that the Annotator doesn?t include results from this ontology. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/164

? and am looking into the parsing errors.

Kind regards.
Jennifer



On Apr 25, 2020, at 2:19 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jay Franklin

Email: frankj7 at rpi.edu<mailto:frankj7 at rpi.edu>

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

Feedback:

Hi,

It seems as though the Clinical Measurements Ontology (CMO) is not working correctly with the Annotator tool right now. Although I can select CMO in the drop-down list of ontologies, when I input biomedical text to be annotated CMO is never returned. For example, "diastolic blood pressure" does not return its corresponding IRI "http://purl.obolibrary.org/obo/CMO_0000004".

Is this an error within the Annotator, or am I misusing the software somehow? I would like to use the Annotator with CMO, so please let me know if something can be done about this.

Thanks,
Jay Franklin
Rensselaer Polytechnic Institute

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

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From vendetti at stanford.edu  Mon Apr 27 11:11:59 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 27 Apr 2020 18:11:59 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jay Franklin
In-Reply-To: <BB18EE09-65F3-4F62-9CFB-4EB645339953@stanford.edu>
References: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail>
 <BB18EE09-65F3-4F62-9CFB-4EB645339953@stanford.edu>
Message-ID: <D83CD11B-DAD1-4BF7-9819-9A082A2A7A34@stanford.edu>

Hi again Jay,

I found the error in the ontology source file that is causing the parsing error, and have asked the maintainers if they could repair it:

https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues/3

If I don?t get a response shortly, I?ll attempt to fix it on our end and reprocess.

Jennifer


On Apr 27, 2020, at 10:26 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Jay,

I looked at CMO in our system and it appears that the latest version (uploaded on January 7th) failed to parse. The status is showing as "Error Rdf?. This is the underlying reason that the Annotator doesn?t include results from this ontology. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/164

? and am looking into the parsing errors.

Kind regards.
Jennifer



On Apr 25, 2020, at 2:19 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jay Franklin

Email: frankj7 at rpi.edu<mailto:frankj7 at rpi.edu>

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

Feedback:

Hi,

It seems as though the Clinical Measurements Ontology (CMO) is not working correctly with the Annotator tool right now. Although I can select CMO in the drop-down list of ontologies, when I input biomedical text to be annotated CMO is never returned. For example, "diastolic blood pressure" does not return its corresponding IRI "http://purl.obolibrary.org/obo/CMO_0000004".

Is this an error within the Annotator, or am I misusing the software somehow? I would like to use the Annotator with CMO, so please let me know if something can be done about this.

Thanks,
Jay Franklin
Rensselaer Polytechnic Institute

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

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

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From vendetti at stanford.edu  Mon Apr 27 11:52:59 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 27 Apr 2020 18:52:59 +0000
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <92d937d82850397ea6d36aab9f7bc85a@rpi.edu>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
 <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
 <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>
 <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu>
 <30a7355d5a089c13602f7139326bb4eb@rpi.edu>
 <AF01D482-E80D-4D26-9A96-C05BE383ADE4@stanford.edu>
 <92d937d82850397ea6d36aab9f7bc85a@rpi.edu>
Message-ID: <E803EC66-209C-4EFD-905D-629F049CF901@stanford.edu>

Hello Shruthi

Your ontology has been fully converted to standalone vs. a view. I?ve also reprocessed your ontology so that you can use it with the Annotator functionality.

Kind regards,
Jennifer



> On Apr 25, 2020, at 1:38 PM, Shruthi Chari <charis at rpi.edu> wrote:
> 
> Hi John,
> 
> Thanks a bunch the logs you sent me were a lifesaver. I was able to reupload our ontology and now the classes show up. I should have reached out to support a year earlier, but never too late.
> 
> I am still waiting on the ontology view fix as in to revert this to be a stand-alone ontology and not a view. This would then allow our ontology to be queryable by the BioAnnotator.
> 
> Thanks for your assistance and looking forward to getting this last issue resolved.
> 
> -Thanks,
> Shruthi
> 
> On 2020-04-24 19:48, John Graybeal wrote:
>> Hi Shruthi,
>> I had a look at the logs. There appear to be two locations in the file
>> that say "rdf:resoure" (instead of rdf:resource). Just a warning in
>> the OWLAPI parser, but our Rapper software
>> (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if
>> fixing those makes it better, yes?
>> John
>>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>> Hi John,
>>> I don't want it to be a view yes. Thanks for making the change.
>>> As for the RDF parsing error, I am not sure what is happening. Can
>>> you send me the log as I don't see to it on my end. I don't see
>>> errors on Protege per se it opens there. I am attaching a screenshot
>>> for your reference.
>>> However, I want to make some import clean up changes so I will work
>>> on that and hopefully it should render better?
>>> Not sure why it doesn't render on Bioportal though.
>>> -Thanks,
>>> Shruthi
>>> On 2020-04-24 19:06, John Graybeal wrote:
>>> Ah, that explains it, thank you.
>>> I have changed the setting to not be View, and saved that. (It
>>> would
>>> have showed up previously, if you enabled the Views checkbox. But
>>> if
>>> it isn't a view that isn't what you want!)
>>> There may be some additional processing required as a result; I'll
>>> ask
>>> our expert on such things when she is back on Monday.
>>> I notice there are no classes being displayed, due to an RDF
>>> parsing
>>> error; do you understand why that is? Let us know if you need help
>>> figuring that out?my basic rule of thumb is to try opening it in
>>> Protege to see if that reports any errors, and fix all those first.
>>> If
>>> it works there but not in BioPortal, let us know and we'll try to
>>> hep.
>>> John
>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>> Hi John,
>>> Thanks so much for reassigning ownership to me, with this, I am
>>> able to upload a new version. I have a problem in that my ontology
>>> doesn't show up on Bioportal's main page as an ontology page as I
>>> accidentally made it an ontology view. Can you help revert this
>>> option and instead set it as an ontology?
>>> -Thanks,
>>> Shruthi
>>> On 2020-04-24 18:09, John Graybeal wrote:
>>> Hi Shruthi,
>>> I am happy to help you, and just want to clarify the situation.
>>> I can see a public ontology called SCO that fits your description,
>>> with you as the contact, and it seems to be publicly visible. So if
>>> you are still having trouble seeing this ontology, can you please
>>> provide further details about what you are doing?
>>> It appears the owner of the ontology may have been mis-assigned
>>> (possibly an operator error on our side); I have re-assigned you as
>>> the owner.
>>> My apologies for this issue. Please try to access it and let me
>>> know
>>> if you have any difficulty.
>>> john
>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote:
>>> Name: shruthichari
>>> Email: charis at rpi.edu
>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1]
>>> [1]%2Fontologies
>>> FEEDBACK:
>>> Hi Sir/Madam,
>>> I had an ontology on Bioportal under the name, Study Cohort
>>> Ontology
>>> and acronym, SCO. Not only can I not find it anymore but I can't
>>> resubmit as somebody else has made a submission. I attest that I am
>>> the author of this ontology and we even have a paper in the
>>> International Semantic Web Conference (ISWC) last year:
>>> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help
>>> me
>>> resubmit my ontology?
>>> Feel free to reach out to me at charis at rpi.edu
>>> -Thanks,
>>> Shruthi
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> [2]
>>> ========================
>>> 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
>>> Links:
>>> ------
>>> [1] http://2Fbioportal.bioontology.org [3] [1]
>>> [2] https://arxiv.org/abs/1907.04358 [1] [2]
>>> ========================
>>> 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
>>> Links:
>>> ------
>>> [1] http://2fbioportal.bioontology.org/ [3]
>>> [2] https://arxiv.org/abs/1907.04358 [1]
>> <Screenshot 2020-04-24 at 7.15.07 PM.png>
>> ========================
>> 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
>> Links:
>> ------
>> [1] https://arxiv.org/abs/1907.04358
>> [2] https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> [3] http://2fbioportal.bioontology.org/
>> [4] http://librdf.org/raptor/rapper.html
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


From charis at rpi.edu  Mon Apr 27 12:28:30 2020
From: charis at rpi.edu (Shruthi Chari)
Date: Mon, 27 Apr 2020 15:28:30 -0400
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <E803EC66-209C-4EFD-905D-629F049CF901@stanford.edu>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
 <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
 <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>
 <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu>
 <30a7355d5a089c13602f7139326bb4eb@rpi.edu>
 <AF01D482-E80D-4D26-9A96-C05BE383ADE4@stanford.edu>
 <92d937d82850397ea6d36aab9f7bc85a@rpi.edu>
 <E803EC66-209C-4EFD-905D-629F049CF901@stanford.edu>
Message-ID: <c8c5b9276761b68d17e31f83077c3248@rpi.edu>

Hi Jennifer,

Thanks so much for this update. I have a quick question if we resubmit a 
version of the ontology - do we need to take extra steps to ensure that 
it is usable via the Annotator functionality?

