From sougato_das at hotmail.com  Tue May  1 07:32:52 2018
From: sougato_das at hotmail.com (Sougato Das)
Date: Tue, 1 May 2018 14:32:52 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das
In-Reply-To: <063CD9B0-6680-4450-BDDB-DAE629B1425F@stanford.edu>
References: <5a2d6b61b527b_52103f98f56fad3873e0@ncbo-prd-app-09.stanford.edu.mail>
 <F69B646B-B67A-4C76-8BA7-6E5783A42E1C@stanford.edu>
 <8691DE0D-2385-468E-92BF-1E89F1361E33@stanford.edu>
 <BLUPR14MB00364AA83618FF5DBC7D52B592B00@BLUPR14MB0036.namprd14.prod.outlook.com>,
 <063CD9B0-6680-4450-BDDB-DAE629B1425F@stanford.edu>
Message-ID: <BLUPR14MB003605B44B416779542CCA8492810@BLUPR14MB0036.namprd14.prod.outlook.com>

I have read through the API documentation and I am sorry to say that I cannot figure out how to get the "classifies" and "Classified as" values of a given term through the API. I would be grateful if you could show me a sample API call that pulls the "classifies" and "Classified as" value of a given term.


Kind regards,

Sougato

________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Monday, April 16, 2018 5:51 PM
To: bioontology-support at lists.stanford.edu
Cc: Sougato Das
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

Hello Sougato,

Apologies that we don?t currently offer mappings as a file download. They're only accessible programmatically via our REST API, e.g.:

http://data.bioontology.org/mappings?ontologies=MESH,MEDDRA

This is more performant version of the REST call if you?re not interested in seeing the hypermedia links:

http://data.bioontology.org/mappings?ontologies=MESH,MEDDRA&display_links=false

Kind regards,
Jennifer



On Apr 16, 2018, at 10:17 AM, Sougato Das <sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>> wrote:

Hello Samson,

Is there anyway to download the mappings, particularly the one between MeSH and MedDRA? I can see how to access it in the user interface, but there does not appear to be anyway to export it. Perhaps this is available in the API?

Kind regards
Sougato

________________________________
From: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>
Sent: Tuesday, December 12, 2017 2:57 PM
To: Jennifer Vendetti
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

?SIB? is a UMLS abbreviation for "has sibling relationship in a Metathesaurus source vocabulary? [1].

With best regards,
Samson

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nlm.nih.gov%2Fresearch%2Fumls%2Fknowledge_sources%2Fmetathesaurus%2Frelease%2Fabbreviations.html&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=PgT6RqR8HpKztRXJmXSOCQbnRMidKTmPqO%2BmoBgX30Q%3D&reserved=0>

On Dec 11, 2017, at 9:04 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Sougato,

Could you please be more specific about what class, in which ontology you?re looking at? The URL you sent results in a 404 error (http://bioportal.bioontology.org/404?p=classes&conceptid=SIB<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioportal.bioontology.org%2F404%3Fp%3Dclasses%26conceptid%3DSIB&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=bQgTRXD1MlpCl82yJN10fOPvdQ2SIYxDxawJJY%2FQHmE%3D&reserved=0>).

Jennifer



On Dec 10, 2017, at 9:14 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Sougato Das
Email: sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>
Location: http%3A%2F%2Fbioportal.bioontology.org<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=h%2B%2BzuX4xvYMQRn6XeUqiPXPy1Bw1bD8z75chnLaAMAU%3D&reserved=0>%2F404%3Fp%3Dclasses%26conceptid%3DSIB

Feedback:
What does "Inverse of SIB" mean? I've googled extensively for the definition of this term and have not had any luck. Thanks.

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=y1S4QWLs0WvIi0imtUGIxBisNr95mb9Sj%2B1L1PxOa9c%3D&reserved=0>

_______________________________________________
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From vendetti at stanford.edu  Tue May  1 11:24:39 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 1 May 2018 18:24:39 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das
In-Reply-To: <BLUPR14MB003605B44B416779542CCA8492810@BLUPR14MB0036.namprd14.prod.outlook.com>
References: <5a2d6b61b527b_52103f98f56fad3873e0@ncbo-prd-app-09.stanford.edu.mail>
 <F69B646B-B67A-4C76-8BA7-6E5783A42E1C@stanford.edu>
 <8691DE0D-2385-468E-92BF-1E89F1361E33@stanford.edu>
 <BLUPR14MB00364AA83618FF5DBC7D52B592B00@BLUPR14MB0036.namprd14.prod.outlook.com>
 <063CD9B0-6680-4450-BDDB-DAE629B1425F@stanford.edu>
 <BLUPR14MB003605B44B416779542CCA8492810@BLUPR14MB0036.namprd14.prod.outlook.com>
Message-ID: <9A2A5A2F-1114-427E-809C-9FBFDED0726A@stanford.edu>

Hello Sougato,

Could you please include what ontology you are working with, as well as the name of a term that you are trying to retrieve these properties for?

Jennifer


On May 1, 2018, at 7:32 AM, Sougato Das <sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>> wrote:

I have read through the API documentation and I am sorry to say that I cannot figure out how to get the "classifies" and "Classified as" values of a given term through the API. I would be grateful if you could show me a sample API call that pulls the "classifies" and "Classified as" value of a given term.

Kind regards,
Sougato

________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Monday, April 16, 2018 5:51 PM
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Sougato Das
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

Hello Sougato,

Apologies that we don?t currently offer mappings as a file download. They're only accessible programmatically via our REST API, e.g.:

http://data.bioontology.org/mappings?ontologies=MESH,MEDDRA

This is more performant version of the REST call if you?re not interested in seeing the hypermedia links:

http://data.bioontology.org/mappings?ontologies=MESH,MEDDRA&display_links=false

Kind regards,
Jennifer



On Apr 16, 2018, at 10:17 AM, Sougato Das <sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>> wrote:

Hello Samson,

Is there anyway to download the mappings, particularly the one between MeSH and MedDRA? I can see how to access it in the user interface, but there does not appear to be anyway to export it. Perhaps this is available in the API?

Kind regards
Sougato

________________________________
From: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>
Sent: Tuesday, December 12, 2017 2:57 PM
To: Jennifer Vendetti
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

?SIB? is a UMLS abbreviation for "has sibling relationship in a Metathesaurus source vocabulary? [1].

With best regards,
Samson

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nlm.nih.gov%2Fresearch%2Fumls%2Fknowledge_sources%2Fmetathesaurus%2Frelease%2Fabbreviations.html&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=PgT6RqR8HpKztRXJmXSOCQbnRMidKTmPqO%2BmoBgX30Q%3D&reserved=0>

On Dec 11, 2017, at 9:04 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Sougato,

Could you please be more specific about what class, in which ontology you?re looking at? The URL you sent results in a 404 error (http://bioportal.bioontology.org/404?p=classes&conceptid=SIB<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioportal.bioontology.org%2F404%3Fp%3Dclasses%26conceptid%3DSIB&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=bQgTRXD1MlpCl82yJN10fOPvdQ2SIYxDxawJJY%2FQHmE%3D&reserved=0>).

Jennifer



On Dec 10, 2017, at 9:14 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Sougato Das
Email: sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>
Location: http%3A%2F%2Fbioportal.bioontology.org<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=h%2B%2BzuX4xvYMQRn6XeUqiPXPy1Bw1bD8z75chnLaAMAU%3D&reserved=0>%2F404%3Fp%3Dclasses%26conceptid%3DSIB

Feedback:
What does "Inverse of SIB" mean? I've googled extensively for the definition of this term and have not had any luck. Thanks.

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=y1S4QWLs0WvIi0imtUGIxBisNr95mb9Sj%2B1L1PxOa9c%3D&reserved=0>

_______________________________________________
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 xindi.guo at sagebase.org  Tue May  1 12:21:01 2018
From: xindi.guo at sagebase.org (Xindi Guo)
Date: Tue, 1 May 2018 12:21:01 -0700
Subject: [bioontology-support] Error - Cannot add custom ontology set
Message-ID: <CACWz4Si+TrkgHK02_9j4bNyiDEGMYGBenunp9Lpo2pJ3J8udXg@mail.gmail.com>

Hi,

I was trying to add the NCIT
<https://bioportal.bioontology.org/ontologies/NCIT> ontology to my custom
ontology set. However, it went to the error page (image attached) when I
clicked on "Save Custom Ontologies". Also, my colleague has tried to add it
as well in her account. She saw the same error page when trying to access
the NCIT link (https://bioportal.bioontology.org/ontologies/NCIT) and she
was not even able to find NCIT in the list of the custom ontology set.

Can you kindly give us some guidance on what we should do?

Thank you in advance.

Best,
Xindi
*--*
*Xindi (Cindy) Guo*
Research Associate, Computational Oncology
Sage Bionetworks
sagebionetworks.org
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From vendetti at stanford.edu  Tue May  1 12:33:11 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 1 May 2018 19:33:11 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Sougato Das
In-Reply-To: <BLUPR14MB003606014F4057C96A272FBA92810@BLUPR14MB0036.namprd14.prod.outlook.com>
References: <5a2d6b61b527b_52103f98f56fad3873e0@ncbo-prd-app-09.stanford.edu.mail>
 <F69B646B-B67A-4C76-8BA7-6E5783A42E1C@stanford.edu>
 <8691DE0D-2385-468E-92BF-1E89F1361E33@stanford.edu>
 <BLUPR14MB00364AA83618FF5DBC7D52B592B00@BLUPR14MB0036.namprd14.prod.outlook.com>
 <063CD9B0-6680-4450-BDDB-DAE629B1425F@stanford.edu>
 <BLUPR14MB003605B44B416779542CCA8492810@BLUPR14MB0036.namprd14.prod.outlook.com>
 <9A2A5A2F-1114-427E-809C-9FBFDED0726A@stanford.edu>
 <BLUPR14MB003606014F4057C96A272FBA92810@BLUPR14MB0036.namprd14.prod.outlook.com>
Message-ID: <2319BCD6-F8DB-45C1-8973-9E8353F9ABA6@stanford.edu>

Hello Sougato

Here?s an example of a call you can use to retrieve the properties and their values for the ?melanoma? class in MEDDRA:

http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10053571?include=all<http://data.bioontology.org/ontologies/MEDDRA/classes/http://purl.bioontology.org/ontology/MEDDRA/10053571?include=all>

Their will be a properties entry in the JSON results, which you?d need to iterate over to get the value of the ?classified_as? property.

Similarly, you can use this call to retrieve the value of ?classifies? on the ?headache? class:

http://data.bioontology.org/ontologies/MEDDRA/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMEDDRA%2F10019211?include=all<http://data.bioontology.org/ontologies/MEDDRA/classes/http://purl.bioontology.org/ontology/MEDDRA/10019211?include=all>

Kind regards,
Jennifer



On May 1, 2018, at 12:21 PM, Sougato Das <sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>> wrote:

The ontology is MEDDRA and the first term is "melanoma" and the second term is "headache"


________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Tuesday, May 1, 2018 2:24 PM
To: Sougato Das
Cc: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

Hello Sougato,

Could you please include what ontology you are working with, as well as the name of a term that you are trying to retrieve these properties for?

Jennifer


On May 1, 2018, at 7:32 AM, Sougato Das <sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>> wrote:

I have read through the API documentation and I am sorry to say that I cannot figure out how to get the "classifies" and "Classified as" values of a given term through the API. I would be grateful if you could show me a sample API call that pulls the "classifies" and "Classified as" value of a given term.

Kind regards,
Sougato

________________________________
From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Monday, April 16, 2018 5:51 PM
To: bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Cc: Sougato Das
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

Hello Sougato,

Apologies that we don?t currently offer mappings as a file download. They're only accessible programmatically via our REST API, e.g.:

http://data.bioontology.org/mappings?ontologies=MESH,MEDDRA

This is more performant version of the REST call if you?re not interested in seeing the hypermedia links:

http://data.bioontology.org/mappings?ontologies=MESH,MEDDRA&display_links=false

Kind regards,
Jennifer



On Apr 16, 2018, at 10:17 AM, Sougato Das <sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>> wrote:

Hello Samson,

Is there anyway to download the mappings, particularly the one between MeSH and MedDRA? I can see how to access it in the user interface, but there does not appear to be anyway to export it. Perhaps this is available in the API?

Kind regards
Sougato

________________________________
From: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>
Sent: Tuesday, December 12, 2017 2:57 PM
To: Jennifer Vendetti
Cc: Samson Tu; support at bioontology.org<mailto:support at bioontology.org>; sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Sougato Das

?SIB? is a UMLS abbreviation for "has sibling relationship in a Metathesaurus source vocabulary? [1].

With best regards,
Samson

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/abbreviations.html<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nlm.nih.gov%2Fresearch%2Fumls%2Fknowledge_sources%2Fmetathesaurus%2Frelease%2Fabbreviations.html&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=PgT6RqR8HpKztRXJmXSOCQbnRMidKTmPqO%2BmoBgX30Q%3D&reserved=0>

On Dec 11, 2017, at 9:04 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Sougato,

Could you please be more specific about what class, in which ontology you?re looking at? The URL you sent results in a 404 error (http://bioportal.bioontology.org/404?p=classes&conceptid=SIB<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioportal.bioontology.org%2F404%3Fp%3Dclasses%26conceptid%3DSIB&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=bQgTRXD1MlpCl82yJN10fOPvdQ2SIYxDxawJJY%2FQHmE%3D&reserved=0>).

Jennifer



On Dec 10, 2017, at 9:14 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Sougato Das
Email: sougato_das at hotmail.com<mailto:sougato_das at hotmail.com>
Location: http%3A%2F%2Fbioportal.bioontology.org<https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=h%2B%2BzuX4xvYMQRn6XeUqiPXPy1Bw1bD8z75chnLaAMAU%3D&reserved=0>%2F404%3Fp%3Dclasses%26conceptid%3DSIB

Feedback:
What does "Inverse of SIB" mean? I've googled extensively for the definition of this term and have not had any luck. Thanks.

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support<https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7C%7C6e9dd23e213741ebc95508d5419a9ad4%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636487054633591452&sdata=y1S4QWLs0WvIi0imtUGIxBisNr95mb9Sj%2B1L1PxOa9c%3D&reserved=0>

_______________________________________________
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From support at bioontology.org  Wed May  2 05:52:55 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 02 May 2018 05:52:55 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Derrick Lottich
Message-ID: <5ae9b4a7329bb_6c463faaa4ab8ab8758d4@ncbo-prd-app-08.stanford.edu.mail>

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From p0928201 at 126.com  Wed May  2 02:02:10 2018
From: p0928201 at 126.com (panhongjie)
Date: Wed, 2 May 2018 17:02:10 +0800
Subject: [bioontology-support] Class Mapping addition and collection
Message-ID: <5AE97E91.84286E.32146@m50-111.126.com>

Dear Sir/Madam,

Many thanks for your reply in the GitHub.  I?m very sorry for my ill-consideration, here are some details for my questions about BioPoral:
When  I  searched the mapping relations between ICD10 and ICD10CM, I found that the two main mapping relations between the two ontology is LOOM and CUI:



And all the mapping relations statistic was calculated automatically to the ?Mappings? button of ICD10, including all the LOOM and CUI mappings.




But when uploaded my ontology(ICD10CN, a Chinese-translated version of ICD10) to BioPortal,  something strange happed, just as following:
(1) For each class, the major CUI relations calculated automatically and presented in each class of ICD10CN:



But the mapping statistic didn?t record automatically in the ?Mappings? button of ICD10CN:



(2) When I added some special mapping relations to some class in my ontology, the mappings presented in ?Class Mapping (5) ? in the related class,



but the total mapping record in ?Mapping? of the ontology didn?t appear any difference:



The total Mappings between ICD10CN and ICD10 was still not showed in BioPortal.

Look forward to your reply.

Your sincerely,
Eve Pan

??? Windows 10 ?????

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From vendetti at stanford.edu  Wed May  2 10:43:26 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 2 May 2018 17:43:26 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Derrick Lottich
In-Reply-To: <5ae9b4a7329bb_6c463faaa4ab8ab8758d4@ncbo-prd-app-08.stanford.edu.mail>
References: <5ae9b4a7329bb_6c463faaa4ab8ab8758d4@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <A1474743-7171-4F3D-981B-F695A2107F1F@stanford.edu>

Hi Derrick,


On May 2, 2018, at 5:52 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

We have a quick question regarding ontology versions. Is it possible to release a version of our ontology in preproduction? For example, we are wondering if we can release our first OWL version of our ontology and test it out before we push it to production for everyone to see. I noticed there is a ?Status? field on the Add New Submission form that has the values of alpha, beta, production, and retired. Do these control the visibility of the ontology at all or are they just labels for the submission?

These are just labels for the submission.

If you want to control the visibility of your ontology, you could change the viewing restriction to ?Private?, and give read access to only the user accounts that you want to view the content during your pre-production phase.

If you have an existing ontology in BioPortal, you can go the summary page and click the ?Edit ontology information? link. This will bring up a form where you can change the viewing restrictions, and add/remove accounts that are allowed to view (screen shot below). At the time that you?re ready to allow everyone to see the ontology, you can change the viewing restrictions back to ?Public?.

If you?re creating a new ontology in BioPortal, you can go to the Tools -> Ontology Browser page [1], click the ?Submit New Ontology? button, and you will see the same form as in the screen shot below.

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/ontologies


[cid:3868A5D0-6F24-4820-A106-767CF2E62562 at stanford.edu]




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From vendetti at stanford.edu  Wed May  2 10:50:08 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 2 May 2018 17:50:08 +0000
Subject: [bioontology-support] Help with downloading mappings from
 Bioportal
In-Reply-To: <2c8646e4d3154f2293110dc00a245cad@osthus.com>
References: <04b820a21265440883353d8a93937505@osthus.com>
 <BF80A734-8707-40FB-8DAC-09B477D97859@stanford.edu>
 <2c8646e4d3154f2293110dc00a245cad@osthus.com>
Message-ID: <DEBBA123-BEDE-437B-A3A4-FCC2C944EC8F@stanford.edu>

Hello Irmgard,


On May 1, 2018, at 11:12 PM, Irmgard Teschke <irmgard.teschke at osthus.com<mailto:irmgard.teschke at osthus.com>> wrote:

Dear Jennifer,
Thanks for the tip?the link was helpful. I am not well-versed in using REST APIs and I was hoping to find an ?easier? way to download the ontologies in a format such as owl. Your link at least provided me with a way to get the json format so I will see if I can find a workaround to transform it to owl.


I believe that you can download an OWL version of the DOID ontology from the OBO Foundry website:

http://www.obofoundry.org/ontology/doid.html

In BioPortal, we host the OBO version of the ontology, as this is the ontology author?s preference.

It?s the same situation for the HP ontology. An OWL version is available for HP on the OBO Foundry website:

 http://www.obofoundry.org/ontology/hp.html

On a related note, we do have a REST API call for most ontologies in BioPortal that allows you to download the ontology source files, e.g.:

http://data.bioontology.org/ontologies/HP/download

Kind regards,
Jennifer


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From vendetti at stanford.edu  Wed May  2 11:19:15 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Wed, 2 May 2018 18:19:15 +0000
Subject: [bioontology-support] Error - Cannot add custom ontology set
In-Reply-To: <CACWz4Si+TrkgHK02_9j4bNyiDEGMYGBenunp9Lpo2pJ3J8udXg@mail.gmail.com>
References: <CACWz4Si+TrkgHK02_9j4bNyiDEGMYGBenunp9Lpo2pJ3J8udXg@mail.gmail.com>
Message-ID: <45621FA2-7292-44CA-9E29-DC196C4BD4FE@stanford.edu>

Hi Xindi,


On May 1, 2018, at 12:21 PM, Xindi Guo <xindi.guo at sagebase.org<mailto:xindi.guo at sagebase.org>> wrote:

I was trying to add the NCIT<https://bioportal.bioontology.org/ontologies/NCIT> ontology to my custom ontology set. However, it went to the error page (image attached) when I clicked on "Save Custom Ontologies". Also, my colleague has tried to add it as well in her account.


As of yet, I haven?t been able to reproduce this error where clicking the ?Save Custom Ontologies? button results in a 404 error.


She saw the same error page when trying to access the NCIT link (https://bioportal.bioontology.org/ontologies/NCIT) and she was not even able to find NCIT in the list of the custom ontology set.


I modified my personal account to use a custom ontology set of NCIT, and I was able to reproduce this secondary error where trying to view the NCIT ontology results in a 500 error. There appears to be a bug in the BioPortal software that prevents users with custom ontology sets from accessing certain ontologies. I?ve entered an issue in our tracker with more detail:

https://github.com/ncbo/ontologies_api/issues/47

You can follow our progress there in terms of when we?re able to release a fix.

Apologies that I?m not aware of any workaround at the moment other than removing your custom ontology set. If you navigate to the Account Settings page for your account, you should be able to click ?clear selection? link in the Custom Ontology Set section and click the ?Save Custom Ontologies? button to clear the set of custom ontologies. This restores your account to the previous state in BioPortal where all public ontologies are visible / accessible.

Kind regards,
Jennifer

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From xindi.guo at sagebase.org  Wed May  2 11:24:50 2018
From: xindi.guo at sagebase.org (Xindi Guo)
Date: Wed, 2 May 2018 11:24:50 -0700
Subject: [bioontology-support] Error - Cannot add custom ontology set
In-Reply-To: <45621FA2-7292-44CA-9E29-DC196C4BD4FE@stanford.edu>
References: <CACWz4Si+TrkgHK02_9j4bNyiDEGMYGBenunp9Lpo2pJ3J8udXg@mail.gmail.com>
 <45621FA2-7292-44CA-9E29-DC196C4BD4FE@stanford.edu>
Message-ID: <CACWz4Sj4TTrvMpTex9-8rBX_tMhVx0rXrMmyEtTmE0qSFhXoKQ@mail.gmail.com>

Hi Jennifer,

Thank you!

As long as the reproducible error can be fixed, we will be able to move
forward with our project. I will follow the progress on Github.

Thanks again.

Best,
Xindi

*--*
*Xindi (Cindy) Guo*
Research Associate, Computational Oncology
Sage Bionetworks
sagebionetworks.org

On Wed, May 2, 2018 at 11:19 AM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi Xindi,
>
>
> On May 1, 2018, at 12:21 PM, Xindi Guo <xindi.guo at sagebase.org> wrote:
>
> I was trying to add the NCIT
> <https://bioportal.bioontology.org/ontologies/NCIT> ontology to my custom
> ontology set. However, it went to the error page (image attached) when I
> clicked on "Save Custom Ontologies". Also, my colleague has tried to add it
> as well in her account.
>
>
>
> As of yet, I haven?t been able to reproduce this error where clicking the
> ?Save Custom Ontologies? button results in a 404 error.
>
>
> She saw the same error page when trying to access the NCIT link (
> https://bioportal.bioontology.org/ontologies/NCIT) and she was not even
> able to find NCIT in the list of the custom ontology set.
>
>
>
> I modified my personal account to use a custom ontology set of NCIT, and I
> was able to reproduce this secondary error where trying to view the NCIT
> ontology results in a 500 error. There appears to be a bug in the BioPortal
> software that prevents users with custom ontology sets from accessing
> certain ontologies. I?ve entered an issue in our tracker with more detail:
>
> https://github.com/ncbo/ontologies_api/issues/47
>
> You can follow our progress there in terms of when we?re able to release a
> fix.
>
> Apologies that I?m not aware of any workaround at the moment other than
> removing your custom ontology set. If you navigate to the Account Settings
> page for your account, you should be able to click ?clear selection? link
> in the Custom Ontology Set section and click the ?Save Custom Ontologies?
> button to clear the set of custom ontologies. This restores your account to
> the previous state in BioPortal where all public ontologies are visible /
> accessible.
>
> Kind regards,
> Jennifer
>
>
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From jgraybeal at stanford.edu  Wed May  2 14:28:47 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Wed, 2 May 2018 21:28:47 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Derrick Lottich
In-Reply-To: <A1474743-7171-4F3D-981B-F695A2107F1F@stanford.edu>
References: <5ae9b4a7329bb_6c463faaa4ab8ab8758d4@ncbo-prd-app-08.stanford.edu.mail>
 <A1474743-7171-4F3D-981B-F695A2107F1F@stanford.edu>
Message-ID: <BD60B636-7BF4-4635-89CD-ABFFD93657AB@stanford.edu>

If I understand correctly, an ontology that was previously public is changed to private, that will essentially make the ontology "disappear" for users who do not have access. So the before the first publication this approach will work, but subsequently it would make the ontology regularly disappear.

In which case I think the only satisfactory workflow would be to submit the draft ontology under a different acronym, where it is set to private with permission given to the desired users, as you describe. That acronym could then host a succession of draft ontologies, while the ultimately published ontologies would permanently use the original ontology acronym.

John

On May 2, 2018, at 10:43 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Derrick,


On May 2, 2018, at 5:52 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

We have a quick question regarding ontology versions. Is it possible to release a version of our ontology in preproduction? For example, we are wondering if we can release our first OWL version of our ontology and test it out before we push it to production for everyone to see. I noticed there is a ?Status? field on the Add New Submission form that has the values of alpha, beta, production, and retired. Do these control the visibility of the ontology at all or are they just labels for the submission?

These are just labels for the submission.

If you want to control the visibility of your ontology, you could change the viewing restriction to ?Private?, and give read access to only the user accounts that you want to view the content during your pre-production phase.

If you have an existing ontology in BioPortal, you can go the summary page and click the ?Edit ontology information? link. This will bring up a form where you can change the viewing restrictions, and add/remove accounts that are allowed to view (screen shot below). At the time that you?re ready to allow everyone to see the ontology, you can change the viewing restrictions back to ?Public?.

If you?re creating a new ontology in BioPortal, you can go to the Tools -> Ontology Browser page [1], click the ?Submit New Ontology? button, and you will see the same form as in the screen shot below.

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/ontologies


<Screenshot 2018-05-02 10.36.57.png>




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

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


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From support at bioontology.org  Wed May  2 13:18:09 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 02 May 2018 13:18:09 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Michal Lijowski
Message-ID: <5aea1d012f7e7_4a8d3f9891dfcc081173a@ncbo-prd-app-08.stanford.edu.mail>

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From support at bioontology.org  Thu May  3 06:41:32 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 03 May 2018 06:41:32 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Tatsuya Kushida
Message-ID: <5aeb118c380cd_10c93ff8d33a70e494860@ncbo-prd-app-09.stanford.edu.mail>

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From amassengale at rsna.org  Thu May  3 06:57:01 2018
From: amassengale at rsna.org (Andrew Massengale)
Date: Thu, 3 May 2018 13:57:01 +0000
Subject: [bioontology-support] Bio Portal down
Message-ID: <163ECC4C-CF0B-49D3-AEBF-1FDF12E9AFA0@rsna.org>

Hi all,

I am a software engineer for RSNA. We are integrating with bio portal for one of our applications, and it appears that bio portal is currently down. Below are some screenshots of errors we are getting:

https://data.bioontology.org/search?ontology=RADLEX&apikey=58bb5724-cad7-45ed-a949-5570fa89a01e&q=cecum&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000
[cid:image001.png at 01D3E2BC.B3162BA0]

Trying to select the ?RADLEX? ontology in the ?Find an ontology? search box on BioPortal?s main site (it has been ?Loading Ontology?? for about 20 minutes now)
[cid:image002.png at 01D3E2BC.B3162BA0]

If you could give me an estimate for how long this will take to fix, that would be great.

Thanks!

Andrew M

Andrew Massengale
Senior Software Engineer
IT: Development
amassengale at rsna.org<mailto:amassengale at rsna.org>
CEL: 815-614-8296
TEL: 630-481-1012
FAX: 630-571-7837
Radiological Society of North America
820 Jorie Blvd, Oak Brook, IL 60523
TEL 1-630-571-2670
FAX 1-630-571-7837
RSNA.org<http://www.rsna.org>

Facebook<http://www.facebook.com/RSNAfans>
Twitter<http://twitter.com/RSNA>
RSNA 2018 Annual Meeting<http://www.rsna.org/Annual_Meeting.aspx>
November 25th ? 30th
McCormick Place, Chicago
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From vendetti at stanford.edu  Thu May  3 11:08:24 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 3 May 2018 18:08:24 +0000
Subject: [bioontology-support] Bio Portal down
In-Reply-To: <163ECC4C-CF0B-49D3-AEBF-1FDF12E9AFA0@rsna.org>
References: <163ECC4C-CF0B-49D3-AEBF-1FDF12E9AFA0@rsna.org>
Message-ID: <710B7A6D-7EDC-4407-AD52-4F1DB944B58C@stanford.edu>

Hello Andrew,

We had some issues with the site / REST API between 6 and 8:45am PST. Everything is back up - please let us know if you?re still experiencing issues.

Kind regards,
Jennifer



On May 3, 2018, at 6:57 AM, Andrew Massengale <amassengale at rsna.org<mailto:amassengale at rsna.org>> wrote:

Hi all,

I am a software engineer for RSNA. We are integrating with bio portal for one of our applications, and it appears that bio portal is currently down. Below are some screenshots of errors we are getting:

https://data.bioontology.org/search?ontology=RADLEX&apikey=58bb5724-cad7-45ed-a949-5570fa89a01e&q=cecum&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000
<image001.png>

Trying to select the ?RADLEX? ontology in the ?Find an ontology? search box on BioPortal?s main site (it has been ?Loading Ontology?? for about 20 minutes now)
<image002.png>

If you could give me an estimate for how long this will take to fix, that would be great.

Thanks!

Andrew M

Andrew Massengale
Senior Software Engineer
IT: Development
amassengale at rsna.org<mailto:amassengale at rsna.org>
CEL: 815-614-8296
TEL: 630-481-1012
FAX: 630-571-7837
Radiological Society of North America
820 Jorie Blvd, Oak Brook, IL 60523
TEL 1-630-571-2670
FAX 1-630-571-7837
RSNA.org<http://www.rsna.org/>

Facebook<http://www.facebook.com/RSNAfans>
Twitter<http://twitter.com/RSNA>
RSNA 2018 Annual Meeting<http://www.rsna.org/Annual_Meeting.aspx>
November 25th ? 30th
McCormick Place, Chicago _______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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From vendetti at stanford.edu  Thu May  3 11:10:39 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 3 May 2018 18:10:39 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Tatsuya Kushida
In-Reply-To: <5aeb118c380cd_10c93ff8d33a70e494860@ncbo-prd-app-09.stanford.edu.mail>
References: <5aeb118c380cd_10c93ff8d33a70e494860@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <0CDD8DAF-3DB8-451D-8004-80172DFBA3F7@stanford.edu>

Hello Tatsuya,

There were some issues with the BIoPortal website from roughly 6am to 8:45am PST. The site is restored and I?ve tested logging in / out, and it?s functioning properly. Please try again and let us know if you?re still experiencing problems with your account.

Kind regards,
Jennifer



On May 3, 2018, at 6:41 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Tatsuya Kushida

Email: kushida at biosciencedbc.jp<mailto:kushida at biosciencedbc.jp>

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

Feedback:

Hi,
I can't log in to my account.
Please tell me why.
My account is kushida
Best wishes.
Tatsuya Kushida

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

_______________________________________________
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From vendetti at stanford.edu  Thu May  3 11:55:09 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 3 May 2018 18:55:09 +0000
Subject: [bioontology-support] Problem with ontology parsing
In-Reply-To: <14F88C2B-F491-4E48-BED3-21D44291EB3C@upmc.fr>
References: <8EDDF5B3-474E-4532-89FE-58EDAC7A0794@lirmm.fr>
 <43EA4856-90C5-4D0F-9D34-EB50DB8EB393@stanford.edu>
 <4202D83D-5A5C-4D0E-9D5E-F8D1F73F1D51@lirmm.fr>
 <14F88C2B-F491-4E48-BED3-21D44291EB3C@upmc.fr>
Message-ID: <82FCF9C7-2EE3-49F3-A124-0D29E9E76067@stanford.edu>

Hello Jean,

We had some issues with BioPortal from roughly 6 to 8:45AM PST. It looks like your new submission was uploaded around that time, and failed to parse as a result. I reprocessed the submission and your ontology is parsed / available in BioPortal now.

I assume you?d like us to delete the previous 9 submissions, none of which parsed due to the prefLabel you mentioned below?