-Thanks,
Shruthi

On 2020-04-27 14:52, Jennifer Leigh Vendetti wrote:
> Hello Shruthi
> 
> Your ontology has been fully converted to standalone vs. a view. I?ve
> also reprocessed your ontology so that you can use it with the
> Annotator functionality.
> 
> Kind regards,
> Jennifer
> 
> 
> 
>> On Apr 25, 2020, at 1:38 PM, Shruthi Chari <charis at rpi.edu> wrote:
>> 
>> Hi John,
>> 
>> Thanks a bunch the logs you sent me were a lifesaver. I was able to 
>> reupload our ontology and now the classes show up. I should have 
>> reached out to support a year earlier, but never too late.
>> 
>> I am still waiting on the ontology view fix as in to revert this to be 
>> a stand-alone ontology and not a view. This would then allow our 
>> ontology to be queryable by the BioAnnotator.
>> 
>> Thanks for your assistance and looking forward to getting this last 
>> issue resolved.
>> 
>> -Thanks,
>> Shruthi
>> 
>> On 2020-04-24 19:48, John Graybeal wrote:
>>> Hi Shruthi,
>>> I had a look at the logs. There appear to be two locations in the 
>>> file
>>> that say "rdf:resoure" (instead of rdf:resource). Just a warning in
>>> the OWLAPI parser, but our Rapper software
>>> (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if
>>> fixing those makes it better, yes?
>>> John
>>>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>>> Hi John,
>>>> I don't want it to be a view yes. Thanks for making the change.
>>>> As for the RDF parsing error, I am not sure what is happening. Can
>>>> you send me the log as I don't see to it on my end. I don't see
>>>> errors on Protege per se it opens there. I am attaching a screenshot
>>>> for your reference.
>>>> However, I want to make some import clean up changes so I will work
>>>> on that and hopefully it should render better?
>>>> Not sure why it doesn't render on Bioportal though.
>>>> -Thanks,
>>>> Shruthi
>>>> On 2020-04-24 19:06, John Graybeal wrote:
>>>> Ah, that explains it, thank you.
>>>> I have changed the setting to not be View, and saved that. (It
>>>> would
>>>> have showed up previously, if you enabled the Views checkbox. But
>>>> if
>>>> it isn't a view that isn't what you want!)
>>>> There may be some additional processing required as a result; I'll
>>>> ask
>>>> our expert on such things when she is back on Monday.
>>>> I notice there are no classes being displayed, due to an RDF
>>>> parsing
>>>> error; do you understand why that is? Let us know if you need help
>>>> figuring that out?my basic rule of thumb is to try opening it in
>>>> Protege to see if that reports any errors, and fix all those first.
>>>> If
>>>> it works there but not in BioPortal, let us know and we'll try to
>>>> hep.
>>>> John
>>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>>> Hi John,
>>>> Thanks so much for reassigning ownership to me, with this, I am
>>>> able to upload a new version. I have a problem in that my ontology
>>>> doesn't show up on Bioportal's main page as an ontology page as I
>>>> accidentally made it an ontology view. Can you help revert this
>>>> option and instead set it as an ontology?
>>>> -Thanks,
>>>> Shruthi
>>>> On 2020-04-24 18:09, John Graybeal wrote:
>>>> Hi Shruthi,
>>>> I am happy to help you, and just want to clarify the situation.
>>>> I can see a public ontology called SCO that fits your description,
>>>> with you as the contact, and it seems to be publicly visible. So if
>>>> you are still having trouble seeing this ontology, can you please
>>>> provide further details about what you are doing?
>>>> It appears the owner of the ontology may have been mis-assigned
>>>> (possibly an operator error on our side); I have re-assigned you as
>>>> the owner.
>>>> My apologies for this issue. Please try to access it and let me
>>>> know
>>>> if you have any difficulty.
>>>> john
>>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote:
>>>> Name: shruthichari
>>>> Email: charis at rpi.edu
>>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1]
>>>> [1]%2Fontologies
>>>> FEEDBACK:
>>>> Hi Sir/Madam,
>>>> I had an ontology on Bioportal under the name, Study Cohort
>>>> Ontology
>>>> and acronym, SCO. Not only can I not find it anymore but I can't
>>>> resubmit as somebody else has made a submission. I attest that I am
>>>> the author of this ontology and we even have a paper in the
>>>> International Semantic Web Conference (ISWC) last year:
>>>> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help
>>>> me
>>>> resubmit my ontology?
>>>> Feel free to reach out to me at charis at rpi.edu
>>>> -Thanks,
>>>> Shruthi
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>> [2]
>>>> ========================
>>>> 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
>>>> Links:
>>>> ------
>>>> [1] http://2Fbioportal.bioontology.org [3] [1]
>>>> [2] https://arxiv.org/abs/1907.04358 [1] [2]
>>>> ========================
>>>> 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
>>>> Links:
>>>> ------
>>>> [1] http://2fbioportal.bioontology.org/ [3]
>>>> [2] https://arxiv.org/abs/1907.04358 [1]
>>> <Screenshot 2020-04-24 at 7.15.07 PM.png>
>>> ========================
>>> 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
>>> Links:
>>> ------
>>> [1] https://arxiv.org/abs/1907.04358
>>> [2] https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> [3] http://2fbioportal.bioontology.org/
>>> [4] http://librdf.org/raptor/rapper.html
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

From vendetti at stanford.edu  Mon Apr 27 12:36:06 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 27 Apr 2020 19:36:06 +0000
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <c8c5b9276761b68d17e31f83077c3248@rpi.edu>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
 <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
 <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>
 <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu>
 <30a7355d5a089c13602f7139326bb4eb@rpi.edu>
 <AF01D482-E80D-4D26-9A96-C05BE383ADE4@stanford.edu>
 <92d937d82850397ea6d36aab9f7bc85a@rpi.edu>
 <E803EC66-209C-4EFD-905D-629F049CF901@stanford.edu>
 <c8c5b9276761b68d17e31f83077c3248@rpi.edu>
Message-ID: <D789CF41-DC1A-45D4-88D1-E82022CF2388@stanford.edu>

Hello Shruthi,

No, you don?t need to take extra steps. BioPortal only serves data from the most recent version of an ontology.

Please note though - when you submit a new version of your ontology it goes into the queue for ontology processing, and there may be a time delay of an hour or two before the new version is fully processed and available in our system. If you notice any irregularities, feel free to contact us again via this support list.

Kind regards,
Jennifer



> On Apr 27, 2020, at 12:28 PM, Shruthi Chari <charis at rpi.edu> wrote:
> 
> Hi Jennifer,
> 
> Thanks so much for this update. I have a quick question if we resubmit a version of the ontology - do we need to take extra steps to ensure that it is usable via the Annotator functionality?
> 
> -Thanks,
> Shruthi
> 
> On 2020-04-27 14:52, Jennifer Leigh Vendetti wrote:
>> Hello Shruthi
>> Your ontology has been fully converted to standalone vs. a view. I?ve
>> also reprocessed your ontology so that you can use it with the
>> Annotator functionality.
>> Kind regards,
>> Jennifer
>>> On Apr 25, 2020, at 1:38 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>> Hi John,
>>> Thanks a bunch the logs you sent me were a lifesaver. I was able to reupload our ontology and now the classes show up. I should have reached out to support a year earlier, but never too late.
>>> I am still waiting on the ontology view fix as in to revert this to be a stand-alone ontology and not a view. This would then allow our ontology to be queryable by the BioAnnotator.
>>> Thanks for your assistance and looking forward to getting this last issue resolved.
>>> -Thanks,
>>> Shruthi
>>> On 2020-04-24 19:48, John Graybeal wrote:
>>>> Hi Shruthi,
>>>> I had a look at the logs. There appear to be two locations in the file
>>>> that say "rdf:resoure" (instead of rdf:resource). Just a warning in
>>>> the OWLAPI parser, but our Rapper software
>>>> (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if
>>>> fixing those makes it better, yes?
>>>> John
>>>>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>>>> Hi John,
>>>>> I don't want it to be a view yes. Thanks for making the change.
>>>>> As for the RDF parsing error, I am not sure what is happening. Can
>>>>> you send me the log as I don't see to it on my end. I don't see
>>>>> errors on Protege per se it opens there. I am attaching a screenshot
>>>>> for your reference.
>>>>> However, I want to make some import clean up changes so I will work
>>>>> on that and hopefully it should render better?
>>>>> Not sure why it doesn't render on Bioportal though.
>>>>> -Thanks,
>>>>> Shruthi
>>>>> On 2020-04-24 19:06, John Graybeal wrote:
>>>>> Ah, that explains it, thank you.
>>>>> I have changed the setting to not be View, and saved that. (It
>>>>> would
>>>>> have showed up previously, if you enabled the Views checkbox. But
>>>>> if
>>>>> it isn't a view that isn't what you want!)
>>>>> There may be some additional processing required as a result; I'll
>>>>> ask
>>>>> our expert on such things when she is back on Monday.
>>>>> I notice there are no classes being displayed, due to an RDF
>>>>> parsing
>>>>> error; do you understand why that is? Let us know if you need help
>>>>> figuring that out?my basic rule of thumb is to try opening it in
>>>>> Protege to see if that reports any errors, and fix all those first.
>>>>> If
>>>>> it works there but not in BioPortal, let us know and we'll try to
>>>>> hep.
>>>>> John
>>>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>>>> Hi John,
>>>>> Thanks so much for reassigning ownership to me, with this, I am
>>>>> able to upload a new version. I have a problem in that my ontology
>>>>> doesn't show up on Bioportal's main page as an ontology page as I
>>>>> accidentally made it an ontology view. Can you help revert this
>>>>> option and instead set it as an ontology?
>>>>> -Thanks,
>>>>> Shruthi
>>>>> On 2020-04-24 18:09, John Graybeal wrote:
>>>>> Hi Shruthi,
>>>>> I am happy to help you, and just want to clarify the situation.
>>>>> I can see a public ontology called SCO that fits your description,
>>>>> with you as the contact, and it seems to be publicly visible. So if
>>>>> you are still having trouble seeing this ontology, can you please
>>>>> provide further details about what you are doing?
>>>>> It appears the owner of the ontology may have been mis-assigned
>>>>> (possibly an operator error on our side); I have re-assigned you as
>>>>> the owner.
>>>>> My apologies for this issue. Please try to access it and let me
>>>>> know
>>>>> if you have any difficulty.
>>>>> john
>>>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote:
>>>>> Name: shruthichari
>>>>> Email: charis at rpi.edu
>>>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1]
>>>>> [1]%2Fontologies
>>>>> FEEDBACK:
>>>>> Hi Sir/Madam,
>>>>> I had an ontology on Bioportal under the name, Study Cohort
>>>>> Ontology
>>>>> and acronym, SCO. Not only can I not find it anymore but I can't
>>>>> resubmit as somebody else has made a submission. I attest that I am
>>>>> the author of this ontology and we even have a paper in the
>>>>> International Semantic Web Conference (ISWC) last year:
>>>>> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help
>>>>> me
>>>>> resubmit my ontology?
>>>>> Feel free to reach out to me at charis at rpi.edu
>>>>> -Thanks,
>>>>> Shruthi
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> bioontology-support at lists.stanford.edu
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>> [2]
>>>>> ========================
>>>>> 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
>>>>> Links:
>>>>> ------
>>>>> [1] http://2Fbioportal.bioontology.org [3] [1]
>>>>> [2] https://arxiv.org/abs/1907.04358 [1] [2]
>>>>> ========================
>>>>> 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
>>>>> Links:
>>>>> ------
>>>>> [1] http://2fbioportal.bioontology.org/ [3]
>>>>> [2] https://arxiv.org/abs/1907.04358 [1]
>>>> <Screenshot 2020-04-24 at 7.15.07 PM.png>
>>>> ========================
>>>> 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
>>>> Links:
>>>> ------
>>>> [1] https://arxiv.org/abs/1907.04358
>>>> [2] https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>> [3] http://2fbioportal.bioontology.org/
>>>> [4] http://librdf.org/raptor/rapper.html
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