Kind regards,
Jennifer



> On May 3, 2018, at 8:35 AM, Charlet Jean <jean.charlet at upmc.fr> wrote:
> 
> Hi Jennifer,
> 
> 1. Good news, Cl?ment found the problem with my ontology: the definition of a ? fr-parl? ? lang for prefLabel(s)
>              (in <skos:prefLabel xml:lang="fr-parl?">besoin big-big</skos:prefLabel>)
> 2. Bad news, I upload a new version of an extract of my ontology in Bioportal in order to verify the good news number one and? it fails (attached screen copy) :-))
> 
> I imagine that you will easily correct the second problem?
> 
> Regards,
> Jean.
> 
> 
> <Capture d?e?cran 2018-05-03 a? 16.04.58.png>
> 


From jean.charlet at upmc.fr  Thu May  3 12:40:39 2018
From: jean.charlet at upmc.fr (Charlet Jean)
Date: Thu, 3 May 2018 21:40:39 +0200
Subject: [bioontology-support] Problem with ontology parsing
In-Reply-To: <82FCF9C7-2EE3-49F3-A124-0D29E9E76067@stanford.edu>
References: <8EDDF5B3-474E-4532-89FE-58EDAC7A0794@lirmm.fr>
 <43EA4856-90C5-4D0F-9D34-EB50DB8EB393@stanford.edu>
 <4202D83D-5A5C-4D0E-9D5E-F8D1F73F1D51@lirmm.fr>
 <14F88C2B-F491-4E48-BED3-21D44291EB3C@upmc.fr>
 <82FCF9C7-2EE3-49F3-A124-0D29E9E76067@stanford.edu>
Message-ID: <DAD07107-70EE-467F-A8F0-50A4571D862C@upmc.fr>

Hello Jennifer,

Yes, after I will upload a real new version.

Thank you.

Regards,
Jean.

> Le 3 mai 2018 ? 20:55, Jennifer Leigh Vendetti <vendetti at stanford.edu> a ?crit :
> 
> Hello Jean,
> 
> We had some issues with BioPortal from roughly 6 to 8:45AM PST. It looks like your new submission was uploaded around that time, and failed to parse as a result. I reprocessed the submission and your ontology is parsed / available in BioPortal now.
> 
> I assume you?d like us to delete the previous 9 submissions, none of which parsed due to the prefLabel you mentioned below?
> 
> Kind regards,
> Jennifer
> 
> 
> 
>> On May 3, 2018, at 8:35 AM, Charlet Jean <jean.charlet at upmc.fr> wrote:
>> 
>> Hi Jennifer,
>> 
>> 1. Good news, Cl?ment found the problem with my ontology: the definition of a ? fr-parl? ? lang for prefLabel(s)
>>             (in <skos:prefLabel xml:lang="fr-parl?">besoin big-big</skos:prefLabel>)
>> 2. Bad news, I upload a new version of an extract of my ontology in Bioportal in order to verify the good news number one and? it fails (attached screen copy) :-))
>> 
>> I imagine that you will easily correct the second problem?
>> 
>> Regards,
>> Jean.
>> 
>> 
>> <Capture d?e?cran 2018-05-03 a? 16.04.58.png>
>> 
> 

           ,,,,
          (o-o)
--------oOO-(_)-OOo------------------------------------------o0O-OOo----
      Jean Charlet                          M?l : Jean.Charlet at upmc.fr
    INSERM UMR_S 1142                        T?l : +33/0 1 44 27 91 09
15, rue de l'?cole de M?decine              URL : http://www.limics.fr/
  75006 Paris, France 
                 Assistance publique - H?pitaux de Paris
               LIMICS - Univ. Paris VI - Univ. Paris XIII
----------o0O-OOo------------------------------------------oOO-( )-OOo--
                                                             (o-o)
                                                              ````


From vendetti at stanford.edu  Thu May  3 15:41:38 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 3 May 2018 22:41:38 +0000
Subject: [bioontology-support] Problem with ontology parsing
In-Reply-To: <DAD07107-70EE-467F-A8F0-50A4571D862C@upmc.fr>
References: <8EDDF5B3-474E-4532-89FE-58EDAC7A0794@lirmm.fr>
 <43EA4856-90C5-4D0F-9D34-EB50DB8EB393@stanford.edu>
 <4202D83D-5A5C-4D0E-9D5E-F8D1F73F1D51@lirmm.fr>
 <14F88C2B-F491-4E48-BED3-21D44291EB3C@upmc.fr>
 <82FCF9C7-2EE3-49F3-A124-0D29E9E76067@stanford.edu>
 <DAD07107-70EE-467F-A8F0-50A4571D862C@upmc.fr>
Message-ID: <F0D7DC34-9884-4FCB-A2BB-94676052E876@stanford.edu>

OK - thanks for the reply Jean. The first 9 submission that didn?t parse have been deleted from the system.

Kind regards,
Jennifer


On May 3, 2018, at 12:40 PM, Charlet Jean <jean.charlet at upmc.fr<mailto:jean.charlet at upmc.fr>> wrote:

Hello Jennifer,

Yes, after I will upload a real new version.

Thank you.

Regards,
Jean.

Le 3 mai 2018 ? 20:55, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> a ?crit :

Hello Jean,

We had some issues with BioPortal from roughly 6 to 8:45AM PST. It looks like your new submission was uploaded around that time, and failed to parse as a result. I reprocessed the submission and your ontology is parsed / available in BioPortal now.

I assume you?d like us to delete the previous 9 submissions, none of which parsed due to the prefLabel you mentioned below?

Kind regards,
Jennifer



On May 3, 2018, at 8:35 AM, Charlet Jean <jean.charlet at upmc.fr<mailto:jean.charlet at upmc.fr>> wrote:

Hi Jennifer,

1. Good news, Cl?ment found the problem with my ontology: the definition of a ? fr-parl? ? lang for prefLabel(s)
           (in <skos:prefLabel xml:lang="fr-parl?">besoin big-big</skos:prefLabel>)
2. Bad news, I upload a new version of an extract of my ontology in Bioportal in order to verify the good news number one and? it fails (attached screen copy) :-))

I imagine that you will easily correct the second problem?

Regards,
Jean.


<Capture d?e?cran 2018-05-03 a? 16.04.58.png>



          ,,,,
         (o-o)
--------oOO-(_)-OOo------------------------------------------o0O-OOo----
     Jean Charlet                          M?l : Jean.Charlet at upmc.fr<mailto:Jean.Charlet at upmc.fr>
   INSERM UMR_S 1142                        T?l : +33/0 1 44 27 91 09
15, rue de l'?cole de M?decine              URL : http://www.limics.fr/
 75006 Paris, France
                Assistance publique - H?pitaux de Paris
              LIMICS - Univ. Paris VI - Univ. Paris XIII
----------o0O-OOo------------------------------------------oOO-( )-OOo--
                                                            (o-o)
                                                             ````

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From amassengale at rsna.org  Fri May  4 06:48:10 2018
From: amassengale at rsna.org (Andrew Massengale)
Date: Fri, 4 May 2018 13:48:10 +0000
Subject: [bioontology-support] Bio Portal down
In-Reply-To: <710B7A6D-7EDC-4407-AD52-4F1DB944B58C@stanford.edu>
References: <163ECC4C-CF0B-49D3-AEBF-1FDF12E9AFA0@rsna.org>
 <710B7A6D-7EDC-4407-AD52-4F1DB944B58C@stanford.edu>
Message-ID: <5BC8C0A8-6EC6-4C9C-B786-0C4578F61749@rsna.org>

Thanks Jennifer!

It appears to be up now.

Andrew M

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Thursday, May 3, 2018 at 1:08 PM
To: Andrew Massengale <amassengale at rsna.org>
Cc: "bioontology-support at lists.stanford.edu" <bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] Bio Portal down

Hello Andrew,

We had some issues with the site / REST API between 6 and 8:45am PST. Everything is back up - please let us know if you?re still experiencing issues.

Kind regards,
Jennifer




On May 3, 2018, at 6:57 AM, Andrew Massengale <amassengale at rsna.org<mailto:amassengale at rsna.org>> wrote:

Hi all,

I am a software engineer for RSNA. We are integrating with bio portal for one of our applications, and it appears that bio portal is currently down. Below are some screenshots of errors we are getting:

https://data.bioontology.org/search?ontology=RADLEX&apikey=58bb5724-cad7-45ed-a949-5570fa89a01e&q=cecum&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdata.bioontology.org%2Fsearch%3Fontology%3DRADLEX%26apikey%3D58bb5724-cad7-45ed-a949-5570fa89a01e%26q%3Dcecum%26format%3Djson%26subtree_root_id%3Dhttp%3A%252F%252Fwww.radlex.org%252FRID%252F%2523RID3%26roots_only%3Dtrue%26page%3D1%26pagesize%3D1000&data=02%7C01%7Camassengale%40rsna.org%7C72482e1e67574b23863408d5b120e08a%7Cfb5fefcd7ca642f3b443917c2a68cecd%7C1%7C0%7C636609677129889794&sdata=MWGncJ4EFVTVI7QzJBpph0uOrhOiOPLAHm32cpu50HY%3D&reserved=0>
<image001.png>

Trying to select the ?RADLEX? ontology in the ?Find an ontology? search box on BioPortal?s main site (it has been ?Loading Ontology?? for about 20 minutes now)
<image002.png>

If you could give me an estimate for how long this will take to fix, that would be great.

Thanks!

Andrew M

Andrew Massengale
Senior Software Engineer
IT: Development
amassengale at rsna.org<mailto:amassengale at rsna.org>
CEL: 815-614-8296
TEL: 630-481-1012
FAX: 630-571-7837
Radiological Society of North America
820 Jorie Blvd, Oak Brook, IL 60523
TEL 1-630-571-2670
FAX 1-630-571-7837
RSNA.org<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rsna.org%2F&data=02%7C01%7Camassengale%40rsna.org%7C72482e1e67574b23863408d5b120e08a%7Cfb5fefcd7ca642f3b443917c2a68cecd%7C1%7C0%7C636609677129889794&sdata=6tLMBWVrKAcyMBO%2BxEAYS4s0wvbMfIbnl201%2BEghgp0%3D&reserved=0>

Facebook<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.facebook.com%2FRSNAfans&data=02%7C01%7Camassengale%40rsna.org%7C72482e1e67574b23863408d5b120e08a%7Cfb5fefcd7ca642f3b443917c2a68cecd%7C1%7C0%7C636609677129889794&sdata=sf4OL0ai0eh2GWotFLnH0YwCNbLb7%2F2T4oeFMB7EjzQ%3D&reserved=0>
Twitter<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftwitter.com%2FRSNA&data=02%7C01%7Camassengale%40rsna.org%7C72482e1e67574b23863408d5b120e08a%7Cfb5fefcd7ca642f3b443917c2a68cecd%7C1%7C0%7C636609677129889794&sdata=GYGN1T8MsTt69144zgF5NtWAVvQrOr4s4DjQxdpw4cY%3D&reserved=0>
RSNA 2018 Annual Meeting<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rsna.org%2FAnnual_Meeting.aspx&data=02%7C01%7Camassengale%40rsna.org%7C72482e1e67574b23863408d5b120e08a%7Cfb5fefcd7ca642f3b443917c2a68cecd%7C1%7C0%7C636609677129889794&sdata=U6o2h2w5KT6dpPnK49uPo4itS9oaMQxYlvN9%2BwSSAXk%3D&reserved=0>
November 25th ? 30th
McCormick Place, Chicago _______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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Radiological Society of North America
820 Jorie Blvd, Oak Brook, IL 60523
TEL 1-630-571-2670
FAX 1-630-571-7837
RSNA.org<http://www.rsna.org>

Facebook<http://www.facebook.com/RSNAfans>
Twitter<http://twitter.com/RSNA>
RSNA 2018 Annual Meeting<http://www.rsna.org/Annual_Meeting.aspx>
November 25th ? 30th
McCormick Place, Chicago
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From phil.kiossoglou at gmail.com  Sat May  5 20:08:31 2018
From: phil.kiossoglou at gmail.com (Phil Kiossoglou)
Date: Sun, 6 May 2018 13:08:31 +1000
Subject: [bioontology-support] [BioPortal] Feedback from Phil Kiossoglou
In-Reply-To: <08C81DDD-1F87-47E4-9176-BD94E384D428@stanford.edu>
References: <5aacb8f1c75f5_52fb3f8b656ed96451467@ncbo-prd-app-08.stanford.edu.mail>
 <94339F1F-DB7E-4948-8E09-9DC5E2C755A2@stanford.edu>
 <CAODuxUR3OYRWY2x0T3K9-bPLCEjBJ7wPVczFHd9bOhGgeoHUvQ@mail.gmail.com>
 <0540F4D3-E4A6-409B-9AD0-5F4C316758E0@stanford.edu>
 <6E89B18B-6E0E-405B-A943-36165CFA50E2@stanford.edu>
 <08C81DDD-1F87-47E4-9176-BD94E384D428@stanford.edu>
Message-ID: <CAODuxUQRk4+AKsYUKk8oVNskgYFk1irMCPp23pXENR1WTJhkzQ@mail.gmail.com>

Can confirm it's working on my end.

Thanks for all the help,

Phil

On 27 April 2018 at 09:28, Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Phil,
>
> Just FYI, this problem has been fixed. Let me know if you experience
> further issues.
>
> Thanks,
>
> Michael
>
>
> On Apr 17, 2018, at 4:11 PM, Michael Dorf <mdorf at stanford.edu> wrote:
>
> Just FYI, the issue is tracked here:
>
> https://github.com/ncbo/ncbo_ontology_recommender/issues/7
>
> Michael
>
> On Apr 17, 2018, at 3:22 PM, Michael Dorf <mdorf at stanford.edu> wrote:
>
> Hi Phil,
>
> Thanks for keeping in touch. This definitely appears to be a bug in our
> system. There is no reason for the Recommender to blow up when given the
> word ?concept? (or any input for that matter). I am still hunting for the
> root cause. The fix will most likely require a code release. I?ll keep you
> posted when I have more details.
>
> Thanks!
>
> Michael
>
>
> On Apr 15, 2018, at 7:35 PM, Phil Kiossoglou <phil.kiossoglou at gmail.com>
> wrote:
>
> Hi John,
>
> Thanks for the insight.  Just ran again and still getting the error
> (related to the term "concept", deleting it manages to make it work in this
> particular instance).
>
> Just wondering if there's anything I can contribute to help with a fix?
> (I'm aware the answer to this is probably "not really").
>
> Thanks and regards,
>
> Phil
>
>
> On 18 March 2018 at 03:41, John Graybeal <jgraybeal at stanford.edu> wrote:
>
>> Phil, thank you for sending your issue, sorry it was a pain for so long.
>>
>> After some trial and error, I found the problem word in your text is
>> 'concept'. Delete that word and you can have recommendations for the rest
>> of this text.
>>
>> As a more permanent fix, we'll have to look in the index to see what has
>> been corrupted. I think this will be straightforward, but it may be a few
>> days before we can get to it. We'll send an email once fixed.
>>
>> john
>>
>> On Mar 16, 2018, at 11:42 PM, support at bioontology.org wrote:
>>
>> Name: Phil Kiossoglou
>>
>> Email: phil.kiossoglou at gmail.com
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org
>> <http://2fbioportal.bioontology.org/>%2Frecommender
>>
>>
>> *Feedback:*
>>
>> Attempting to use the NCBO recommender, both via the API and via the
>> online web app is generating errors. In the case of the API, these are HTTP
>> 500 errors.
>>
>> This issue has been persisting for > 1 week.
>>
>> The text I am supplying is (without quotes):
>>
>> "Inflammatory bowel disease (IBD) including Crohn's disease (CD) and
>> ulcerative colitis (UC), is an immunologically mediated chronic disease.
>> The key underlying pathology is a deregulated immune response to commensal
>> flora in a genetically susceptible host. Advances in genomics, epigenomics
>> and understanding of the microbiome have brought forth the role of these
>> spheres in the pathogenesis of IBD. Yet these factors explain only a small
>> fraction of disease risk and our ability to predict relapses and response
>> to treatment remains dismal. The external environment plays an important
>> role in modifying the risk of IBD and in precipitating relapses in patients
>> with established disease. The term 'exposome' was proposed to reflect a
>> life-course of environmental influences beginning in-utero and proceeding
>> right through childhood to adulthood. While the exposome is still a concept
>> which needs practical perspective to enable better patient care, this
>> review examines the gaps in our understanding that the IBD exposome helps
>> explain. We further highlight the definition and parameters of this metric
>> which can be incorporated for its application in research and clinical
>> practice"
>>
>> I have supplied this data to the recommender in the past and it has
>> worked successfully. Can you please advise if there is a fault at the
>> moment?
>>
>> Thanks and regards,
>>
>> Phil
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>> ========================
>> John Graybeal
>> Technical Program Manager
>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>> 650-736-1632
>>
>>
>>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> _______________________________________________
> 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 May  7 08:20:49 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 07 May 2018 08:20:49 -0700
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
Message-ID: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Mon May  7 09:01:54 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 7 May 2018 16:01:54 +0000
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
In-Reply-To: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
References: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>

Hello Ahmed,

I?m not sure I understand exactly what you?re looking for. You can browse MEDDRA via the BioPortal application here:

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

Or, you can use our REST API to programmatically access the ontology:

http://data.bioontology.org/ontologies/MEDDRA

Use of the REST API requires that you have an API key. Instructions for getting an API key are available on our wiki:

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

The API is documented here:

http://data.bioontology.org/documentation

Kind regards
Jennifer



On May 7, 2018, at 8:20 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: afarhat

Email: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>

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

Feedback:

Hi,
I need "Bioontology URL" for MEDDRA to use it through ClinCapture EDC System.

We already have an MSSO account

Appreciate your help.

Thanks
Ahmed Farhat

_______________________________________________
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 ahmed.farhat at clinart.net  Mon May  7 09:44:44 2018
From: ahmed.farhat at clinart.net (Ahmed Farhat)
Date: Mon, 7 May 2018 18:44:44 +0200
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
In-Reply-To: <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>
References: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
 <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>
Message-ID: <6b675e554c4cc7ddb2187ef7bd14de03@mail.gmail.com>

Dear Jennifer,

Many thanks for your prompt reply.



Kindly find the below snapshot from my BioPortal account and from
ClinCapture EDC System







Is the entered data correct?



Thanks



Regards,



*Ahmed Farhat *
IT Supervisor
[image: Clinart MENA Logo]
2nd  Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th
Settlement, New Cairo, Egypt
Phone: +20228117526 | Fax: +20228117527
Mobile: +20 1145161634 | Skype: farhat.clinart
*Email:* ahmed.farhat at clinart.net | www.clinart.net



*From:* Jennifer Leigh Vendetti <vendetti at stanford.edu>
*Sent:* 7 May, 2018 6:02 PM
*To:* NCBO User Support <support at bioontology.org>
*Cc:* ahmed.farhat at clinart.net
*Subject:* Re: [bioontology-support] [BioPortal] Feedback from afarhat



Hello Ahmed,



I?m not sure I understand exactly what you?re looking for. You can browse
MEDDRA via the BioPortal application here:



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



Or, you can use our REST API to programmatically access the ontology:



http://data.bioontology.org/ontologies/MEDDRA



Use of the REST API requires that you have an API key. Instructions for
getting an API key are available on our wiki:



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



The API is documented here:



http://data.bioontology.org/documentation



Kind regards

Jennifer







On May 7, 2018, at 8:20 AM, support at bioontology.org wrote:



Name: afarhat

Email: ahmed.farhat at clinart.net <ahmed.farhat at clinart.net>

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


*Feedback:*

Hi,
I need "Bioontology URL" for MEDDRA to use it through ClinCapture EDC
System.

We already have an MSSO account

Appreciate your help.

Thanks
Ahmed Farhat



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

-- 
??

The contents of
this e-mail may contain confidential information. If 
you are not the intended
recipient of this message and its contents, please 
inform us by return and
delete it from your system.





Any unauthorized

use, copying or disclosure of the contents of this message is strictly

prohibited.


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From vendetti at stanford.edu  Mon May  7 10:12:24 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 7 May 2018 17:12:24 +0000
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
In-Reply-To: <6b675e554c4cc7ddb2187ef7bd14de03@mail.gmail.com>
References: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
 <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>
 <6b675e554c4cc7ddb2187ef7bd14de03@mail.gmail.com>
Message-ID: <CF4F8228-ED64-44BA-911D-1CC65A9952CB@stanford.edu>

Hello Ahmed,

Apologies, but I have no knowledge of what the ClinCapture system is, so I can?t comment on whether you?ve correctly entered data there.

What I can tell you is how to test whether your BioPortal account is working properly. You should be able to enter a URL for our REST API in a browser and see response data displayed. For example, if you enter the following URL in a browser (enter your API key at the end where I?ve indicated):

http://data.bioontology.org/ontologies/MEDDRA?apikey=your_api_key_goes_here

You should see a JSON response like this:


[cid:EBB7B747-FABE-4BE3-989C-97FD1FA74D51 at stanford.edu]
Kind regards,
Jennifer




On May 7, 2018, at 9:44 AM, Ahmed Farhat <ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>> wrote:

Dear Jennifer,
Many thanks for your prompt reply.

Kindly find the below snapshot from my BioPortal account and from ClinCapture EDC System

<image003.png>

<image001.png>

Is the entered data correct?

Thanks

Regards,

Ahmed Farhat
IT Supervisor
<image002.jpg>
2nd  Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th Settlement, New Cairo, Egypt
Phone: +20228117526 | Fax: +20228117527
Mobile: +20 1145161634 | Skype: farhat.clinart
Email: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net> | www.clinart.net<http://www.clinart.net/>

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: 7 May, 2018 6:02 PM
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>
Subject: Re: [bioontology-support] [BioPortal] Feedback from afarhat

Hello Ahmed,

I?m not sure I understand exactly what you?re looking for. You can browse MEDDRA via the BioPortal application here:

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

Or, you can use our REST API to programmatically access the ontology:

http://data.bioontology.org/ontologies/MEDDRA

Use of the REST API requires that you have an API key. Instructions for getting an API key are available on our wiki:

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

The API is documented here:

http://data.bioontology.org/documentation

Kind regards
Jennifer




On May 7, 2018, at 8:20 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: afarhat
Email: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies

Feedback:
Hi,
I need "Bioontology URL" for MEDDRA to use it through ClinCapture EDC System.
We already have an MSSO account
Appreciate your help.
Thanks
Ahmed Farhat

_______________________________________________
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


  [http://clinart.net/wp-content/uploads/2017/05/ISO-9001-blue-TM-e1495018831397.jpg]

The contents of this e-mail may contain confidential information. If you are not the intended recipient of this message and its contents, please inform us by return and delete it from your system.


Any unauthorized use, copying or disclosure of the contents of this message is strictly prohibited.

________________________________



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From jgraybeal at stanford.edu  Mon May  7 12:22:52 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Mon, 7 May 2018 19:22:52 +0000
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
In-Reply-To: <CF4F8228-ED64-44BA-911D-1CC65A9952CB@stanford.edu>
References: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
 <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>
 <6b675e554c4cc7ddb2187ef7bd14de03@mail.gmail.com>
 <CF4F8228-ED64-44BA-911D-1CC65A9952CB@stanford.edu>
Message-ID: <C3482ED0-7BE3-462B-9BCB-4B712CA2CF57@stanford.edu>

Ahmed, as your API key got shared in a publically visible mailing list, can you please change it? The means to do so is on your profile page.

Thanks!

John


On May 7, 2018, at 10:12 AM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Ahmed,

Apologies, but I have no knowledge of what the ClinCapture system is, so I can?t comment on whether you?ve correctly entered data there.

What I can tell you is how to test whether your BioPortal account is working properly. You should be able to enter a URL for our REST API in a browser and see response data displayed. For example, if you enter the following URL in a browser (enter your API key at the end where I?ve indicated):

http://data.bioontology.org/ontologies/MEDDRA?apikey=your_api_key_goes_here

You should see a JSON response like this:


<Screenshot 2018-05-07 10.10.54.png>
Kind regards,
Jennifer




On May 7, 2018, at 9:44 AM, Ahmed Farhat <ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>> wrote:

Dear Jennifer,
Many thanks for your prompt reply.

Kindly find the below snapshot from my BioPortal account and from ClinCapture EDC System

<image003.png>

<image001.png>

Is the entered data correct?

Thanks

Regards,

Ahmed Farhat
IT Supervisor
<image002.jpg>
2nd  Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th Settlement, New Cairo, Egypt
Phone: +20228117526 | Fax: +20228117527
Mobile: +20 1145161634 | Skype: farhat.clinart
Email: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net> | www.clinart.net<http://www.clinart.net/>

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: 7 May, 2018 6:02 PM
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>
Subject: Re: [bioontology-support] [BioPortal] Feedback from afarhat

Hello Ahmed,

I?m not sure I understand exactly what you?re looking for. You can browse MEDDRA via the BioPortal application here:

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

Or, you can use our REST API to programmatically access the ontology:

http://data.bioontology.org/ontologies/MEDDRA

Use of the REST API requires that you have an API key. Instructions for getting an API key are available on our wiki:

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

The API is documented here:

http://data.bioontology.org/documentation

Kind regards
Jennifer




On May 7, 2018, at 8:20 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: afarhat
Email: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies

Feedback:
Hi,
I need "Bioontology URL" for MEDDRA to use it through ClinCapture EDC System.
We already have an MSSO account
Appreciate your help.
Thanks
Ahmed Farhat

_______________________________________________
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


  [http://clinart.net/wp-content/uploads/2017/05/ISO-9001-blue-TM-e1495018831397.jpg]

The contents of this e-mail may contain confidential information. If you are not the intended recipient of this message and its contents, please inform us by return and delete it from your system.


Any unauthorized use, copying or disclosure of the contents of this message is strictly prohibited.

________________________________



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

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


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From ahmed.farhat at clinart.net  Tue May  8 01:53:44 2018
From: ahmed.farhat at clinart.net (Ahmed Farhat)
Date: Tue, 8 May 2018 10:53:44 +0200
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
In-Reply-To: <CF4F8228-ED64-44BA-911D-1CC65A9952CB@stanford.edu>
References: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
 <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>
 <6b675e554c4cc7ddb2187ef7bd14de03@mail.gmail.com>
 <CF4F8228-ED64-44BA-911D-1CC65A9952CB@stanford.edu>
Message-ID: <a15bb6c070be91c4b0771b9f46a9a0e6@mail.gmail.com>

Hi Jennifer,

Yes, I got the JSON response.





But when I click on download it gives me the below message





We already have a license, where I can add the license details?



Thanks



Regards,



*Ahmed Farhat *
IT Supervisor
[image: Clinart MENA Logo]
2nd  Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th
Settlement, New Cairo, Egypt
Phone: +20228117526 | Fax: +20228117527
Mobile: +20 1145161634 | Skype: farhat.clinart
*Email:* ahmed.farhat at clinart.net | www.clinart.net



*From:* Jennifer Leigh Vendetti <vendetti at stanford.edu>
*Sent:* 7 May, 2018 7:12 PM
*To:* Ahmed Farhat <ahmed.farhat at clinart.net>
*Cc:* NCBO User Support <support at bioontology.org>
*Subject:* Re: [bioontology-support] [BioPortal] Feedback from afarhat



Hello Ahmed,



Apologies, but I have no knowledge of what the ClinCapture system is, so I
can?t comment on whether you?ve correctly entered data there.



What I can tell you is how to test whether your BioPortal account is
working properly. You should be able to enter a URL for our REST API in a
browser and see response data displayed. For example, if you enter the
following URL in a browser (enter your API key at the end where I?ve
indicated):



http://data.bioontology.org/ontologies/MEDDRA?apikey=your_api_key_goes_here



You should see a JSON response like this:





Kind regards,

Jennifer









On May 7, 2018, at 9:44 AM, Ahmed Farhat <ahmed.farhat at clinart.net> wrote:



Dear Jennifer,

Many thanks for your prompt reply.



Kindly find the below snapshot from my BioPortal account and from
ClinCapture EDC System



<image003.png>



<image001.png>



Is the entered data correct?



Thanks



Regards,



*Ahmed Farhat *
IT Supervisor
<image002.jpg>
2nd  Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th
Settlement, New Cairo, Egypt
Phone: +20228117526 | Fax: +20228117527
Mobile: +20 1145161634 | Skype: farhat.clinart
*Email: *ahmed.farhat at clinart.net | www.clinart.net



*From:* Jennifer Leigh Vendetti <vendetti at stanford.edu>
*Sent:* 7 May, 2018 6:02 PM
*To:* NCBO User Support <support at bioontology.org>
*Cc:* ahmed.farhat at clinart.net
*Subject:* Re: [bioontology-support] [BioPortal] Feedback from afarhat



Hello Ahmed,



I?m not sure I understand exactly what you?re looking for. You can browse
MEDDRA via the BioPortal application here:



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



Or, you can use our REST API to programmatically access the ontology:



http://data.bioontology.org/ontologies/MEDDRA



Use of the REST API requires that you have an API key. Instructions for
getting an API key are available on our wiki:



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



The API is documented here:



http://data.bioontology.org/documentation



Kind regards

Jennifer







On May 7, 2018, at 8:20 AM, support at bioontology.org wrote:



Name: afarhat

Email: ahmed.farhat at clinart.net <ahmed.farhat at clinart.net>

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


*Feedback:*

Hi,
I need "Bioontology URL" for MEDDRA to use it through ClinCapture EDC
System.

We already have an MSSO account

Appreciate your help.

Thanks
Ahmed Farhat



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






The contents of this e-mail may contain confidential information. If you
are not the intended recipient of this message and its contents, please
inform us by return and delete it from your system.



Any unauthorized use, copying or disclosure of the contents of this message
is strictly prohibited.
------------------------------

-- 
??

The contents of
this e-mail may contain confidential information. If 
you are not the intended
recipient of this message and its contents, please 
inform us by return and
delete it from your system.





Any unauthorized

use, copying or disclosure of the contents of this message is strictly

prohibited.


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From vendetti at stanford.edu  Tue May  8 10:38:09 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 8 May 2018 17:38:09 +0000
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
In-Reply-To: <a15bb6c070be91c4b0771b9f46a9a0e6@mail.gmail.com>
References: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
 <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>
 <6b675e554c4cc7ddb2187ef7bd14de03@mail.gmail.com>
 <CF4F8228-ED64-44BA-911D-1CC65A9952CB@stanford.edu>
 <a15bb6c070be91c4b0771b9f46a9a0e6@mail.gmail.com>
Message-ID: <31D75CE1-E0AD-49F7-8B6B-F5B3808E7CB3@stanford.edu>

Hello Ahmed,

Roughly twice per year, we import a set of ontologies from the National Library of Medicine's UMLS [1], of which MEDDRA is one. Due to licensing restrictions imposed by the NLM, end users are allowed browse the contents of these ontologies, but we are prohibited from making the ontology source files available as downloads directly from the BioPortal application, or from our REST API.

For example, REST API calls to retrieve class data will return results:

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

? but the download link returns a 403 forbidden response, as you mention below.

If you have a current UMLS license [2], please contact us off-list (vendetti at stanford.edu<http://stanford.edu>) for options with regard to retrieving a copy of the ontology source file.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/
[2] https://www.nlm.nih.gov/databases/umls.html



On May 8, 2018, at 1:53 AM, Ahmed Farhat <ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>> wrote:

Hi Jennifer,
Yes, I got the JSON response.

<image001.png>

But when I click on download it gives me the below message

<image002.png>

We already have a license, where I can add the license details?

Thanks

Regards,

Ahmed Farhat
IT Supervisor
<image003.jpg>
2nd  Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th Settlement, New Cairo, Egypt
Phone: +20228117526 | Fax: +20228117527
Mobile: +20 1145161634 | Skype: farhat.clinart
Email: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net> | www.clinart.net<http://www.clinart.net/>

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: 7 May, 2018 7:12 PM
To: Ahmed Farhat <ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>>
Cc: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from afarhat

Hello Ahmed,

Apologies, but I have no knowledge of what the ClinCapture system is, so I can?t comment on whether you?ve correctly entered data there.

What I can tell you is how to test whether your BioPortal account is working properly. You should be able to enter a URL for our REST API in a browser and see response data displayed. For example, if you enter the following URL in a browser (enter your API key at the end where I?ve indicated):

http://data.bioontology.org/ontologies/MEDDRA?apikey=your_api_key_goes_here

You should see a JSON response like this:


<image004.png>
Kind regards,
Jennifer





On May 7, 2018, at 9:44 AM, Ahmed Farhat <ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>> wrote:

Dear Jennifer,
Many thanks for your prompt reply.

Kindly find the below snapshot from my BioPortal account and from ClinCapture EDC System

<image003.png>

<image001.png>

Is the entered data correct?

Thanks

Regards,

Ahmed Farhat
IT Supervisor
<image002.jpg>
2nd  Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th Settlement, New Cairo, Egypt
Phone: +20228117526 | Fax: +20228117527
Mobile: +20 1145161634 | Skype: farhat.clinart
Email: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net> | www.clinart.net<http://www.clinart.net/>

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: 7 May, 2018 6:02 PM
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>
Subject: Re: [bioontology-support] [BioPortal] Feedback from afarhat

Hello Ahmed,

I?m not sure I understand exactly what you?re looking for. You can browse MEDDRA via the BioPortal application here:

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

Or, you can use our REST API to programmatically access the ontology:

http://data.bioontology.org/ontologies/MEDDRA

Use of the REST API requires that you have an API key. Instructions for getting an API key are available on our wiki:

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

The API is documented here:

http://data.bioontology.org/documentation

Kind regards
Jennifer



On May 7, 2018, at 8:20 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: afarhat
Email: ahmed.farhat at clinart.net<mailto:ahmed.farhat at clinart.net>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies

Feedback:
Hi,
I need "Bioontology URL" for MEDDRA to use it through ClinCapture EDC System.
We already have an MSSO account
Appreciate your help.
Thanks
Ahmed Farhat

_______________________________________________
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


  [http://clinart.net/wp-content/uploads/2017/05/ISO-9001-blue-TM-e1495018831397.jpg]
The contents of this e-mail may contain confidential information. If you are not the intended recipient of this message and its contents, please inform us by return and delete it from your system.