From charis at rpi.edu  Mon Apr 27 12:42:00 2020
From: charis at rpi.edu (Shruthi Chari)
Date: Mon, 27 Apr 2020 15:42:00 -0400
Subject: [bioontology-support] [BioPortal] Feedback from shruthichari
In-Reply-To: <D789CF41-DC1A-45D4-88D1-E82022CF2388@stanford.edu>
References: <5ea34258a0d01_e9e2c1777499430@ncbo-prd-app-09.stanford.edu.mail>
 <B4C925B0-5F9C-42B3-A417-80428A84CF11@stanford.edu>
 <3a6aaff5ea82d285c037a0dd0c9229d2@rpi.edu>
 <1A58CA31-404F-450B-9830-B42800331A6D@stanford.edu>
 <30a7355d5a089c13602f7139326bb4eb@rpi.edu>
 <AF01D482-E80D-4D26-9A96-C05BE383ADE4@stanford.edu>
 <92d937d82850397ea6d36aab9f7bc85a@rpi.edu>
 <E803EC66-209C-4EFD-905D-629F049CF901@stanford.edu>
 <c8c5b9276761b68d17e31f83077c3248@rpi.edu>
 <D789CF41-DC1A-45D4-88D1-E82022CF2388@stanford.edu>
Message-ID: <2549f3ec30dded55bdbd6b8c70557899@rpi.edu>

Hi Jennifer,

Thanks for your response, it helps clear my doubts and it is really good 
to know that there is an active support team out there. Stay safe and 
healthy.

Looking forward to continuing to use Bioportal. Thanks for helping with 
our issues and to get our ontology up and running on the site.

-Thanks,
Shruthi

  On 2020-04-27 15:36, Jennifer Leigh Vendetti wrote:
> Hello Shruthi,
> 
> No, you don?t need to take extra steps. BioPortal only serves data
> from the most recent version of an ontology.
> 
> Please note though - when you submit a new version of your ontology it
> goes into the queue for ontology processing, and there may be a time
> delay of an hour or two before the new version is fully processed and
> available in our system. If you notice any irregularities, feel free
> to contact us again via this support list.
> 
> Kind regards,
> Jennifer
> 
> 
> 
>> On Apr 27, 2020, at 12:28 PM, Shruthi Chari <charis at rpi.edu> wrote:
>> 
>> Hi Jennifer,
>> 
>> Thanks so much for this update. I have a quick question if we resubmit 
>> a version of the ontology - do we need to take extra steps to ensure 
>> that it is usable via the Annotator functionality?
>> 
>> -Thanks,
>> Shruthi
>> 
>> On 2020-04-27 14:52, Jennifer Leigh Vendetti wrote:
>>> Hello Shruthi
>>> Your ontology has been fully converted to standalone vs. a view. I?ve
>>> also reprocessed your ontology so that you can use it with the
>>> Annotator functionality.
>>> Kind regards,
>>> Jennifer
>>>> On Apr 25, 2020, at 1:38 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>>> Hi John,
>>>> Thanks a bunch the logs you sent me were a lifesaver. I was able to 
>>>> reupload our ontology and now the classes show up. I should have 
>>>> reached out to support a year earlier, but never too late.
>>>> I am still waiting on the ontology view fix as in to revert this to 
>>>> be a stand-alone ontology and not a view. This would then allow our 
>>>> ontology to be queryable by the BioAnnotator.
>>>> Thanks for your assistance and looking forward to getting this last 
>>>> issue resolved.
>>>> -Thanks,
>>>> Shruthi
>>>> On 2020-04-24 19:48, John Graybeal wrote:
>>>>> Hi Shruthi,
>>>>> I had a look at the logs. There appear to be two locations in the 
>>>>> file
>>>>> that say "rdf:resoure" (instead of rdf:resource). Just a warning in
>>>>> the OWLAPI parser, but our Rapper software
>>>>> (http://librdf.org/raptor/rapper.html [4]) didn't like it. See if
>>>>> fixing those makes it better, yes?
>>>>> John
>>>>>> On Apr 24, 2020, at 4:23 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>>>>> Hi John,
>>>>>> I don't want it to be a view yes. Thanks for making the change.
>>>>>> As for the RDF parsing error, I am not sure what is happening. Can
>>>>>> you send me the log as I don't see to it on my end. I don't see
>>>>>> errors on Protege per se it opens there. I am attaching a 
>>>>>> screenshot
>>>>>> for your reference.
>>>>>> However, I want to make some import clean up changes so I will 
>>>>>> work
>>>>>> on that and hopefully it should render better?
>>>>>> Not sure why it doesn't render on Bioportal though.
>>>>>> -Thanks,
>>>>>> Shruthi
>>>>>> On 2020-04-24 19:06, John Graybeal wrote:
>>>>>> Ah, that explains it, thank you.
>>>>>> I have changed the setting to not be View, and saved that. (It
>>>>>> would
>>>>>> have showed up previously, if you enabled the Views checkbox. But
>>>>>> if
>>>>>> it isn't a view that isn't what you want!)
>>>>>> There may be some additional processing required as a result; I'll
>>>>>> ask
>>>>>> our expert on such things when she is back on Monday.
>>>>>> I notice there are no classes being displayed, due to an RDF
>>>>>> parsing
>>>>>> error; do you understand why that is? Let us know if you need help
>>>>>> figuring that out?my basic rule of thumb is to try opening it in
>>>>>> Protege to see if that reports any errors, and fix all those 
>>>>>> first.
>>>>>> If
>>>>>> it works there but not in BioPortal, let us know and we'll try to
>>>>>> hep.
>>>>>> John
>>>>>> On Apr 24, 2020, at 3:50 PM, Shruthi Chari <charis at rpi.edu> wrote:
>>>>>> Hi John,
>>>>>> Thanks so much for reassigning ownership to me, with this, I am
>>>>>> able to upload a new version. I have a problem in that my ontology
>>>>>> doesn't show up on Bioportal's main page as an ontology page as I
>>>>>> accidentally made it an ontology view. Can you help revert this
>>>>>> option and instead set it as an ontology?
>>>>>> -Thanks,
>>>>>> Shruthi
>>>>>> On 2020-04-24 18:09, John Graybeal wrote:
>>>>>> Hi Shruthi,
>>>>>> I am happy to help you, and just want to clarify the situation.
>>>>>> I can see a public ontology called SCO that fits your description,
>>>>>> with you as the contact, and it seems to be publicly visible. So 
>>>>>> if
>>>>>> you are still having trouble seeing this ontology, can you please
>>>>>> provide further details about what you are doing?
>>>>>> It appears the owner of the ontology may have been mis-assigned
>>>>>> (possibly an operator error on our side); I have re-assigned you 
>>>>>> as
>>>>>> the owner.
>>>>>> My apologies for this issue. Please try to access it and let me
>>>>>> know
>>>>>> if you have any difficulty.
>>>>>> john
>>>>>> On Apr 24, 2020, at 12:47 PM, support at bioontology.org wrote:
>>>>>> Name: shruthichari
>>>>>> Email: charis at rpi.edu
>>>>>> Location: https%3A%2F%2Fbioportal.bioontology.org [1]
>>>>>> [1]%2Fontologies
>>>>>> FEEDBACK:
>>>>>> Hi Sir/Madam,
>>>>>> I had an ontology on Bioportal under the name, Study Cohort
>>>>>> Ontology
>>>>>> and acronym, SCO. Not only can I not find it anymore but I can't
>>>>>> resubmit as somebody else has made a submission. I attest that I 
>>>>>> am
>>>>>> the author of this ontology and we even have a paper in the
>>>>>> International Semantic Web Conference (ISWC) last year:
>>>>>> https://arxiv.org/abs/1907.04358 [1] [2] [2]. Can you please help
>>>>>> me
>>>>>> resubmit my ontology?
>>>>>> Feel free to reach out to me at charis at rpi.edu
>>>>>> -Thanks,
>>>>>> Shruthi
>>>>>> _______________________________________________
>>>>>> bioontology-support mailing list
>>>>>> bioontology-support at lists.stanford.edu
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>> [2]
>>>>>> ========================
>>>>>> 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
>>>>>> Links:
>>>>>> ------
>>>>>> [1] http://2Fbioportal.bioontology.org [3] [1]
>>>>>> [2] https://arxiv.org/abs/1907.04358 [1] [2]
>>>>>> ========================
>>>>>> 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
>>>>>> Links:
>>>>>> ------
>>>>>> [1] http://2fbioportal.bioontology.org/ [3]
>>>>>> [2] https://arxiv.org/abs/1907.04358 [1]
>>>>> <Screenshot 2020-04-24 at 7.15.07 PM.png>
>>>>> ========================
>>>>> 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
>>>>> Links:
>>>>> ------
>>>>> [1] https://arxiv.org/abs/1907.04358
>>>>> [2] 
>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>> [3] http://2fbioportal.bioontology.org/
>>>>> [4] http://librdf.org/raptor/rapper.html
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