Any unauthorized use, copying or disclosure of the contents of this message is strictly prohibited.
________________________________





  [http://clinart.net/wp-content/uploads/2017/05/ISO-9001-blue-TM-e1495018831397.jpg]

The contents of this e-mail may contain confidential information. If you are not the intended recipient of this message and its contents, please inform us by return and delete it from your system.


Any unauthorized use, copying or disclosure of the contents of this message is strictly prohibited.

________________________________



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From Sina.Madani at vumc.org  Tue May  8 12:40:07 2018
From: Sina.Madani at vumc.org (Madani, Sina)
Date: Tue, 8 May 2018 19:40:07 +0000
Subject: [bioontology-support] Visualization limit
Message-ID: <1EC55D15-42E8-4774-A61B-BD659D3AD2F3@contoso.com>


Hi,

It seems there is a limitation on the number of concepts (alphabetically) shown in a given branch.
I have 4 concepts in my ontology that start with ?Abdomen-? but only one of them is being listed when I start browsing the branch. I can see all 4 only if I start typing in the ?Jump to? box.
Is the number of concepts shown in a given branch configurable?

Thanks!
Sina


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From david at dbooth.org  Tue May  8 14:49:04 2018
From: david at dbooth.org (David Booth)
Date: Tue, 8 May 2018 17:49:04 -0400
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
In-Reply-To: <31D75CE1-E0AD-49F7-8B6B-F5B3808E7CB3@stanford.edu>
References: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
 <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>
 <6b675e554c4cc7ddb2187ef7bd14de03@mail.gmail.com>
 <CF4F8228-ED64-44BA-911D-1CC65A9952CB@stanford.edu>
 <a15bb6c070be91c4b0771b9f46a9a0e6@mail.gmail.com>
 <31D75CE1-E0AD-49F7-8B6B-F5B3808E7CB3@stanford.edu>
Message-ID: <c25e8a6f-ac4b-aa1d-6cd8-58568d9970f3@dbooth.org>

On 05/08/2018 01:38 PM, Jennifer Leigh Vendetti wrote:
> Hello Ahmed,
> 
> Roughly twice per year, we import a set of ontologies from the National 
> Library of Medicine's UMLS [1], of which MEDDRA is one. Due to licensing 
> restrictions imposed by the NLM, 

Can you clarify please?   I thought the licensing restrictions were 
imposed *on* the NLM, by the owners of the various source ontologies, 
rather than being imposed *by* the NLM.
https://www.meddra.org/subscription/special-licences

Thanks,
David Booth

end users are allowed browse the
> contents of these ontologies, but we are prohibited from making the 
> ontology source files available as downloads directly from the BioPortal 
> application, or from our REST API.
> 
> For example, REST API calls to retrieve class data will return results:
> 
> http://data.bioontology.org/ontologies/MEDDRA/classes
> 
> ? but the download link returns a 403 forbidden response, as you mention 
> below.
> 
> If you have a current UMLS license [2], please contact us off-list 
> (vendetti at stanford.edu <http://stanford.edu>) for options with regard 
> to retrieving a copy of the ontology source file.
> 
> Kind regards,
> Jennifer
> 
> [1] https://www.nlm.nih.gov/research/umls/
> [2] https://www.nlm.nih.gov/databases/umls.html
> 
> 
> 
>> On May 8, 2018, at 1:53 AM, Ahmed Farhat <ahmed.farhat at clinart.net 
>> <mailto:ahmed.farhat at clinart.net>> wrote:
>>
>> Hi Jennifer,
>> Yes, I got the JSON response.
>>
>> <image001.png>
>>
>> But when I click on download it gives me the below message
>>
>> <image002.png>
>>
>> We already have a license, where I can add the license details?
>>
>> Thanks
>>
>> Regards,
>>
>> *Ahmed?Farhat *
>> IT Supervisor
>> <image003.jpg>
>> 2^nd ^Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th 
>> Settlement, New Cairo, Egypt
>> Phone:?+20228117526?|?Fax:?+20228117527
>> Mobile:?+20 1145161634?|?Skype:?farhat.clinart
>> *Email:***ahmed.farhat at clinart.net 
>> <mailto:ahmed.farhat at clinart.net>?|**www.clinart.net 
>> <http://www.clinart.net/>
>>
>> *From:*Jennifer Leigh Vendetti <vendetti at stanford.edu 
>> <mailto:vendetti at stanford.edu>>
>> *Sent:*7 May, 2018 7:12 PM
>> *To:*Ahmed Farhat <ahmed.farhat at clinart.net 
>> <mailto:ahmed.farhat at clinart.net>>
>> *Cc:*NCBO User Support <support at bioontology.org 
>> <mailto:support at bioontology.org>>
>> *Subject:*Re: [bioontology-support] [BioPortal] Feedback from afarhat
>>
>> Hello Ahmed,
>>
>> Apologies, but I have no knowledge of what the ClinCapture system is, 
>> so I can?t comment on whether you?ve correctly entered data there.
>>
>> What I can tell you is how to test whether your BioPortal account is 
>> working properly. You should be able to enter a URL for our REST API 
>> in a browser and see response data displayed. For example, if you 
>> enter the following URL in a browser (enter your API key at the end 
>> where I?ve indicated):
>>
>> http://data.bioontology.org/ontologies/MEDDRA?apikey=your_api_key_goes_here
>>
>> You should see a JSON response like this:
>>
>> <image004.png>
>> Kind regards,
>> Jennifer
>>
>>
>>
>>> On May 7, 2018, at 9:44 AM, Ahmed Farhat <ahmed.farhat at clinart.net 
>>> <mailto:ahmed.farhat at clinart.net>> wrote:
>>>
>>> Dear Jennifer,
>>> Many thanks for your prompt reply.
>>>
>>> Kindly find the below snapshot from my BioPortal account and from 
>>> ClinCapture EDC System
>>>
>>> <image003.png>
>>>
>>> <image001.png>
>>>
>>> Is the entered datacorrect?
>>>
>>> Thanks
>>>
>>> Regards,
>>>
>>> *Ahmed?Farhat *
>>> IT Supervisor
>>> <image002.jpg>
>>> 2^nd ^Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th 
>>> Settlement, New Cairo, Egypt
>>> Phone:?+20228117526?|?Fax:?+20228117527
>>> Mobile:?+20 1145161634?|?Skype:?farhat.clinart
>>> *Email:*ahmed.farhat at clinart.net 
>>> <mailto:ahmed.farhat at clinart.net>?|**www.clinart.net 
>>> <http://www.clinart.net/>
>>>
>>> *From:*Jennifer Leigh Vendetti <vendetti at stanford.edu 
>>> <mailto:vendetti at stanford.edu>>
>>> *Sent:*7 May, 2018 6:02 PM
>>> *To:*NCBO User Support <support at bioontology.org 
>>> <mailto:support at bioontology.org>>
>>> *Cc:*ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>
>>> *Subject:*Re: [bioontology-support] [BioPortal] Feedback from afarhat
>>>
>>> Hello Ahmed,
>>>
>>> I?m not sure I understand exactly what you?re looking for. You can 
>>> browse MEDDRA via the BioPortal application here:
>>>
>>> http://bioportal.bioontology.org/ontologies/MEDDRA
>>>
>>> Or, you can use our REST API to programmatically access the ontology:
>>>
>>> http://data.bioontology.org/ontologies/MEDDRA
>>>
>>> Use of the REST API requires that you have an API key. Instructions 
>>> for getting an API key are available on our wiki:
>>>
>>> https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key
>>>
>>> The API is documented here:
>>>
>>> http://data.bioontology.org/documentation
>>>
>>> Kind regards
>>> Jennifer
>>>
>>>
>>>> On May 7, 2018, at 8:20 AM,support at bioontology.org 
>>>> <mailto:support at bioontology.org>wrote:
>>>>
>>>> Name: afarhat
>>>> Email: ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>
>>>> Location: https%3A%2F%2Fbioportal.bioontology.org 
>>>> <http://2fbioportal.bioontology.org/>%2Fontologies
>>>>
>>>> *Feedback:*
>>>> Hi,
>>>> I need "Bioontology URL" for MEDDRA to use it through ClinCapture 
>>>> EDC System.
>>>> We already have an MSSO account
>>>> Appreciate your help.
>>>> Thanks
>>>> Ahmed Farhat
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>>> The contents of this e-mail may contain confidential information. If 
>>> you are not the intended recipient of this message and its contents, 
>>> please inform us by return and delete it from your system.
>>>
>>> Any unauthorized use, copying or disclosure of the contents of this 
>>> message is strictly prohibited.
>>> ------------------------------------------------------------------------
>>>
>>>
>>
>> The contents of this e-mail may contain confidential information. If 
>> you are not the intended recipient of this message and its contents, 
>> please inform us by return and delete it from your system.
>>
>>
>> Any unauthorized use, copying or disclosure of the contents of this 
>> message is strictly prohibited.
>>
>> ------------------------------------------------------------------------
>>
>>
>>
> 
> 
> 
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 

From vendetti at stanford.edu  Tue May  8 15:01:56 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 8 May 2018 22:01:56 +0000
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
In-Reply-To: <c25e8a6f-ac4b-aa1d-6cd8-58568d9970f3@dbooth.org>
References: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
 <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>
 <6b675e554c4cc7ddb2187ef7bd14de03@mail.gmail.com>
 <CF4F8228-ED64-44BA-911D-1CC65A9952CB@stanford.edu>
 <a15bb6c070be91c4b0771b9f46a9a0e6@mail.gmail.com>
 <31D75CE1-E0AD-49F7-8B6B-F5B3808E7CB3@stanford.edu>
 <c25e8a6f-ac4b-aa1d-6cd8-58568d9970f3@dbooth.org>
Message-ID: <C2A7D419-0A3E-4F80-A657-7FD82A094B9B@stanford.edu>

Sorry that I didn?t word that very well. I?m a developer working on the BioPortal software and am not an expert on the particulars of where the license text originates from. We?ve been importing UMLS releases into BioPortal for roughly five years, which is longer that I?ve been in the group. The download restrictions were in place before I joined.

I read the license text on the page you link to, and it appears that we are in compliance:

"Special licences allow MedDRA?s use without charge in a non-downloadable format within agency electronic (software) tools designed to allow a company to meet their regulatory (adverse reaction) reporting requirements.?

In other words, you can browse MedDRA?s content free of charge via BioPortal or the REST API, but we restrict downloads.

If anyone else subscribed to the list has further insight, feel free to comment.

Jennifer
  

> On May 8, 2018, at 2:49 PM, David Booth <david at dbooth.org> wrote:
> 
> On 05/08/2018 01:38 PM, Jennifer Leigh Vendetti wrote:
>> Hello Ahmed,
>> Roughly twice per year, we import a set of ontologies from the National Library of Medicine's UMLS [1], of which MEDDRA is one. Due to licensing restrictions imposed by the NLM, 
> 
> Can you clarify please?   I thought the licensing restrictions were imposed *on* the NLM, by the owners of the various source ontologies, rather than being imposed *by* the NLM.
> https://www.meddra.org/subscription/special-licences
> 
> Thanks,
> David Booth
> 
> end users are allowed browse the
>> contents of these ontologies, but we are prohibited from making the ontology source files available as downloads directly from the BioPortal application, or from our REST API.
>> For example, REST API calls to retrieve class data will return results:
>> http://data.bioontology.org/ontologies/MEDDRA/classes
>> ? but the download link returns a 403 forbidden response, as you mention below.
>> If you have a current UMLS license [2], please contact us off-list (vendetti at stanford.edu <http://stanford.edu>) for options with regard to retrieving a copy of the ontology source file.
>> Kind regards,
>> Jennifer
>> [1] https://www.nlm.nih.gov/research/umls/
>> [2] https://www.nlm.nih.gov/databases/umls.html
>>> On May 8, 2018, at 1:53 AM, Ahmed Farhat <ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>> wrote:
>>> 
>>> Hi Jennifer,
>>> Yes, I got the JSON response.
>>> 
>>> <image001.png>
>>> 
>>> But when I click on download it gives me the below message
>>> 
>>> <image002.png>
>>> 
>>> We already have a license, where I can add the license details?
>>> 
>>> Thanks
>>> 
>>> Regards,
>>> 
>>> *Ahmed Farhat *
>>> IT Supervisor
>>> <image003.jpg>
>>> 2^nd ^Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th Settlement, New Cairo, Egypt
>>> Phone: +20228117526 | Fax: +20228117527
>>> Mobile: +20 1145161634 | Skype: farhat.clinart
>>> *Email:***ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net> |**www.clinart.net <http://www.clinart.net/>
>>> 
>>> *From:*Jennifer Leigh Vendetti <vendetti at stanford.edu <mailto:vendetti at stanford.edu>>
>>> *Sent:*7 May, 2018 7:12 PM
>>> *To:*Ahmed Farhat <ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>>
>>> *Cc:*NCBO User Support <support at bioontology.org <mailto:support at bioontology.org>>
>>> *Subject:*Re: [bioontology-support] [BioPortal] Feedback from afarhat
>>> 
>>> Hello Ahmed,
>>> 
>>> Apologies, but I have no knowledge of what the ClinCapture system is, so I can?t comment on whether you?ve correctly entered data there.
>>> 
>>> What I can tell you is how to test whether your BioPortal account is working properly. You should be able to enter a URL for our REST API in a browser and see response data displayed. For example, if you enter the following URL in a browser (enter your API key at the end where I?ve indicated):
>>> 
>>> http://data.bioontology.org/ontologies/MEDDRA?apikey=your_api_key_goes_here
>>> 
>>> You should see a JSON response like this:
>>> 
>>> <image004.png>
>>> Kind regards,
>>> Jennifer
>>> 
>>> 
>>> 
>>>> On May 7, 2018, at 9:44 AM, Ahmed Farhat <ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>> wrote:
>>>> 
>>>> Dear Jennifer,
>>>> Many thanks for your prompt reply.
>>>> 
>>>> Kindly find the below snapshot from my BioPortal account and from ClinCapture EDC System
>>>> 
>>>> <image003.png>
>>>> 
>>>> <image001.png>
>>>> 
>>>> Is the entered datacorrect?
>>>> 
>>>> Thanks
>>>> 
>>>> Regards,
>>>> 
>>>> *Ahmed Farhat *
>>>> IT Supervisor
>>>> <image002.jpg>
>>>> 2^nd ^Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th Settlement, New Cairo, Egypt
>>>> Phone: +20228117526 | Fax: +20228117527
>>>> Mobile: +20 1145161634 | Skype: farhat.clinart
>>>> *Email:*ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net> |**www.clinart.net <http://www.clinart.net/>
>>>> 
>>>> *From:*Jennifer Leigh Vendetti <vendetti at stanford.edu <mailto:vendetti at stanford.edu>>
>>>> *Sent:*7 May, 2018 6:02 PM
>>>> *To:*NCBO User Support <support at bioontology.org <mailto:support at bioontology.org>>
>>>> *Cc:*ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>
>>>> *Subject:*Re: [bioontology-support] [BioPortal] Feedback from afarhat
>>>> 
>>>> Hello Ahmed,
>>>> 
>>>> I?m not sure I understand exactly what you?re looking for. You can browse MEDDRA via the BioPortal application here:
>>>> 
>>>> http://bioportal.bioontology.org/ontologies/MEDDRA
>>>> 
>>>> Or, you can use our REST API to programmatically access the ontology:
>>>> 
>>>> http://data.bioontology.org/ontologies/MEDDRA
>>>> 
>>>> Use of the REST API requires that you have an API key. Instructions for getting an API key are available on our wiki:
>>>> 
>>>> https://www.bioontology.org/wiki/index.php/BioPortal_Help#Getting_an_API_key
>>>> 
>>>> The API is documented here:
>>>> 
>>>> http://data.bioontology.org/documentation
>>>> 
>>>> Kind regards
>>>> Jennifer
>>>> 
>>>> 
>>>>> On May 7, 2018, at 8:20 AM,support at bioontology.org <mailto:support at bioontology.org>wrote:
>>>>> 
>>>>> Name: afarhat
>>>>> Email: ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>
>>>>> Location: https%3A%2F%2Fbioportal.bioontology.org <http://2fbioportal.bioontology.org/>%2Fontologies
>>>>> 
>>>>> *Feedback:*
>>>>> Hi,
>>>>> I need "Bioontology URL" for MEDDRA to use it through ClinCapture EDC System.
>>>>> We already have an MSSO account
>>>>> Appreciate your help.
>>>>> Thanks
>>>>> Ahmed Farhat
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>>> 
>>>> 
>>>> The contents of this e-mail may contain confidential information. If you are not the intended recipient of this message and its contents, please inform us by return and delete it from your system.
>>>> 
>>>> Any unauthorized use, copying or disclosure of the contents of this message is strictly prohibited.
>>>> ------------------------------------------------------------------------
>>>> 
>>>> 
>>> 
>>> The contents of this e-mail may contain confidential information. If you are not the intended recipient of this message and its contents, please inform us by return and delete it from your system.
>>> 
>>> 
>>> Any unauthorized use, copying or disclosure of the contents of this message is strictly prohibited.
>>> 
>>> ------------------------------------------------------------------------
>>> 
>>> 
>>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support


From jgraybeal at stanford.edu  Tue May  8 16:31:49 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Tue, 8 May 2018 23:31:49 +0000
Subject: [bioontology-support] [BioPortal] Feedback from afarhat
In-Reply-To: <C2A7D419-0A3E-4F80-A657-7FD82A094B9B@stanford.edu>
References: <5af06ed17d64a_4f233fe5e4d956ac48981@ncbo-prd-app-09.stanford.edu.mail>
 <2ADD05A9-D084-4720-88F8-2E329C0C4CA5@stanford.edu>
 <6b675e554c4cc7ddb2187ef7bd14de03@mail.gmail.com>
 <CF4F8228-ED64-44BA-911D-1CC65A9952CB@stanford.edu>
 <a15bb6c070be91c4b0771b9f46a9a0e6@mail.gmail.com>
 <31D75CE1-E0AD-49F7-8B6B-F5B3808E7CB3@stanford.edu>
 <c25e8a6f-ac4b-aa1d-6cd8-58568d9970f3@dbooth.org>
 <C2A7D419-0A3E-4F80-A657-7FD82A094B9B@stanford.edu>
Message-ID: <8DFB46F4-F776-41CF-8A72-87800945732F@stanford.edu>

Hi David and Jennifer,

I would like to suggest we take the rather arcane discussion of licenses off the main BioPortal support list.