From vendetti at stanford.edu  Mon Apr 27 15:59:21 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 27 Apr 2020 22:59:21 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Thomas Lemberger
In-Reply-To: <74258F94-CB04-4A2D-A226-DCBECB66919F@embo.org>
References: <5ea68633fb1e_56be2b660c88145e@ncbo-prd-app-08.stanford.edu.mail>
 <0CFC2970-5C49-49C2-B2E4-E87922E982ED@stanford.edu>
 <74258F94-CB04-4A2D-A226-DCBECB66919F@embo.org>
Message-ID: <C8EB8BBF-6E32-4CA8-BA58-043F67F205A8@stanford.edu>

Hi Thomas,

Thank you for providing additional detail. Please see my answers inline below.


On Apr 27, 2020, at 1:18 PM, Thomas Lemberger <thomas.lemberger at embo.org<mailto:thomas.lemberger at embo.org>> wrote:

Dear Jennifer,

Many thanks for getting back to me and apologies if my description was confusing. Maybe it is just my misunderstanding.

Let?s take the example of the term bao:BAO_0002424 for the assay ?western blot?.

In the CSV file (http://data.bioontology.org/ontologies/BAO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=csv), ?western blot? is described in row 172

Class ID        Preferred Label Synonyms        Definitions     Obsolete        CUI     Semantic Types  Parents alternative term        alternative_term        axiom_lost_from_external_ontology       based on normalization  bearer of       catalyzed by    connected to    contains process        contributor     curator notes   database_cross_reference        definition      definition      definition source       derives from    derives into    detects detects phenotype       development_notes       editor note     editor preferred term~editor preferred label    encodes example of usage        external_definition     external_ontology_notes fma_set_term    function_notes  has absorbance wavelength value has activity threshold value    has alternate assay conditions  has alternate assay format      has alternate assay type        has alternate cell line assay   has alternate confirmatory assay        has alternate organism assay    has alternate target assay      has anti-sense strand sequence  has antibody source     has artificial regulatory region copy number    has assay control       has assay deposition date       has assay design method has assay footprint     has assay format        has assay kit   has assay kit component has assay medium        has assay method        has assay phase characteristic  has assay pressure value        has assay protocol      has assay readout content       has assay readout content parametricity has assay readout type  has assay serum has assay source        has assay stage has assay supporting method     has assay temperature value     has assay title has associated disease  has binding site        has bioassay type       has biosafety level     has cDNA copy number    has cell count  has cell line   has cell modification temperature value has cell modification time value        has compound aggregation assay  has compound fluorescence assay has compound redox-activity assay       has compound toxicity assay     has concentration       has concentration throughput    has concentration unit  has confirmatory assay  has copy number has counter assay       has coupled substrate incubation temperature value      has coupled substrate incubation time value     has curation status     has curve fit specification     has detected entity     has detection method    has DNA sequence        has emission wavelength value   has endpoint    has endpoint modifier   has enzyme reaction temperature value   has enzyme reaction time value  has excitation wavelength value has form        has function    has function in has gene symbol has id value    has identical assay     has incubation time value       has indicator   has inducer     has lead optimization assay     has ligand incubation time value        has manufacturer        has marker      has measure group       has measured entity     has mode of action      has molecular phenotype has morphological phenotype     has negative control    has nucleic acid sequence       has organism    has orthogonal assay design     has orthogonal assay technology has parental cell line assay    has part        has participant has passage number      has percent response    has percent response value      has perturbagen has perturbagen incubation temperature value    has perturbagen incubation time value   has phenotype   has physicochemical profiling assay     has positive control    has preparation method  has primary assay       has protein sequence    has purity unit has quality     has recommended name    has repetition point-number     has repetition throughput       has response unit       has response value      has RNA sequence        has role        has selectivity assay   has sense strand sequence       has sequence    has sequence position   has shRNA probe sense sequence position has shRNA sense sequence        has signal direction    has siRNA probe sense sequence position has specification       has substrate   has substrate incubation temperature value      has substrate incubation time value     has summary assay       has target      has temperature unit    has temperature value   has time unit   has transcription factor        has unit        has value       has variant construct assay     has wavelength value    has_alternative_id      has_broad_synonym       has_exact_synonym       has_narrow_synonym      has_obo_namespace       has_related_synonym     has_relational_adjective        homology_notes  http://data.bioontology.org/metadata/prefixIRI  http://purl.obolibrary.org/obo/hasDbXref        http://purl.obolibrary.org/obo/hasOBONamespace  http://purl.obolibrary.org/obo/IAO_0000231      http://purl.obolibrary.org/obo/id       http://purl.obolibrary.org/obo/is_metadata_tag  http://purl.obolibrary.org/obo/RO_0002161       http://purl.obolibrary.org/obo/RO_0002174       http://purl.obolibrary.org/obo/shorthand        http://purl.obolibrary.org/obo/uberon/core#dubious_for_taxon    http://purl.obolibrary.org/obo/uberon/core#fma_set_term http://purl.obolibrary.org/obo/uberon/core#homologous_in        http://purl.obolibrary.org/obo/uberon/core#spatially_disjoint_from      http://purl.org/dc/elements/1.1/date    http://purl.org/dc/elements/1.1/license http://purl.org/dc/elements/1.1/relation        http://purl.org/dc/elements/1.1/source  http://www.ebi.ac.uk/cellline/definition        http://www.ebi.ac.uk/cellline/definition_editor http://www.ebi.ac.uk/efo/bioportal_provenance   http://www.ebi.ac.uk/efo/definition_citation    http://www.ebi.ac.uk/efo/EV_definition_citation http://www.ebi.ac.uk/efo/EVM_definition_citation        http://www.ebi.ac.uk/efo/FBdv_definition_citation       http://www.ebi.ac.uk/efo/MAT_definition_citation        http://www.ebi.ac.uk/efo/MSH_definition_citation        http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation      http://www.ebi.ac.uk/efo/NIFSTD_definition_citation     http://www.ebi.ac.uk/efo/obsoleted_in_version   http://www.ebi.ac.uk/efo/organizational_class   http://www.ebi.ac.uk/efo/reason_for_obsolescence        http://www.ebi.ac.uk/efo/SNOMEDCT_definition_citation   http://www.ebi.ac.uk/efo/WBls_definition_citation       http://www.ebi.ac.uk/efo/XAO_definition_citation        http://www.ebi.ac.uk/efo/ZFS_definition_citation        http://www.geneontology.org/formats/oboInOwl#created_by http://www.geneontology.org/formats/oboInOwl#creation_date      http://www.geneontology.org/formats/oboInOwl#hasDefinition      http://www.geneontology.org/formats/oboInOwl#id http://www.geneontology.org/formats/oboInOwl#is_class_level     http://www.geneontology.org/formats/oboInOwl#is_metadata_tag    http://www.w3.org/2000/01/rdf-schema#comment    http://www.w3.org/2000/01/rdf-schema#isDefinedBy        http://www.w3.org/2000/01/rdf-schema#seeAlso    http://www.w3.org/2002/07/owl#deprecated        http://www.w3.org/2002/07/owl#topDataProperty   http://www.w3.org/2002/07/owl#topObjectProperty http://www.w3.org/2004/02/skos/core#notation    http://xmlns.com/foaf/0.1/depicted_by   imported from   in_subset       inheres in      involves biological process     involves molecular function     is alternate assay conditions of        is alternate assay format of    is alternate assay type of      is alternate cell line assay of is alternate confirmatory assay of      is alternate organism assay of  is alternate target assay of    is assay format of      is assay method of      is assay protocol of    is associated disease of        is binding site of      is bioassay type of     is cell line of is compound aggregation assay of        is compound fluorescence assay of       is compound redox-activity assay of     is compound toxicity assay of   is confirmatory assay of        is counter assay of     is derived from is described by is detected by  is detection method of  is endpoint of  is grown in     is identical assay of   is indicator of is input data value of  is lead optimization assay of   is localized in is marker of    is measure group of     is measured entity of   is opposite_of  is orthogonal assay design of   is orthogonal assay technology of       is parental cell line assay of  is perturbagen of       is phenotype of is physicochemical profiling assay of   is primary assay of     is regulated by is regulator of is related assay to     is role of      is selectivity assay of is specification of     is substrate of is summary assay of     is target of    is transfected into     is unit of      is variant construct assay of   label   LINCS ID        occurs in       part of participates in phenotype of    PubChem AID     quantifies      recombinantly expressed in      reports reports assay measurment value  shorthand       silences        stains  structure_notes taxon_notes     term editor     term replaced by        uses as substrate       uses assay kit  uses detection instrument
http://www.bioassayontology.org/bao#BAO_0002424 western blot            The western blot (alternatively, protein immunoblot) is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.     FALSE                   http://www.bioassayontology.org/bao#BAO_0002422                                                         The western blot (alternatively, protein immunoblot) is an analytical technique used to detect specific proteins in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     bao:BAO_0002424                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 western blot



I think this term is absent from the owl file (http://data.bioontology.org/ontologies/BAO/submissions/36/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb).


The ontology source file for BAO (bao_complete.owl) has two import statements near the top of the file:

<owl:imports rdf:resource="http://www.bioassayontology.org/bao/bao_core.owl"/>
<owl:imports rdf:resource="http://www.bioassayontology.org/bao/bao_external.owl"/>

At processing time, BioPortal reads those import statements and dynamically pulls in the content from the imported ontologies. So, yes - you are correct that the ?western blot? term doesn?t appear in the root ontology (bao_complete.owl). However, it does appear in one of the ontologies that BAO imports, which is why you see that data in BioPortal. The BAO ontology has a fairy complicated import structure. I opened it in the Protege ontology editor (https://protege.stanford.edu/) where you can see a graphical representations of the imports:


[cid:F2D14877-A216-4A61-901D-300DB8CACA4E at stanford.edu]


Furthermore, other terms that are in the owl file, for example bao:BAO_0000978 ?NP-40? seem to include only the class/sub class hierarchy but no other information (no definition, no label etc?)

<!-- http://www.bioassayontology.org/bao#BAO_0000978 -->
<owl:Class rdf:about="http://www.bioassayontology.org/bao#BAO_0000978">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0003102"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_27780"/>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>

The equivalent term in the CSV (row 1640) is:

Class ID        Preferred Label Synonyms        Definitions     Obsolete        CUI     Semantic Types  Parents alternative term        alternative_term        axiom_lost_from_external_ontology       based on normalization  bearer of       catalyzed by    connected to    contains process        contributor     curator notes   database_cross_reference        definition      definition      definition source       derives from    derives into    detects detects phenotype       development_notes       editor note     editor preferred term~editor preferred label    encodes example of usage        external_definition     external_ontology_notes fma_set_term    function_notes  has absorbance wavelength value has activity threshold value    has alternate assay conditions  has alternate assay format      has alternate assay type        has alternate cell line assay   has alternate confirmatory assay        has alternate organism assay    has alternate target assay      has anti-sense strand sequence  has antibody source     has artificial regulatory region copy number    has assay control       has assay deposition date       has assay design method has assay footprint     has assay format        has assay kit   has assay kit component has assay medium        has assay method        has assay phase characteristic  has assay pressure value        has assay protocol      has assay readout content       has assay readout content parametricity has assay readout type  has assay serum has assay source        has assay stage has assay supporting method     has assay temperature value     has assay title has associated disease  has binding site        has bioassay type       has biosafety level     has cDNA copy number    has cell count  has cell line   has cell modification temperature value has cell modification time value        has compound aggregation assay  has compound fluorescence assay has compound redox-activity assay       has compound toxicity assay     has concentration       has concentration throughput    has concentration unit  has confirmatory assay  has copy number has counter assay       has coupled substrate incubation temperature value      has coupled substrate incubation time value     has curation status     has curve fit specification     has detected entity     has detection method    has DNA sequence        has emission wavelength value   has endpoint    has endpoint modifier   has enzyme reaction temperature value   has enzyme reaction time value  has excitation wavelength value has form        has function    has function in has gene symbol has id value    has identical assay     has incubation time value       has indicator   has inducer     has lead optimization assay     has ligand incubation time value        has manufacturer        has marker      has measure group       has measured entity     has mode of action      has molecular phenotype has morphological phenotype     has negative control    has nucleic acid sequence       has organism    has orthogonal assay design     has orthogonal assay technology has parental cell line assay    has part        has participant has passage number      has percent response    has percent response value      has perturbagen has perturbagen incubation temperature value    has perturbagen incubation time value   has phenotype   has physicochemical profiling assay     has positive control    has preparation method  has primary assay       has protein sequence    has purity unit has quality     has recommended name    has repetition point-number     has repetition throughput       has response unit       has response value      has RNA sequence        has role        has selectivity assay   has sense strand sequence       has sequence    has sequence position   has shRNA probe sense sequence position has shRNA sense sequence        has signal direction    has siRNA probe sense sequence position has specification       has substrate   has substrate incubation temperature value      has substrate incubation time value     has summary assay       has target      has temperature unit    has temperature value   has time unit   has transcription factor        has unit        has value       has variant construct assay     has wavelength value    has_alternative_id      has_broad_synonym       has_exact_synonym       has_narrow_synonym      has_obo_namespace       has_related_synonym     has_relational_adjective        homology_notes  http://data.bioontology.org/metadata/prefixIRI  http://purl.obolibrary.org/obo/hasDbXref        http://purl.obolibrary.org/obo/hasOBONamespace  http://purl.obolibrary.org/obo/IAO_0000231      http://purl.obolibrary.org/obo/id       http://purl.obolibrary.org/obo/is_metadata_tag  http://purl.obolibrary.org/obo/RO_0002161       http://purl.obolibrary.org/obo/RO_0002174       http://purl.obolibrary.org/obo/shorthand        http://purl.obolibrary.org/obo/uberon/core#dubious_for_taxon    http://purl.obolibrary.org/obo/uberon/core#fma_set_term http://purl.obolibrary.org/obo/uberon/core#homologous_in        http://purl.obolibrary.org/obo/uberon/core#spatially_disjoint_from      http://purl.org/dc/elements/1.1/date    http://purl.org/dc/elements/1.1/license http://purl.org/dc/elements/1.1/relation        http://purl.org/dc/elements/1.1/source  http://www.ebi.ac.uk/cellline/definition        http://www.ebi.ac.uk/cellline/definition_editor http://www.ebi.ac.uk/efo/bioportal_provenance   http://www.ebi.ac.uk/efo/definition_citation    http://www.ebi.ac.uk/efo/EV_definition_citation http://www.ebi.ac.uk/efo/EVM_definition_citation        http://www.ebi.ac.uk/efo/FBdv_definition_citation       http://www.ebi.ac.uk/efo/MAT_definition_citation        http://www.ebi.ac.uk/efo/MSH_definition_citation        http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation      http://www.ebi.ac.uk/efo/NIFSTD_definition_citation     http://www.ebi.ac.uk/efo/obsoleted_in_version   http://www.ebi.ac.uk/efo/organizational_class   http://www.ebi.ac.uk/efo/reason_for_obsolescence        http://www.ebi.ac.uk/efo/SNOMEDCT_definition_citation   http://www.ebi.ac.uk/efo/WBls_definition_citation       http://www.ebi.ac.uk/efo/XAO_definition_citation        http://www.ebi.ac.uk/efo/ZFS_definition_citation        http://www.geneontology.org/formats/oboInOwl#created_by http://www.geneontology.org/formats/oboInOwl#creation_date      http://www.geneontology.org/formats/oboInOwl#hasDefinition      http://www.geneontology.org/formats/oboInOwl#id http://www.geneontology.org/formats/oboInOwl#is_class_level     http://www.geneontology.org/formats/oboInOwl#is_metadata_tag    http://www.w3.org/2000/01/rdf-schema#comment    http://www.w3.org/2000/01/rdf-schema#isDefinedBy        http://www.w3.org/2000/01/rdf-schema#seeAlso    http://www.w3.org/2002/07/owl#deprecated        http://www.w3.org/2002/07/owl#topDataProperty   http://www.w3.org/2002/07/owl#topObjectProperty http://www.w3.org/2004/02/skos/core#notation    http://xmlns.com/foaf/0.1/depicted_by   imported from   in_subset       inheres in      involves biological process     involves molecular function     is alternate assay conditions of        is alternate assay format of    is alternate assay type of      is alternate cell line assay of is alternate confirmatory assay of      is alternate organism assay of  is alternate target assay of    is assay format of      is assay method of      is assay protocol of    is associated disease of        is binding site of      is bioassay type of     is cell line of is compound aggregation assay of        is compound fluorescence assay of       is compound redox-activity assay of     is compound toxicity assay of   is confirmatory assay of        is counter assay of     is derived from is described by is detected by  is detection method of  is endpoint of  is grown in     is identical assay of   is indicator of is input data value of  is lead optimization assay of   is localized in is marker of    is measure group of     is measured entity of   is opposite_of  is orthogonal assay design of   is orthogonal assay technology of       is parental cell line assay of  is perturbagen of       is phenotype of is physicochemical profiling assay of   is primary assay of     is regulated by is regulator of is related assay to     is role of      is selectivity assay of is specification of     is substrate of is summary assay of     is target of    is transfected into     is unit of      is variant construct assay of   label   LINCS ID        occurs in       part of participates in phenotype of    PubChem AID     quantifies      recombinantly expressed in      reports reports assay measurment value  shorthand       silences        stains  structure_notes taxon_notes     term editor     term replaced by        uses as substrate       uses assay kit  uses detection instrument
http://www.bioassayontology.org/bao#BAO_0000978 NP-40           NP-40 is a commercially available detergent. The full name of NP-40 is Tergitol-type NP-40, which is nonyl phenoxypolyethoxylethanol.   FALSE                   http://www.bioassayontology.org/bao#BAO_0003043                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         bao:BAO_0000978                                                                                                                                                                                                                                                                                                                         NP-40 is a commercially available detergent. The full name of NP-40 is Tergitol-type NP-40, which is nonyl phenoxypolyethoxylethanol.                                                                                                                                                                                                                                                                                                                                                                                                                                                                           NP-40