If someone on the list wants to present their argument about why our treatment of the licenses is unnecessarily strict, I welcome your input. (Especially useful if your email starts "I *am* a lawyer" :->).

If you have a concern that we are not strict enough, please contact me directly, so we can a discussion going among the principals.

Thanks,

John

On May 8, 2018, at 3:01 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Sorry that I didn?t word that very well. I?m a developer working on the BioPortal software and am not an expert on the particulars of where the license text originates from. We?ve been importing UMLS releases into BioPortal for roughly five years, which is longer that I?ve been in the group. The download restrictions were in place before I joined.

I read the license text on the page you link to, and it appears that we are in compliance:

"Special licences allow MedDRA?s use without charge in a non-downloadable format within agency electronic (software) tools designed to allow a company to meet their regulatory (adverse reaction) reporting requirements.?

In other words, you can browse MedDRA?s content free of charge via BioPortal or the REST API, but we restrict downloads.

If anyone else subscribed to the list has further insight, feel free to comment.

Jennifer


On May 8, 2018, at 2:49 PM, David Booth <david at dbooth.org<mailto:david at dbooth.org>> wrote:

On 05/08/2018 01:38 PM, Jennifer Leigh Vendetti wrote:
Hello Ahmed,
Roughly twice per year, we import a set of ontologies from the National Library of Medicine's UMLS [1], of which MEDDRA is one. Due to licensing restrictions imposed by the NLM,

Can you clarify please?   I thought the licensing restrictions were imposed *on* the NLM, by the owners of the various source ontologies, rather than being imposed *by* the NLM.
https://www.meddra.org/subscription/special-licences

Thanks,
David Booth

end users are allowed browse the
contents of these ontologies, but we are prohibited from making the ontology source files available as downloads directly from the BioPortal application, or from our REST API.
For example, REST API calls to retrieve class data will return results:
http://data.bioontology.org/ontologies/MEDDRA/classes
? but the download link returns a 403 forbidden response, as you mention below.
If you have a current UMLS license [2], please contact us off-list (vendetti at stanford.edu <http://stanford.edu>) for options with regard to retrieving a copy of the ontology source file.
Kind regards,
Jennifer
[1] https://www.nlm.nih.gov/research/umls/
[2] https://www.nlm.nih.gov/databases/umls.html
On May 8, 2018, at 1:53 AM, Ahmed Farhat <ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>> wrote:

Hi Jennifer,
Yes, I got the JSON response.

<image001.png>

But when I click on download it gives me the below message

<image002.png>

We already have a license, where I can add the license details?

Thanks

Regards,

*Ahmed Farhat *
IT Supervisor
<image003.jpg>
2^nd ^Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th Settlement, New Cairo, Egypt
Phone: +20228117526 | Fax: +20228117527
Mobile: +20 1145161634 | Skype: farhat.clinart
*Email:***ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net> |**www.clinart.net <http://www.clinart.net/>

*From:*Jennifer Leigh Vendetti <vendetti at stanford.edu <mailto:vendetti at stanford.edu>>
*Sent:*7 May, 2018 7:12 PM
*To:*Ahmed Farhat <ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>>
*Cc:*NCBO User Support <support at bioontology.org <mailto:support at bioontology.org>>
*Subject:*Re: [bioontology-support] [BioPortal] Feedback from afarhat

Hello Ahmed,

Apologies, but I have no knowledge of what the ClinCapture system is, so I can?t comment on whether you?ve correctly entered data there.

What I can tell you is how to test whether your BioPortal account is working properly. You should be able to enter a URL for our REST API in a browser and see response data displayed. For example, if you enter the following URL in a browser (enter your API key at the end where I?ve indicated):

http://data.bioontology.org/ontologies/MEDDRA?apikey=your_api_key_goes_here

You should see a JSON response like this:

<image004.png>
Kind regards,
Jennifer



On May 7, 2018, at 9:44 AM, Ahmed Farhat <ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>> wrote:

Dear Jennifer,
Many thanks for your prompt reply.

Kindly find the below snapshot from my BioPortal account and from ClinCapture EDC System

<image003.png>

<image001.png>

Is the entered datacorrect?

Thanks

Regards,

*Ahmed Farhat *
IT Supervisor
<image002.jpg>
2^nd ^Floor, 106 Town Center, 1st Commercial sector (Banks Zone), 5th Settlement, New Cairo, Egypt
Phone: +20228117526 | Fax: +20228117527
Mobile: +20 1145161634 | Skype: farhat.clinart
*Email:*ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net> |**www.clinart.net <http://www.clinart.net/>

*From:*Jennifer Leigh Vendetti <vendetti at stanford.edu <mailto:vendetti at stanford.edu>>
*Sent:*7 May, 2018 6:02 PM
*To:*NCBO User Support <support at bioontology.org <mailto:support at bioontology.org>>
*Cc:*ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>
*Subject:*Re: [bioontology-support] [BioPortal] Feedback from afarhat

Hello Ahmed,

I?m not sure I understand exactly what you?re looking for. You can browse MEDDRA via the BioPortal application here:

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

Or, you can use our REST API to programmatically access the ontology:

http://data.bioontology.org/ontologies/MEDDRA

Use of the REST API requires that you have an API key. Instructions for getting an API key are available on our wiki:

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

The API is documented here:

http://data.bioontology.org/documentation

Kind regards
Jennifer


On May 7, 2018, at 8:20 AM,support at bioontology.org <mailto:support at bioontology.org>wrote:

Name: afarhat
Email: ahmed.farhat at clinart.net <mailto:ahmed.farhat at clinart.net>
Location: https%3A%2F%2Fbioportal.bioontology.org <http://2fbioportal.bioontology.org/>%2Fontologies

*Feedback:*
Hi,
I need "Bioontology URL" for MEDDRA to use it through ClinCapture EDC System.
We already have an MSSO account
Appreciate your help.
Thanks
Ahmed Farhat

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

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


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From support at bioontology.org  Wed May  9 02:01:43 2018
From: support at bioontology.org (support at bioontology.org)
Date: Wed, 09 May 2018 02:01:43 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Martijn Kersloot
Message-ID: <5af2b8f7b6115_5c73fbeb4c06e64918b8@ncbo-prd-app-08.stanford.edu.mail>

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From amassengale at rsna.org  Thu May 10 07:01:31 2018
From: amassengale at rsna.org (Andrew Massengale)
Date: Thu, 10 May 2018 14:01:31 +0000
Subject: [bioontology-support] Bio Portal API route is not working
Message-ID: <FD208B34-B638-4F08-8D31-451A15E7193E@rsna.org>

Hello,

The following API route is not working for us anymore. It looks like the problem is the HTTPS endpoint is not working. Did the HTTPS server get shut down? Or is it supposed to be up, and is not working?

https://data.bioontology.org/search?ontology=RADLEX&apikey=58bb5724-cad7-45ed-a949-5570fa89a01e&q=rectum&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000

vs

http://data.bioontology.org/search?ontology=RADLEX&apikey=58bb5724-cad7-45ed-a949-5570fa89a01e&q=rectum&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000

Thanks,

Andrew M

Andrew Massengale
Senior Software Engineer
IT: Development
amassengale at rsna.org<mailto:amassengale at rsna.org>
CEL: 815-614-8296
TEL: 630-481-1012
FAX: 630-571-7837
Radiological Society of North America
820 Jorie Blvd, Oak Brook, IL 60523
TEL 1-630-571-2670
FAX 1-630-571-7837
RSNA.org<http://www.rsna.org>

Facebook<http://www.facebook.com/RSNAfans>
Twitter<http://twitter.com/RSNA>
RSNA 2018 Annual Meeting<http://www.rsna.org/Annual_Meeting.aspx>
November 25th ? 30th
McCormick Place, Chicago
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From jgraybeal at stanford.edu  Thu May 10 07:26:46 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 10 May 2018 14:26:46 +0000
Subject: [bioontology-support] Bio Portal API route is not working
In-Reply-To: <FD208B34-B638-4F08-8D31-451A15E7193E@rsna.org>
References: <FD208B34-B638-4F08-8D31-451A15E7193E@rsna.org>
Message-ID: <6B7B691A-E117-4EBE-B660-714D3142FCDB@stanford.edu>

Thanks Andrew. We had some significant network hardware issues last night, and it appears some https forwarding capability was lost. We will have a look as soon as we can.

John

On May 10, 2018, at 7:01 AM, Andrew Massengale <amassengale at rsna.org<mailto:amassengale at rsna.org>> wrote:

Hello,

The following API route is not working for us anymore. It looks like the problem is the HTTPS endpoint is not working. Did the HTTPS server get shut down? Or is it supposed to be up, and is not working?

https://data.bioontology.org/search?ontology=RADLEX&q=rectum&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000<https://data.bioontology.org/search?ontology=RADLEX&q=rectum&format=json&subtree_root_id=http://www.radlex.org/RID/#RID3&roots_only=true&page=1&pagesize=1000>

vs

http://data.bioontology.org/search?ontology=RADLEX&q=rectum&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000<http://data.bioontology.org/search?ontology=RADLEX&apikey=58bb5724-cad7-45ed-a949-5570fa89a01e&q=rectum&format=json&subtree_root_id=http://www.radlex.org/RID/#RID3&roots_only=true&page=1&pagesize=1000>

Thanks,

Andrew M

Andrew Massengale
Senior Software Engineer
IT: Development
amassengale at rsna.org<mailto:amassengale at rsna.org>
CEL: 815-614-8296
TEL: 630-481-1012
FAX: 630-571-7837
Radiological Society of North America
820 Jorie Blvd, Oak Brook, IL 60523
TEL 1-630-571-2670
FAX 1-630-571-7837
RSNA.org<http://www.rsna.org/>

Facebook<http://www.facebook.com/RSNAfans>
Twitter<http://twitter.com/RSNA>
RSNA 2018 Annual Meeting<http://www.rsna.org/Annual_Meeting.aspx>
November 25th ? 30th
McCormick Place, Chicago _______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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


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From jgraybeal at stanford.edu  Thu May 10 09:22:17 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 10 May 2018 16:22:17 +0000
Subject: [bioontology-support] Bio Portal API route is not working
In-Reply-To: <6B7B691A-E117-4EBE-B660-714D3142FCDB@stanford.edu>
References: <FD208B34-B638-4F08-8D31-451A15E7193E@rsna.org>
 <6B7B691A-E117-4EBE-B660-714D3142FCDB@stanford.edu>
Message-ID: <213CD03E-F541-406C-9C87-A0F0841CC9AD@stanford.edu>

Andrew,

This issue has now been addressed. Thanks for bringing it to our attention.

John

On May 10, 2018, at 7:26 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Thanks Andrew. We had some significant network hardware issues last night, and it appears some https forwarding capability was lost. We will have a look as soon as we can.

John

On May 10, 2018, at 7:01 AM, Andrew Massengale <amassengale at rsna.org<mailto:amassengale at rsna.org>> wrote:

Hello,

The following API route is not working for us anymore. It looks like the problem is the HTTPS endpoint is not working. Did the HTTPS server get shut down? Or is it supposed to be up, and is not working?

https://data.bioontology.org/search?ontology=RADLEX&q=rectum&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000<https://data.bioontology.org/search?ontology=RADLEX&q=rectum&format=json&subtree_root_id=http://www.radlex.org/RID/#RID3&roots_only=true&page=1&pagesize=1000>

vs

http://data.bioontology.org/search?ontology=RADLEX&q=rectum&format=json&subtree_root_id=http:%2F%2Fwww.radlex.org%2FRID%2F%23RID3&roots_only=true&page=1&pagesize=1000<http://data.bioontology.org/search?ontology=RADLEX&apikey=58bb5724-cad7-45ed-a949-5570fa89a01e&q=rectum&format=json&subtree_root_id=http://www.radlex.org/RID/#RID3&roots_only=true&page=1&pagesize=1000>

Thanks,

Andrew M

Andrew Massengale
Senior Software Engineer
IT: Development
amassengale at rsna.org<mailto:amassengale at rsna.org>
CEL: 815-614-8296
TEL: 630-481-1012
FAX: 630-571-7837
Radiological Society of North America
820 Jorie Blvd, Oak Brook, IL 60523
TEL 1-630-571-2670
FAX 1-630-571-7837
RSNA.org<http://www.rsna.org/>

Facebook<http://www.facebook.com/RSNAfans>
Twitter<http://twitter.com/RSNA>
RSNA 2018 Annual Meeting<http://www.rsna.org/Annual_Meeting.aspx>
November 25th ? 30th
McCormick Place, Chicago _______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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

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


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From pshilling at ucsd.edu  Thu May 10 08:30:24 2018
From: pshilling at ucsd.edu (Shilling, Paul)
Date: Thu, 10 May 2018 15:30:24 +0000
Subject: [bioontology-support] RX norm not working
Message-ID: <66F1079D-DE29-48FB-ABF5-8408690374F8@ucsd.edu>

Hello,


We have been using the bioportal to connect to your  Rxnorm list of medications to populate our medication fields when users at our 21 sites enter a med name.

Users are reporting this AM -  ?no results returned?

Is your server down?

Thanks, Paul


Paul D. Shilling, PhD
9500 Gilman Drive
Department of Psychiatry 0405
La Jolla, CA  92093
Tel: 858-822-2474

From support at bioontology.org  Thu May 10 08:38:17 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 10 May 2018 08:38:17 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Paul Shilling
Message-ID: <5af46769b0cf2_e2c3fd815a88ef0569fc@ncbo-prd-app-08.stanford.edu.mail>

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From jgraybeal at stanford.edu  Thu May 10 09:31:28 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 10 May 2018 16:31:28 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Paul Shilling
In-Reply-To: <5af46769b0cf2_e2c3fd815a88ef0569fc@ncbo-prd-app-08.stanford.edu.mail>
References: <5af46769b0cf2_e2c3fd815a88ef0569fc@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <A5F6DFFC-DA3B-42BB-B014-796A9EFBEAE9@stanford.edu>

Hello Paul,

Thanks for your question.  The https service was down earlier as the side effect of some network outages last night. It is back up now.

If you are still seeing difficulties, please send us an example query that we can use to troubleshoot on our end. Thanks!

John

On May 10, 2018, at 8:38 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Paul Shilling

Email: pshilling at ucsd.edu<mailto:pshilling at ucsd.edu>

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

Feedback:

We have been using the bioportal to connect to your Rxnorm list of medications to populate our medication fields when users at our 21 sites enter a med name.