This is the same situation where the definition is formally declared not in the root ontology, but in one of the ontologies that BAO imports. The BioPortal user interface doesn?t present any information that would help you track down which import the declaration lives in - for that, you would need to use a different tool. If you?re familiar with the Protege application that I mentioned above, you could use the following steps:

1). Open bao_complete.owl
2). Click the Search? button in the top right corner and enter NP-40 in the resulting Search dialog
3). Double click the first match in the result list:

[cid:EC6287D3-3CBC-4901-9D73-784E9E973719 at stanford.edu]

This will navigate to NP-40 in the classes tree where you can view all of the properties attached to the class. If you hover your mouse over the rdfs:comment on the right-hand side in the Class Annotations pane, you?ll see a tooltip pop up that will tell you where the comment was declared. In this case, I see tooltip content of ?Asserted in: http://www.bioassayontology.org/bao/bao_vocabulary_materialentity.owl?.


In the meantime, I found that the RDF/XML file http://data.bioontology.org/ontologies/BAO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=rdf includes the entire ontology, so I am not sure what is the role of the .owl file in the case of BAO. This seems to be different with other ontologies I downloaded.

Maybe I am just misunderstanding something.


The OWL file is the canonical source file that was submitted to BioPortal by the ontology maintainer. The RDF/XML file is generated by BioPortal at processing time and includes everything from the original ontology source file, as well as data from imported ontologies. BioPortal is backed by an RDF store, so we need to have this intermediate step of generating an RDF/XML representation from the various ontology formats that end users are allowed to submit (OWL, OBO, and SKOS).


In the case of other ontologies, for example OBI https://bioportal.bioontology.org/ontologies/OBI, the .owl file (http://data.bioontology.org/ontologies/OBI/submissions/42/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb) does include the whole ontology and not only the class/subclass hierarchy.


I checked OBI and it doesn?t have any imports, which is why the entirety of the ontology content is visible in the original source OWL file.

Hope this information is helpful.

Kind regards,
Jennifer



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From rsingh at pieriandx.com  Tue Apr 28 08:03:27 2020
From: rsingh at pieriandx.com (Radhey Singh)
Date: Tue, 28 Apr 2020 10:03:27 -0500
Subject: [bioontology-support] VMWare Virtual Appliance v2.5 Zip Download
Message-ID: <CAO3boWEVdmc4=JLMZD2OD8q18J=DHf+SBjSizf1PWvPx-hd4MA@mail.gmail.com>

Hello,

We are looking to explore OntoPortal VMWare Virtual Appliance 2.5. Could
you please send us the Download Zip file for the same?

My Username:  rsingh552

Thanks & Regards,

*Radhey Shyam Singh*

DevOps Lead

P: office: 314-628-0035/ cell: 412-298-5345
E: rsingh at pieriandx.com

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From vendetti at stanford.edu  Tue Apr 28 09:51:19 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 28 Apr 2020 16:51:19 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Jay Franklin
In-Reply-To: <D83CD11B-DAD1-4BF7-9819-9A082A2A7A34@stanford.edu>
References: <5ea4a96492d76_492b289a48419331@ncbo-prd-app-08.stanford.edu.mail>
 <BB18EE09-65F3-4F62-9CFB-4EB645339953@stanford.edu>
 <D83CD11B-DAD1-4BF7-9819-9A082A2A7A34@stanford.edu>
Message-ID: <AC0773ED-60B1-4557-84C8-0E1E5358806E@stanford.edu>

I haven?t received a response from the ontology maintainers, so I fixed the small error in the ontology source file that was causing parsing issues and reprocessed it in our system. CMO is fully available in BioPortal now, including the ability to use with the Annotator.

Jennifer



On Apr 27, 2020, at 11:11 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi again Jay,

I found the error in the ontology source file that is causing the parsing error, and have asked the maintainers if they could repair it:

https://github.com/rat-genome-database/CMO-Clinical-Measurement-Ontology/issues/3

If I don?t get a response shortly, I?ll attempt to fix it on our end and reprocess.

Jennifer


On Apr 27, 2020, at 10:26 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Jay,

I looked at CMO in our system and it appears that the latest version (uploaded on January 7th) failed to parse. The status is showing as "Error Rdf?. This is the underlying reason that the Annotator doesn?t include results from this ontology. I?ve entered an issue in our tracker:

https://github.com/ncbo/bioportal-project/issues/164

? and am looking into the parsing errors.

Kind regards.
Jennifer



On Apr 25, 2020, at 2:19 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jay Franklin

Email: frankj7 at rpi.edu<mailto:frankj7 at rpi.edu>

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

Feedback:

Hi,

It seems as though the Clinical Measurements Ontology (CMO) is not working correctly with the Annotator tool right now. Although I can select CMO in the drop-down list of ontologies, when I input biomedical text to be annotated CMO is never returned. For example, "diastolic blood pressure" does not return its corresponding IRI "http://purl.obolibrary.org/obo/CMO_0000004".

Is this an error within the Annotator, or am I misusing the software somehow? I would like to use the Annotator with CMO, so please let me know if something can be done about this.

Thanks,
Jay Franklin
Rensselaer Polytechnic Institute

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From vendetti at stanford.edu  Tue Apr 28 11:56:44 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 28 Apr 2020 18:56:44 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Philip van Damme
In-Reply-To: <5FCF14AD-B0A3-42D7-9FE2-BEC284FF3C4B@stanford.edu>
References: <C8E76070-EF00-40B5-BC2D-8D167A2F45E3@amsterdamumc.nl>
 <5FCF14AD-B0A3-42D7-9FE2-BEC284FF3C4B@stanford.edu>
Message-ID: <B75222E0-CACE-449E-84CE-C1696ED0E6B5@stanford.edu>

Hello Philip,


On Apr 9, 2020, at 2:35 AM, Damme, P. van (Philip) <p.vandamme at amsterdamumc.nl<mailto:p.vandamme at amsterdamumc.nl>> wrote:

Dear Michael, others,

Thank you for your quick response back on the 12th of March, I appreciate it. First and foremost I hope you?re all doing well under the current circumstances.

I stumbled upon something what seems like a discrepancy between the mappings returned by the API calling "/ontologies/:ontology/classes/:cls/mappings? and "/mappings?ontologies=ONT1,ONT2?. When I try to get mappings between a pair of ontologies involving SNOMED CT, I get different results.

For example, I want to check if this mappings exists in BioPortal: http://www.orpha.net/ORDO/Orphanet_3389<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C0%7C637221570442163072&sdata=CE7PbjVrayH7pjA2uwVe2AsX5%2BkL%2FYz%2Fc6pn5g8ovpQ%3D&reserved=0> = http://purl.bioontology.org/ontology/SNOMEDCT/56717001<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F56717001&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442173065&sdata=UGaosLiUz9ZaicxBF1EyqtcdB8tYBtOtmAoFsI9oQIw%3D&reserved=0>. I can use the API calling
http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FORDO%2Fclasses%2Fhttp%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389%2Fmappings&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442183061&sdata=HjpAr3UKN9lvgUGbFC3qCU0syLh922rDU0zrtJRRxeM%3D&reserved=0>
or http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fmappings%3Fontologies%3DORDO%2CSNOMEDCT&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442183061&sdata=3W7%2F1o9DTZNtj5X2DSE0mRRsQs60%2F5eUnowuQek10so%3D&reserved=0> and check if the mapping exists. However, when I compare the returned set from the API calls above with https://bioportal.bioontology.org/ontologies/ORDO?p=classes&conceptid=http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389#mappings<https://eur04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FORDO%3Fp%3Dclasses%26conceptid%3Dhttp%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389%23mappings&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442193057&sdata=lqb4RXc0BwVKbiSIS%2Bn4d7APAQAVtmRiPM%2Bvf6Ng8bQ%3D&reserved=0> I noticed the following:

  *   The mapping exists according to the class mappings on the webpage, referring to URI http://purl.bioontology.org/ontology/SNOMEDCT/56717001<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F56717001&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442193057&sdata=jv%2BxNjoV68ur%2B68An1meF0LjsLcyzZEaXV4V5isAy%2BQ%3D&reserved=0> and SNOMEDCT.


Yes, I confirm that I see the same.



  *   The mapping exists according to http://data.bioontology.org/ontologies/ORDO/classes/http%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389/mappings<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fontologies%2FORDO%2Fclasses%2Fhttp%3A%2F%2Fwww.orpha.net%2FORDO%2FOrphanet_3389%2Fmappings&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442203056&sdata=hsftEAxXI%2FoEX7ZestFYO0jIcTpgmdqp9fx5LwJilRM%3D&reserved=0>, however, using different URI (http://snomed.info/id/56717001<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsnomed.info%2Fid%2F56717001&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442213046&sdata=%2FfJZBnDeafRZ060%2FTpA%2BRm%2BIXJE4FFC%2F7q8%2F4vM%2BuLU%3D&reserved=0>) and referring to ontology SNO_COPY which is not accessible.


I don?t see the same here. I issued the REST call that you list above, and the mapping between the Tuberculosis terms in ORDO and SNOMEDCT does exist in the result set. Here?s a screen shot showing the LOOM mapping:


[cid:CAB488B4-906C-417D-8302-942F2DB18543 at stanford.edu]


I also see the other mapping you referred to, i.e., the LOOM mapping between the Tuberculosis terms in ORDO and SNO_COPY:


[cid:7854C9AF-8DD7-4B34-A1D3-FB605FC4FE02 at stanford.edu]


With regard to this latter case, I see two issues:

1). There's a known issue with the BioPortal REST API where the mappings endpoint returns results that include terms from private ontologies (documented here: https://github.com/ncbo/ontologies_api/issues/52). SNO_COPY is a private ontology, which is why it?s not accessible to you.
2). There appears to be a duplicate of the same LOOM mapping from Tuberculosis in ORDO to Tuberculosis in SNO_COPY. It?s not immediately clear to me why the duplicate exists. I?ve entered a new issue in our tracker: https://github.com/ncbo/ontologies_api/issues/67.



  *   The mappings doesn?t exist according to http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fmappings%3Fontologies%3DORDO%2CSNOMEDCT&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442213046&sdata=R6L3sQQcnVR8dEpAUf33of7tu1S2Hyn2dCBOCFFVVsM%3D&reserved=0>.


Yes, I confirm that I see the same. There?s a known issue with the BioPortal REST API where occasional irregularities exist between result sets from the /mappings and /classes/:cls/mappings endpoints. That issue is documented in our GitHub repository, and I?ve added your observations just now: https://github.com/ncbo/ontologies_api/issues/50#issuecomment-620784355.



I decided to only use mappings from http://data.bioontology.org/mappings?ontologies=ORDO,SNOMEDCT<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fmappings%3Fontologies%3DORDO%2CSNOMEDCT&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442223042&sdata=oDFTyhR44021QpzPUvYoViVzb6MOYvtqbmVD4YZ9Z%2Fs%3D&reserved=0>, but that still makes me wonder why the webpage shows SNOMED CT mappings that are not returned by the API in the same way (point 1 vs. point 2). Am I missing something? I checked http://data.bioontology.org/mappings?ontologies=ORDO,SNO_COPY<https://eur04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdata.bioontology.org%2Fmappings%3Fontologies%3DORDO%2CSNO_COPY&data=02%7C01%7Cp.vandamme%40amsterdamumc.nl%7C96fd498830434d7bf44808d7dda46413%7C68dfab1a11bb4cc6beb528d756984fb6%7C0%7C1%7C637221570442233040&sdata=DC6ZnwEewmNtyEwVnyNDuQsOhGw8bRq5vg6QxwDqZZA%3D&reserved=0>, which is returning an empty set.


No, you?re not missing something. As I mentioned above, you?ve run into a known issue with the API.

Hope these explanations were helpful.

Kind regards,
Jennifer

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From chinghua at us.ibm.com  Wed Apr 29 15:37:27 2020
From: chinghua at us.ibm.com (Ching-Hua Chen)
Date: Wed, 29 Apr 2020 22:37:27 +0000
Subject: [bioontology-support] Annotation GET results
Message-ID: <OF4E7C00F7.937466F2-ON00258559.007BE298-00258559.007C4799@notes.na.collabserv.com>

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From vendetti at stanford.edu  Wed Apr 29 16:24:53 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 29 Apr 2020 23:24:53 +0000
Subject: [bioontology-support] Annotation GET results
In-Reply-To: <OF4E7C00F7.937466F2-ON00258559.007BE298-00258559.007C4799@notes.na.collabserv.com>
References: <OF4E7C00F7.937466F2-ON00258559.007BE298-00258559.007C4799@notes.na.collabserv.com>
Message-ID: <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu>

Hello Ching-Hua,


On Apr 29, 2020, at 3:37 PM, Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> wrote:

I am running the sample code "annotate_txt.py" and experiencing results that I can't understand.

I modified the API call to the following, in order to specifically use the ICD10 ontology:

get_json(REST_URL + "/annotator?ontologies=ICD10&text=" + urllib.parse.quote(text_to_annotate))

When I reference the public bioportal, I get non-zero results for the text_to_annotate provided.


I?m not able to reproduce this on our end. I issued that REST call and public BioPortal returns empty results if you constrain to the ICD10 ontology. This is the specific call that I used:

http://data.bioontology.org/annotator?ontologies=ICD10&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye.

? and I see an empty result set:

[cid:67099FF0-67F6-41E3-80D6-B12A2DAA72E6 at stanford.edu]



However, when I change the URL to reference my local Virtual Appliance, the annotation results are empty, even though ICD10 is listed as one of the ontologies on my virtual appliance.

This discrepancy only occurs for some ontologies, and not others, that are on my virtual appliance. Any suggestions on why this might be happening?


If you?re not seeing expected Annotator results from a particular ontology, one thing to check is whether that ontology has been fully and successfully processed in your appliance instance. In other words, look at the ontology metadata page and see if there are any error statuses for the last submission of the ontology. You should see a list of statuses for the last submission that include ?Parsed, Indexed, Metrics, Annotator?:

[cid:9FCDB055-8868-46ED-B34B-F08CDE085D2F at stanford.edu]


Alternatively, if you have administrative privileges for your appliance instance, you can log in and look at the Admin -> Ontology Administration tab, which will indicate if there are any ontology processing issues.

Kind regards,
Jennifer

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From chinghua at us.ibm.com  Thu Apr 30 07:59:33 2020
From: chinghua at us.ibm.com (Ching-Hua Chen)
Date: Thu, 30 Apr 2020 14:59:33 +0000
Subject: [bioontology-support] Annotation GET results
In-Reply-To: <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu>
References: <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu>,
 <OF4E7C00F7.937466F2-ON00258559.007BE298-00258559.007C4799@notes.na.collabserv.com>
Message-ID: <OFE3811D69.0CD229C8-ON0025855A.004FC18F-0025855A.00525B3B@notes.na.collabserv.com>

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From vendetti at stanford.edu  Thu Apr 30 09:02:40 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 30 Apr 2020 16:02:40 +0000
Subject: [bioontology-support] Annotation GET results
In-Reply-To: <OFE3811D69.0CD229C8-ON0025855A.004FC18F-0025855A.00525B3B@notes.na.collabserv.com>
References: <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu>
 <OF4E7C00F7.937466F2-ON00258559.007BE298-00258559.007C4799@notes.na.collabserv.com>
 <OFE3811D69.0CD229C8-ON0025855A.004FC18F-0025855A.00525B3B@notes.na.collabserv.com>
Message-ID: <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu>

Hi Ching-Hua,

You could use an API call like the following to examine the latest submission of a given ontology:

http://data.bioontology.org/ontologies/ICD10/latest_submission?include=all

In the JSON results, there should be a ?submissionStatus? name/value pair with an array of statuses, e.g.:


[cid:AAB79AAB-3DE6-4EC3-9430-1DDF539B5A07 at stanford.edu]


If any of the processing steps failed, there would be status values with an ?ERROR? string, e.g.:


[cid:098F4D4C-6B11-4CCA-81C8-11AFFE790663 at stanford.edu]


Alternatively, you could issue API calls to get the root classes of an ontology, or all of the classes for an ontology. If the ontology failed to process correctly, you would likely see failures or empty sets when trying to access the ontology content:

http://data.bioontology.org/ontologies/ICD10/classes/roots
http://data.bioontology.org/ontologies/ICD10/classes

Finally, you could look at the log file for a given ontology to see if there were any error during processing. Information about log file location is here:

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

We also have some public documentation of the REST API that you may find helpful:

http://data.bioontology.org/documentation

Kind regards,
Jennifer



On Apr 30, 2020, at 7:59 AM, Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> wrote:

Thanks, Jennifer!