Users are reporting this AM - ?no results returned? when first three letters of med name is entered.

Is your server down?

Thanks, Paul

Paul D. Shilling, PhD
9500 Gilman Drive
Department of Psychiatry 0405
La Jolla, CA 92093
Tel: 858-822-2474

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

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


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From jgraybeal at stanford.edu  Thu May 10 09:37:49 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Thu, 10 May 2018 16:37:49 +0000
Subject: [bioontology-support] Sparql endpoint is not CORS
In-Reply-To: <CALsrFgMA=HaGGujNC+wSU6S7YZkM0ffQU=sG=a7R_ZBMfgC-Fg@mail.gmail.com>
References: <CALsrFgMA=HaGGujNC+wSU6S7YZkM0ffQU=sG=a7R_ZBMfgC-Fg@mail.gmail.com>
Message-ID: <25A64ABB-7FD6-4006-A786-C994241BB683@stanford.edu>

Hello Karima,

It looks like we haven't addressed your query, apologies. I am not sure exactly what you are asking though.

The Beta SPARQL endpoint is not formally maintained (and its data is somewhat old, alas). But I have checked and it is openly accessible from the test front end. Are you saying it is not accessible via API?

And am wondering what you mean by "open it for another domain (CORS)". Is that referring to the ESIP Community Ontology Repository?  Perhaps you can describe your use case in a little more detail?

John


On Apr 26, 2018, at 9:18 AM, Karima Rafes <karima.rafes at gmail.com<mailto:karima.rafes at gmail.com>> wrote:

Hello

Your SPARQL endpoint doesn't allow to request data from another domain.
Is it possible to open it for another domain (CORS) ?
And if possible with a protocol https, it would be perfect.

I works on a new SPARQL editor between several endpoints about biology.

Thanks
Best regards
Karima Rafes


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

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


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From karima.rafes at gmail.com  Thu May 10 10:22:03 2018
From: karima.rafes at gmail.com (Karima Rafes)
Date: Thu, 10 May 2018 19:22:03 +0200
Subject: [bioontology-support] Sparql endpoint is not CORS
In-Reply-To: <25A64ABB-7FD6-4006-A786-C994241BB683@stanford.edu>
References: <CALsrFgMA=HaGGujNC+wSU6S7YZkM0ffQU=sG=a7R_ZBMfgC-Fg@mail.gmail.com>
 <25A64ABB-7FD6-4006-A786-C994241BB683@stanford.edu>
Message-ID: <CALsrFgNS7AgWRqxdau8kS6f+SmhSojmQPPLqY-TvDJmOs3ahNw@mail.gmail.com>

Hello

I uses Javascript via a browser to show the Sparql result of queries. The h
ttp requests  failed if this endpoint Sparql doesn't allow to use it from
another http domain.

I test a web site in order to help Biologists to build online more easily a
Sparql federated query. The quality of data is not very important for my
tests.

You can see a demo here
https://io.datascience-paris-saclay.fr/exampleInsertUpdate.php?ex_id=200&action=copy

Best regards
Karima Rafes

2018-05-10 18:37 GMT+02:00 John Graybeal <jgraybeal at stanford.edu>:

> Hello Karima,
>
> It looks like we haven't addressed your query, apologies. I am not sure
> exactly what you are asking though.
>
> The Beta SPARQL endpoint is not formally maintained (and its data is
> somewhat old, alas). But I have checked and it is openly accessible from
> the test front end. Are you saying it is not accessible via API?
>
> And am wondering what you mean by "open it for another domain (CORS)". Is
> that referring to the ESIP Community Ontology Repository?  Perhaps you can
> describe your use case in a little more detail?
>
> John
>
>
> On Apr 26, 2018, at 9:18 AM, Karima Rafes <karima.rafes at gmail.com> wrote:
>
> Hello
>
> Your SPARQL endpoint doesn't allow to request data from another domain.
> Is it possible to open it for another domain (CORS) ?
> And if possible with a protocol https, it would be perfect.
>
> I works on a new SPARQL editor between several endpoints about biology.
>
> Thanks
> Best regards
> Karima Rafes
>
>
> _______________________________________________
> 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
>
>
>
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From support at bioontology.org  Thu May 10 12:48:55 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 10 May 2018 12:48:55 -0700
Subject: [bioontology-support] [BioPortal] Feedback from David Rogers
Message-ID: <5af4a227463f6_16bd3fcb510dac94709a0@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu May 10 13:17:09 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 10 May 2018 20:17:09 +0000
Subject: [bioontology-support] [BioPortal] Feedback from David Rogers
In-Reply-To: <5af4a227463f6_16bd3fcb510dac94709a0@ncbo-prd-app-08.stanford.edu.mail>
References: <5af4a227463f6_16bd3fcb510dac94709a0@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <7E455E57-A7BF-4B33-AD7F-BDE8F0E1DAF2@stanford.edu>

Hello David,


On May 10, 2018, at 12:48 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: David Rogers

Email: drogers at fredhutch.org<mailto:drogers at fredhutch.org>

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

Feedback:

Is it possible to get versioning for the CTCAE Ontology? For at least one prior version?

Could you be more specific about your needs?

The BioPortal REST API serves content from the latest submission of each of the ontology entries in our system. Currently we?re serving v5.0 of CTCAE. All previous versions (4.0.3, 4.0.2) are still available as file downloads though, e.g.:

http://data.bioontology.org/ontologies/CTCAE/submissions/2/download
http://data.bioontology.org/ontologies/CTCAE/submissions/1/download


Kind regards,
Jennifer

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From drogers at fredhutch.org  Thu May 10 15:40:57 2018
From: drogers at fredhutch.org (Rogers, David W)
Date: Thu, 10 May 2018 22:40:57 +0000
Subject: [bioontology-support] [BioPortal] Feedback from David Rogers
In-Reply-To: <7E455E57-A7BF-4B33-AD7F-BDE8F0E1DAF2@stanford.edu>
References: <5af4a227463f6_16bd3fcb510dac94709a0@ncbo-prd-app-08.stanford.edu.mail>
 <7E455E57-A7BF-4B33-AD7F-BDE8F0E1DAF2@stanford.edu>
Message-ID: <AA93F5A9E9B76E46BE1521CF17AED572012FD58152@adama.fhcrc.org>

Hello Jennifer,

We have numerous projects which use REDCap to select CTCAE ontologies provided through BioPortal. Much like ICD codes, one doesn?t normally switch to a different version (e.g., ICD9 ?> ICD10) in the middle of a research study. My request is for you guys to do the same thing with CTCAE as you have done with ICD codes ? provide multiple versions ? at least the most recent prior version as well as the current version in the api. So I would see CTCAE and CTCAE4 in the list of available ontologies.

Thanks,
David
--
David W. Rogers
Software Developer / Collaborative Data Services / 206.667.7089 / drogers at fredhutch.org / Fred Hutch / Cures Start Here

General CDS help: CdsHelp at fredhutch.org<mailto:CdsHelp at fredhutch.org> or REDCap-specific help: REDCapHelp at fredhutch.org<mailto:REDCapHelp at fredhutch.org>

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Thursday, May 10, 2018 1:17 PM
To: support at bioontology.org
Cc: Rogers, David W <drogers at fredhutch.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from David Rogers

Hello David,



On May 10, 2018, at 12:48 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: David Rogers
Email: drogers at fredhutch.org<mailto:drogers at fredhutch.org>
Location: https%3A%2F%2Fbioportal.bioontology.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__2Fbioportal.bioontology.org&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=uOSdQ7inwHPMjFHBV1swSL2PE77Vwrk-Zovojy2KX4w&s=Gq015MwjmUImQxRO6XRrljmklSvDscRUKmkzy9WPcsQ&e=>%2Fontologies%2FCTCAE

Feedback:
Is it possible to get versioning for the CTCAE Ontology? For at least one prior version?

Could you be more specific about your needs?

The BioPortal REST API serves content from the latest submission of each of the ontology entries in our system. Currently we?re serving v5.0 of CTCAE. All previous versions (4.0.3, 4.0.2) are still available as file downloads though, e.g.:

http://data.bioontology.org/ontologies/CTCAE/submissions/2/download<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_ontologies_CTCAE_submissions_2_download&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=uOSdQ7inwHPMjFHBV1swSL2PE77Vwrk-Zovojy2KX4w&s=EKI8mxTquTsEfs5dpGJIeJ0GBZFgVzQVdVpcMcqz6Vs&e=>
http://data.bioontology.org/ontologies/CTCAE/submissions/1/download<https://urldefense.proofpoint.com/v2/url?u=http-3A__data.bioontology.org_ontologies_CTCAE_submissions_1_download&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=uOSdQ7inwHPMjFHBV1swSL2PE77Vwrk-Zovojy2KX4w&s=MrSGhEj93ue2WrLNaVgV1o7lc6lqdDskN4u8RVW2MLc&e=>


Kind regards,
Jennifer

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From vendetti at stanford.edu  Thu May 10 17:17:55 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 11 May 2018 00:17:55 +0000
Subject: [bioontology-support] [BioPortal] Feedback from David Rogers
In-Reply-To: <AA93F5A9E9B76E46BE1521CF17AED572012FD58152@adama.fhcrc.org>
References: <5af4a227463f6_16bd3fcb510dac94709a0@ncbo-prd-app-08.stanford.edu.mail>
 <7E455E57-A7BF-4B33-AD7F-BDE8F0E1DAF2@stanford.edu>
 <AA93F5A9E9B76E46BE1521CF17AED572012FD58152@adama.fhcrc.org>
Message-ID: <ACFC8273-1A39-4BDD-9FEB-36BA160B542E@stanford.edu>

Hi David,


On May 10, 2018, at 3:40 PM, Rogers, David W <drogers at fredhutch.org<mailto:drogers at fredhutch.org>> wrote:

We have numerous projects which use REDCap to select CTCAE ontologies provided through BioPortal. Much like ICD codes, one doesn?t normally switch to a different version (e.g., ICD9 ?> ICD10) in the middle of a research study. My request is for you guys to do the same thing with CTCAE as you have done with ICD codes ? provide multiple versions ? at least the most recent prior version as well as the current version in the api.


I wanted to offer some clarification with regard to ICD. Roughly 5 years ago, we started doing twice annual imports of the ontologies that are part of the National Library of Medicine?s UMLS [1]. The UMLS includes copies of both ICD9 and ICD10, which is why you see both in BioPortal. In other words, there was no internal decision to offer multiple versions of ICD. This is simply a product of what?s available to import from the UMLS.

Generally speaking, we provide the software infrastructure for publishing biomedical ontologies into our repository. In most cases, we aren?t the authors, and/or maintainers of these ontologies and don?t put restrictions on when ontology authors are allowed to publish new versions. The contact information for CTCAE in BioPortal indicates that it?s maintained by NCI.


So I would see CTCAE and CTCAE4 in the list of available ontologies.


If you?re doing a research study that requires access to a particular version of an ontology, you?re welcome to create a new entry in BioPortal. As the owner/administrator of that entry, you?d be able to ensure that no modifications are made for the duration of your study. To add an entry for an older version of CTCAE in BioPortal, you would need to create an account [2], then navigate to the Tools -> Ontology Browser page, and click the Submit New Ontology button.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/
[2] https://bioportal.bioontology.org/accounts/new

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From jgraybeal at stanford.edu  Thu May 10 19:16:52 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 11 May 2018 02:16:52 +0000
Subject: [bioontology-support] [BioPortal] Feedback from David Rogers
In-Reply-To: <ACFC8273-1A39-4BDD-9FEB-36BA160B542E@stanford.edu>
References: <5af4a227463f6_16bd3fcb510dac94709a0@ncbo-prd-app-08.stanford.edu.mail>
 <7E455E57-A7BF-4B33-AD7F-BDE8F0E1DAF2@stanford.edu>
 <AA93F5A9E9B76E46BE1521CF17AED572012FD58152@adama.fhcrc.org>
 <ACFC8273-1A39-4BDD-9FEB-36BA160B542E@stanford.edu>
Message-ID: <8B20C118-2466-46AC-9770-687C0CA33E18@stanford.edu>

David,

If I may add a few thoughts.

Note that the older version you add would have to have a different acronym than CTCAE (so your REDCAP system and/or users would have to know to use that ontology acronym, not the CTCAE one).

Something else that might be useful: if you make the ontology private, you could give access privileges to the BioPortal users that need to use it. (For example, if it's all served by a single REDCap installation, just the user that owns that API. If it is multiple installations with different user API, that would be harder.)  Then you and your users would be the only ones seeing the older ontology.

It appears that the identifiers in the CTCAE ontology are defined in the ontology. This is good?it means that REDCap is likely to use the same identifiers from your version of the ontology, as the ones originally provided by CTCAE (then the previous version) to your users. So the data would likely be annotated exactly the same way.

One other thought, before you go to that trouble: Have you compared the two versions? It may turn out that the ontology does varies little between them, and you might be able to get away with using the new one.

I hope our contributions have been helpful, I know this is an annoying situation.  If I could wave the wand I would love versions to be configurable in BioPortal, but that would require way more magic than any wand I can wave, sorry!

John

On May 10, 2018, at 5:17 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi David,


On May 10, 2018, at 3:40 PM, Rogers, David W <drogers at fredhutch.org<mailto:drogers at fredhutch.org>> wrote:

We have numerous projects which use REDCap to select CTCAE ontologies provided through BioPortal. Much like ICD codes, one doesn?t normally switch to a different version (e.g., ICD9 ?> ICD10) in the middle of a research study. My request is for you guys to do the same thing with CTCAE as you have done with ICD codes ? provide multiple versions ? at least the most recent prior version as well as the current version in the api.


I wanted to offer some clarification with regard to ICD. Roughly 5 years ago, we started doing twice annual imports of the ontologies that are part of the National Library of Medicine?s UMLS [1]. The UMLS includes copies of both ICD9 and ICD10, which is why you see both in BioPortal. In other words, there was no internal decision to offer multiple versions of ICD. This is simply a product of what?s available to import from the UMLS.

Generally speaking, we provide the software infrastructure for publishing biomedical ontologies into our repository. In most cases, we aren?t the authors, and/or maintainers of these ontologies and don?t put restrictions on when ontology authors are allowed to publish new versions. The contact information for CTCAE in BioPortal indicates that it?s maintained by NCI.


So I would see CTCAE and CTCAE4 in the list of available ontologies.


If you?re doing a research study that requires access to a particular version of an ontology, you?re welcome to create a new entry in BioPortal. As the owner/administrator of that entry, you?d be able to ensure that no modifications are made for the duration of your study. To add an entry for an older version of CTCAE in BioPortal, you would need to create an account [2], then navigate to the Tools -> Ontology Browser page, and click the Submit New Ontology button.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/
[2] https://bioportal.bioontology.org/accounts/new

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

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


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From drogers at fredhutch.org  Thu May 10 17:58:11 2018
From: drogers at fredhutch.org (Rogers, David W)
Date: Fri, 11 May 2018 00:58:11 +0000
Subject: [bioontology-support] [BioPortal] Feedback from David Rogers
In-Reply-To: <ACFC8273-1A39-4BDD-9FEB-36BA160B542E@stanford.edu>
References: <5af4a227463f6_16bd3fcb510dac94709a0@ncbo-prd-app-08.stanford.edu.mail>
 <7E455E57-A7BF-4B33-AD7F-BDE8F0E1DAF2@stanford.edu>
 <AA93F5A9E9B76E46BE1521CF17AED572012FD58152@adama.fhcrc.org>,
 <ACFC8273-1A39-4BDD-9FEB-36BA160B542E@stanford.edu>
Message-ID: <AA93F5A9E9B76E46BE1521CF17AED572012FD58222@adama.fhcrc.org>

Interesting. So the custom ontology would appear in the list when I used my apikey?





Sent from my Verizon, Samsung Galaxy smartphone


-------- Original message --------
From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: 5/10/18 5:18 PM (GMT-08:00)
To: "Rogers, David W" <drogers at fredhutch.org>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] [BioPortal] Feedback from David Rogers

Hi David,


On May 10, 2018, at 3:40 PM, Rogers, David W <drogers at fredhutch.org<mailto:drogers at fredhutch.org>> wrote:

We have numerous projects which use REDCap to select CTCAE ontologies provided through BioPortal. Much like ICD codes, one doesn?t normally switch to a different version (e.g., ICD9 ?> ICD10) in the middle of a research study. My request is for you guys to do the same thing with CTCAE as you have done with ICD codes ? provide multiple versions ? at least the most recent prior version as well as the current version in the api.