My apologies, the text I was actually annotating is:

text_to_annotate = "Relationship among genotype, biochemical phenotype, and cognitive performance in females with phenylalanine hydroxylase deficiency: report from the Maternal Phenylketonuria Collaborative Study. OBJECTIVE  To examine the relationship of phenylalanine hydroxylase ( PAH ) genotypes to biochemical phenotype and cognitive development in maternal phenylketonuria ( PKU ) . METHODOLOGY  PAH gene mutations were examined in 222 hyperphenylalaninemic females enrolled in the Maternal PKU Collaborative Study ( MPKUCS ) . A total of 84 different mutations were detected , and complete genotype was obtained in 199 individuals . Based on previous knowledge about mutation-phenotype associations , 78 of the mutations could be assigned to one of four classes of severity ( severe PKU , moderate PKU , mild PKU , and mild hyperphenylalaninemia [ MHP ] ) . Then , 189 MPKUCS subjects were grouped according to the various combinations of mutation classifications . The sample sizes were large enough for statistical testing in four groups with at least one mutation that completely abolishes enzyme activity . These patients are considered functionally hemizygous . RESULTS  The biochemical phenotype predicted from the genotype in functionally hemizygous patients was related significantly to the assigned phenylalanine level . Cognitive performance ( IQ ) was also significantly related to genotype . The IQ of PAH-deficient mothers with a severe PKU mutation in combination with a MHP mutation or a mild PKU mutation was 99 and 96 , respectively , whereas the IQ of PKU mothers with two severe PKU mutations or with one severe and one moderate PKU mutation was 83 and 84 , respectively . Of the patients with PKU , 92 % had been treated during childhood . Those who were untreated or treated late had lower than average IQ scores for their group of mutation combinations . Females with moderate or mild PKU who were treated early and treated for > 6 years showed IQ scores 10 points above average for their group . CONCLUSIONS  The reproductive outcome in maternal phenylketonuria is dependent on prenatal metabolic control and postnatal environmental circumstances . Both factors depend on the intellectual resources of the mother with PKU . The significant relationship among genotype , biochemical phenotype , and cognitive performance observed in the present study is of importance for the development of an optimal strategy for future treatment of females with PKU who plan pregnancy"


Is there a way to check the status of submitted ontologies without using the UI? (My appliance is not very responsive when I try to access it using the UI. However, when I make API calls it seems to be quite responsive. Maybe the reason I am getting empty results for some ontologies is that the request is timing out....)

Should I be examining the ontology submission status? I'm not very familiar with the API yet, if you are able to provide an example API call that can return the status would be much appreciated!

Best,

Ching-Hua Chen

Computational Health Behavior & Decision Science
IBM, T.J. Watson Research Center
1101 Kitchawan Road, Yorktown Heights, NY 10598

chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>
(914) 945-2061 (o); (845) 519-7582 (m)

"Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson


----- Original message -----
From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
To: Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>>
Cc: "bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>" <bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>>
Subject: [EXTERNAL] Re: [bioontology-support] Annotation GET results
Date: Wed, Apr 29, 2020 7:25 PM

Hello Ching-Hua,


On Apr 29, 2020, at 3:37 PM, Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> wrote:

I am running the sample code "annotate_txt.py" and experiencing results that I can't understand.

I modified the API call to the following, in order to specifically use the ICD10 ontology:

get_json(REST_URL + "/annotator?ontologies=ICD10&text=" + urllib.parse.quote(text_to_annotate))

When I reference the public bioportal, I get non-zero results for the text_to_annotate provided.


I?m not able to reproduce this on our end. I issued that REST call and public BioPortal returns empty results if you constrain to the ICD10 ontology. This is the specific call that I used:

http://data.bioontology.org/annotator?ontologies=ICD10&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye.

? and I see an empty result set:

<Image.67099FF0-67F6-41E3-80D6-B12A2DAA72E6 at stanford.edu.png>



However, when I change the URL to reference my local Virtual Appliance, the annotation results are empty, even though ICD10 is listed as one of the ontologies on my virtual appliance.

This discrepancy only occurs for some ontologies, and not others, that are on my virtual appliance. Any suggestions on why this might be happening?


If you?re not seeing expected Annotator results from a particular ontology, one thing to check is whether that ontology has been fully and successfully processed in your appliance instance. In other words, look at the ontology metadata page and see if there are any error statuses for the last submission of the ontology. You should see a list of statuses for the last submission that include ?Parsed, Indexed, Metrics, Annotator?:

<Image.9FCDB055-8868-46ED-B34B-F08CDE085D2F at stanford.edu.png>


Alternatively, if you have administrative privileges for your appliance instance, you can log in and look at the Admin -> Ontology Administration tab, which will indicate if there are any ontology processing issues.

Kind regards,
Jennifer




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From hoyle at buffalo.edu  Thu Apr 30 13:50:48 2020
From: hoyle at buffalo.edu (Hoyle, Patrick)
Date: Thu, 30 Apr 2020 20:50:48 +0000
Subject: [bioontology-support] Question regarding OntoPortal Virtual
	Appliance 3.0
Message-ID: <07E30CAE-D052-4F7C-BCBF-B06DBD0B1000@buffalo.edu>

Hi--

I currently support a couple of instances of the OntoPortal Virtual Appliance for a professor at the University at Buffalo.  One is version 2.4, and the other is 2.5.  I plan to upgrade both of these to version 3.0 as soon as it is released, since both 2.4 and 2.5 are based on CentOS 6, which reaches end of life on 30 November.  Could you tell me which Linux distro version 3.0 will be based on??

Thanks in advance,

-- 
________________________________________________________________________
Patrick Hoyle
Instructional Support Specialist, CASet
College of Arts and Sciences
University at Buffalo
(716) 645-5638
 


From vendetti at stanford.edu  Thu Apr 30 16:32:42 2020
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 30 Apr 2020 23:32:42 +0000
Subject: [bioontology-support] Question regarding OntoPortal
	Virtual	Appliance 3.0
In-Reply-To: <07E30CAE-D052-4F7C-BCBF-B06DBD0B1000@buffalo.edu>
References: <07E30CAE-D052-4F7C-BCBF-B06DBD0B1000@buffalo.edu>
Message-ID: <42ED7782-BA48-4B72-8A09-78DC758A8309@stanford.edu>

Hi Patrick,

OntoPortal 3.0 is based on CentOS 7.

Kind regards,
Jennifer


> On Apr 30, 2020, at 1:50 PM, Hoyle, Patrick <hoyle at buffalo.edu> wrote:
> 
> Hi--
> 
> I currently support a couple of instances of the OntoPortal Virtual Appliance for a professor at the University at Buffalo.  One is version 2.4, and the other is 2.5.  I plan to upgrade both of these to version 3.0 as soon as it is released, since both 2.4 and 2.5 are based on CentOS 6, which reaches end of life on 30 November.  Could you tell me which Linux distro version 3.0 will be based on??
> 
> Thanks in advance,
> 
> -- 
> ________________________________________________________________________
> Patrick Hoyle
> Instructional Support Specialist, CASet
> College of Arts and Sciences
> University at Buffalo
> (716) 645-5638
> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


From chinghua at us.ibm.com  Thu Apr 30 16:39:20 2020
From: chinghua at us.ibm.com (Ching-Hua Chen)
Date: Thu, 30 Apr 2020 23:39:20 +0000
Subject: [bioontology-support] Annotation GET results
In-Reply-To: <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu>
References: <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu>,
 <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu>
 <OF4E7C00F7.937466F2-ON00258559.007BE298-00258559.007C4799@notes.na.collabserv.com>
 <OFE3811D69.0CD229C8-ON0025855A.004FC18F-0025855A.00525B3B@notes.na.collabserv.com>
Message-ID: <OFA371DB05.D8A0740C-ON0025855A.0080DBCF-0025855A.0081F1D4@notes.na.collabserv.com>

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From chinghua at us.ibm.com  Thu Apr 30 19:23:52 2020
From: chinghua at us.ibm.com (Ching-Hua Chen)
Date: Fri, 1 May 2020 02:23:52 +0000
Subject: [bioontology-support] Annotation GET results
In-Reply-To: <OFA371DB05.D8A0740C-ON0025855A.0080DBCF-0025855A.0081F1D4@LocalDomain>
References: <OFA371DB05.D8A0740C-ON0025855A.0080DBCF-0025855A.0081F1D4@LocalDomain>,
 <76563438-D7B9-4B67-B05D-B72F0458C595@stanford.edu>,
 <113E963C-26A1-4B91-AD50-D35AF584F6ED@stanford.edu>
 <OF4E7C00F7.937466F2-ON00258559.007BE298-00258559.007C4799@notes.na.collabserv.com>
 <OFE3811D69.0CD229C8-ON0025855A.004FC18F-0025855A.00525B3B@notes.na.collabserv.com>
Message-ID: <OF0A00F187.B117233C-ON0025855B.000CEDD2-0025855B.000D2C40@notes.na.collabserv.com>

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