I wanted to offer some clarification with regard to ICD. Roughly 5 years ago, we started doing twice annual imports of the ontologies that are part of the National Library of Medicine?s UMLS [1]. The UMLS includes copies of both ICD9 and ICD10, which is why you see both in BioPortal. In other words, there was no internal decision to offer multiple versions of ICD. This is simply a product of what?s available to import from the UMLS.

Generally speaking, we provide the software infrastructure for publishing biomedical ontologies into our repository. In most cases, we aren?t the authors, and/or maintainers of these ontologies and don?t put restrictions on when ontology authors are allowed to publish new versions. The contact information for CTCAE in BioPortal indicates that it?s maintained by NCI.


So I would see CTCAE and CTCAE4 in the list of available ontologies.


If you?re doing a research study that requires access to a particular version of an ontology, you?re welcome to create a new entry in BioPortal. As the owner/administrator of that entry, you?d be able to ensure that no modifications are made for the duration of your study. To add an entry for an older version of CTCAE in BioPortal, you would need to create an account [2], then navigate to the Tools -> Ontology Browser page, and click the Submit New Ontology button.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nlm.nih.gov_research_umls_knowledge-5Fsources_metathesaurus_&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=v16cO8iN5aJref9Dc01IEJl0-eByniIewnSjRiScoAs&s=beksTC-3a8JKw6nqdF6PiKhzmVTJBuAZiCUB37EzusI&e=>
[2] https://bioportal.bioontology.org/accounts/new<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_accounts_new&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=v16cO8iN5aJref9Dc01IEJl0-eByniIewnSjRiScoAs&s=3_WScNMyFPlU9OLK1t07w3cC7XwOwEWn_KCQu7amTLc&e=>

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From drogers at fredhutch.org  Fri May 11 08:53:11 2018
From: drogers at fredhutch.org (Rogers, David W)
Date: Fri, 11 May 2018 15:53:11 +0000
Subject: [bioontology-support] [BioPortal] Feedback from David Rogers
In-Reply-To: <8B20C118-2466-46AC-9770-687C0CA33E18@stanford.edu>
References: <5af4a227463f6_16bd3fcb510dac94709a0@ncbo-prd-app-08.stanford.edu.mail>
 <7E455E57-A7BF-4B33-AD7F-BDE8F0E1DAF2@stanford.edu>
 <AA93F5A9E9B76E46BE1521CF17AED572012FD58152@adama.fhcrc.org>
 <ACFC8273-1A39-4BDD-9FEB-36BA160B542E@stanford.edu>
 <8B20C118-2466-46AC-9770-687C0CA33E18@stanford.edu>
Message-ID: <AA93F5A9E9B76E46BE1521CF17AED572012FD58516@adama.fhcrc.org>

Thank you, John! I was thinking of using the old version number as a suffix, as in, ?CTCAE_V4?. This would require all of the project owners who want to stay on that version to reconfigure, but presumably they would be happy to have this capability for such a small effort.

I have not compared the two versions. I think I will go back to the project owner and get their  take on the differences. Perhaps this is one of those cases where a knee-jerk reaction to a user request is the wrong way to go.

These ontologies are black boxes to me so I appreciate your analysis of my possible chances of success. Do you have any idea how much time it would take a neophyte to complete this approach? (I have to bill them for my time ? a factor that usually increases their thoughtfulness quite a bit?)

As for a magic wand, you can?t be serious! A simple time-stretching device such as the ?Give Me Just a Little More Time? model 1970 would suffice. ?

Thanks again for your thoughts!
David
--
David W. Rogers
Software Developer / Collaborative Data Services / 206.667.7089 / drogers at fredhutch.org / Fred Hutch / Cures Start Here

General CDS help: CdsHelp at fredhutch.org<mailto:CdsHelp at fredhutch.org> or REDCap-specific help: REDCapHelp at fredhutch.org<mailto:REDCapHelp at fredhutch.org>

From: John Graybeal <jgraybeal at stanford.edu>
Sent: Thursday, May 10, 2018 7:17 PM
To: Rogers, David W <drogers at fredhutch.org>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] [BioPortal] Feedback from David Rogers

David,

If I may add a few thoughts.

Note that the older version you add would have to have a different acronym than CTCAE (so your REDCAP system and/or users would have to know to use that ontology acronym, not the CTCAE one).

Something else that might be useful: if you make the ontology private, you could give access privileges to the BioPortal users that need to use it. (For example, if it's all served by a single REDCap installation, just the user that owns that API. If it is multiple installations with different user API, that would be harder.)  Then you and your users would be the only ones seeing the older ontology.

It appears that the identifiers in the CTCAE ontology are defined in the ontology. This is good?it means that REDCap is likely to use the same identifiers from your version of the ontology, as the ones originally provided by CTCAE (then the previous version) to your users. So the data would likely be annotated exactly the same way.

One other thought, before you go to that trouble: Have you compared the two versions? It may turn out that the ontology does varies little between them, and you might be able to get away with using the new one.

I hope our contributions have been helpful, I know this is an annoying situation.  If I could wave the wand I would love versions to be configurable in BioPortal, but that would require way more magic than any wand I can wave, sorry!

John

On May 10, 2018, at 5:17 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi David,



On May 10, 2018, at 3:40 PM, Rogers, David W <drogers at fredhutch.org<mailto:drogers at fredhutch.org>> wrote:

We have numerous projects which use REDCap to select CTCAE ontologies provided through BioPortal. Much like ICD codes, one doesn?t normally switch to a different version (e.g., ICD9 ?> ICD10) in the middle of a research study. My request is for you guys to do the same thing with CTCAE as you have done with ICD codes ? provide multiple versions ? at least the most recent prior version as well as the current version in the api.


I wanted to offer some clarification with regard to ICD. Roughly 5 years ago, we started doing twice annual imports of the ontologies that are part of the National Library of Medicine?s UMLS [1]. The UMLS includes copies of both ICD9 and ICD10, which is why you see both in BioPortal. In other words, there was no internal decision to offer multiple versions of ICD. This is simply a product of what?s available to import from the UMLS.

Generally speaking, we provide the software infrastructure for publishing biomedical ontologies into our repository. In most cases, we aren?t the authors, and/or maintainers of these ontologies and don?t put restrictions on when ontology authors are allowed to publish new versions. The contact information for CTCAE in BioPortal indicates that it?s maintained by NCI.


So I would see CTCAE and CTCAE4 in the list of available ontologies.


If you?re doing a research study that requires access to a particular version of an ontology, you?re welcome to create a new entry in BioPortal. As the owner/administrator of that entry, you?d be able to ensure that no modifications are made for the duration of your study. To add an entry for an older version of CTCAE in BioPortal, you would need to create an account [2], then navigate to the Tools -> Ontology Browser page, and click the Submit New Ontology button.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nlm.nih.gov_research_umls_knowledge-5Fsources_metathesaurus_&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=O6dFQHEpJW9nMxkywjx7sUUR8ZT2h4NSohkny0LhWaA&s=FflCQa6uObbIK_Q80_Vmq_OpE7dBm0qB5QyUblgH-X0&e=>
[2] https://bioportal.bioontology.org/accounts/new<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_accounts_new&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=O6dFQHEpJW9nMxkywjx7sUUR8ZT2h4NSohkny0LhWaA&s=K1H9YPFo3cHYkoWRuMeRWmyK_GwbAqL85f3R9i7MG1Y&e=>

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

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

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From msgolec at yahoo.com  Fri May 11 11:51:28 2018
From: msgolec at yahoo.com (Marcin Golec)
Date: Fri, 11 May 2018 18:51:28 +0000 (UTC)
Subject: [bioontology-support] how to place an ontology on Bioportal?
References: <431696364.277581.1526064688104.ref@mail.yahoo.com>
Message-ID: <431696364.277581.1526064688104@mail.yahoo.com>

Dear Madams/Sirs,

I would like to ask you how may I register / place the ontology prepared by our group in Bioportal?

What are the crititeria an ontology has to fulfill in order to be registered on Bioportal?

Thank you in advance for your help.

Best regards,

Marcin Golec MD, PhD, MSc

From vendetti at stanford.edu  Fri May 11 12:54:13 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 11 May 2018 19:54:13 +0000
Subject: [bioontology-support] how to place an ontology on Bioportal?
In-Reply-To: <431696364.277581.1526064688104@mail.yahoo.com>
References: <431696364.277581.1526064688104.ref@mail.yahoo.com>
 <431696364.277581.1526064688104@mail.yahoo.com>
Message-ID: <3B0B39AF-9B64-4CFD-812F-4F06AEC55B5F@stanford.edu>

Hello Marcin,


On May 11, 2018, at 11:51 AM, Marcin Golec <msgolec at yahoo.com<mailto:msgolec at yahoo.com>> wrote:

Dear Madams/Sirs,

I would like to ask you how may I register / place the ontology prepared by our group in Bioportal?


To upload an ontology in Bioportal, you?ll need to create an account [1]. Then navigate to the Tools -> Ontology Browser page and click the Submit New Ontology button. From there, fill out the required fields in the resulting forms.

The process is also documented on our wiki [2].



What are the crititeria an ontology has to fulfill in order to be registered on Bioportal?


I?m not aware of any criteria, other than your ontology being related to the field of biomedicine.

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/accounts/new
[2] https://www.bioontology.org/wiki/index.php/BioPortal_Help#Submitting_an_ontology


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From vendetti at stanford.edu  Fri May 11 13:03:26 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 11 May 2018 20:03:26 +0000
Subject: [bioontology-support] how to place an ontology on Bioportal?
In-Reply-To: <3B0B39AF-9B64-4CFD-812F-4F06AEC55B5F@stanford.edu>
References: <431696364.277581.1526064688104.ref@mail.yahoo.com>
 <431696364.277581.1526064688104@mail.yahoo.com>
 <3B0B39AF-9B64-4CFD-812F-4F06AEC55B5F@stanford.edu>
Message-ID: <6C56F156-C1DB-4C4A-AEAA-BF97BD7E834F@stanford.edu>

Hell again Marcin,

Apologies, but I should have mentioned in my initial reply that BioPortal accepts ontologies in OWL, OBO, or SKOS format. Is your ontology available in one of these formats?

Kind regards,
Jennifer



On May 11, 2018, at 12:54 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Marcin,


On May 11, 2018, at 11:51 AM, Marcin Golec <msgolec at yahoo.com<mailto:msgolec at yahoo.com>> wrote:

Dear Madams/Sirs,

I would like to ask you how may I register / place the ontology prepared by our group in Bioportal?


To upload an ontology in Bioportal, you?ll need to create an account [1]. Then navigate to the Tools -> Ontology Browser page and click the Submit New Ontology button. From there, fill out the required fields in the resulting forms.

The process is also documented on our wiki [2].



What are the crititeria an ontology has to fulfill in order to be registered on Bioportal?


I?m not aware of any criteria, other than your ontology being related to the field of biomedicine.

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/accounts/new
[2] https://www.bioontology.org/wiki/index.php/BioPortal_Help#Submitting_an_ontology


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

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From jgraybeal at stanford.edu  Fri May 11 16:17:10 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 11 May 2018 23:17:10 +0000
Subject: [bioontology-support] [BioPortal] Feedback from David Rogers
In-Reply-To: <AA93F5A9E9B76E46BE1521CF17AED572012FD58516@adama.fhcrc.org>
References: <5af4a227463f6_16bd3fcb510dac94709a0@ncbo-prd-app-08.stanford.edu.mail>
 <7E455E57-A7BF-4B33-AD7F-BDE8F0E1DAF2@stanford.edu>
 <AA93F5A9E9B76E46BE1521CF17AED572012FD58152@adama.fhcrc.org>
 <ACFC8273-1A39-4BDD-9FEB-36BA160B542E@stanford.edu>
 <8B20C118-2466-46AC-9770-687C0CA33E18@stanford.edu>
 <AA93F5A9E9B76E46BE1521CF17AED572012FD58516@adama.fhcrc.org>
Message-ID: <7121C402-3976-427C-B96B-6C00D3AE663B@stanford.edu>

If you have access to the version 4 ontology?I'm not sure if the version on BioPortal is the right format  but you could download it and look?getting it into BioPortal under a new acronym should be pretty straightforward. At least people do it fairly often, and you know the ontology should be working OK. Maybe under an hour, plus some waiting time for BioPortal to parse and all. (Plus also your REDCap setup time, and the training of the users if they have access to multiple ontologies.)

If you can ask the project owner, that's definitely the best way to learn about differences, plus it will help make sure they aren't unpleasantly surprised to find it there.

If you do that, the custom ontology will definitely be accessible to your API key. If you set it to PRIVATE, only you and the administrators (and the REDHat that's using your API key) could access it, or even know it's in BioPortal.

John


On May 11, 2018, at 8:53 AM, Rogers, David W <drogers at fredhutch.org<mailto:drogers at fredhutch.org>> wrote:

Thank you, John! I was thinking of using the old version number as a suffix, as in, ?CTCAE_V4?. This would require all of the project owners who want to stay on that version to reconfigure, but presumably they would be happy to have this capability for such a small effort.

I have not compared the two versions. I think I will go back to the project owner and get their  take on the differences. Perhaps this is one of those cases where a knee-jerk reaction to a user request is the wrong way to go.

These ontologies are black boxes to me so I appreciate your analysis of my possible chances of success. Do you have any idea how much time it would take a neophyte to complete this approach? (I have to bill them for my time ? a factor that usually increases their thoughtfulness quite a bit?)

As for a magic wand, you can?t be serious! A simple time-stretching device such as the ?Give Me Just a Little More Time? model 1970 would suffice. ?

Thanks again for your thoughts!
David
--
David W. Rogers
Software Developer / Collaborative Data Services / 206.667.7089 / drogers<mailto:drogers at fredhutch.org>@<mailto:drogers at fredhutch.org>fredhutch.org<mailto:drogers at fredhutch.org> / Fred Hutch / Cures Start Here

General CDS help: CdsHelp at fredhutch.org<mailto:CdsHelp at fredhutch.org> or REDCap-specific help: REDCapHelp at fredhutch.org<mailto:REDCapHelp at fredhutch.org>

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, May 10, 2018 7:17 PM
To: Rogers, David W <drogers at fredhutch.org<mailto:drogers at fredhutch.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from David Rogers

David,

If I may add a few thoughts.

Note that the older version you add would have to have a different acronym than CTCAE (so your REDCAP system and/or users would have to know to use that ontology acronym, not the CTCAE one).

Something else that might be useful: if you make the ontology private, you could give access privileges to the BioPortal users that need to use it. (For example, if it's all served by a single REDCap installation, just the user that owns that API. If it is multiple installations with different user API, that would be harder.)  Then you and your users would be the only ones seeing the older ontology.

It appears that the identifiers in the CTCAE ontology are defined in the ontology. This is good?it means that REDCap is likely to use the same identifiers from your version of the ontology, as the ones originally provided by CTCAE (then the previous version) to your users. So the data would likely be annotated exactly the same way.

One other thought, before you go to that trouble: Have you compared the two versions? It may turn out that the ontology does varies little between them, and you might be able to get away with using the new one.

I hope our contributions have been helpful, I know this is an annoying situation.  If I could wave the wand I would love versions to be configurable in BioPortal, but that would require way more magic than any wand I can wave, sorry!

John

On May 10, 2018, at 5:17 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi David,



On May 10, 2018, at 3:40 PM, Rogers, David W <drogers at fredhutch.org<mailto:drogers at fredhutch.org>> wrote:

We have numerous projects which use REDCap to select CTCAE ontologies provided through BioPortal. Much like ICD codes, one doesn?t normally switch to a different version (e.g., ICD9 ?> ICD10) in the middle of a research study. My request is for you guys to do the same thing with CTCAE as you have done with ICD codes ? provide multiple versions ? at least the most recent prior version as well as the current version in the api.


I wanted to offer some clarification with regard to ICD. Roughly 5 years ago, we started doing twice annual imports of the ontologies that are part of the National Library of Medicine?s UMLS [1]. The UMLS includes copies of both ICD9 and ICD10, which is why you see both in BioPortal. In other words, there was no internal decision to offer multiple versions of ICD. This is simply a product of what?s available to import from the UMLS.

Generally speaking, we provide the software infrastructure for publishing biomedical ontologies into our repository. In most cases, we aren?t the authors, and/or maintainers of these ontologies and don?t put restrictions on when ontology authors are allowed to publish new versions. The contact information for CTCAE in BioPortal indicates that it?s maintained by NCI.


So I would see CTCAE and CTCAE4 in the list of available ontologies.


If you?re doing a research study that requires access to a particular version of an ontology, you?re welcome to create a new entry in BioPortal. As the owner/administrator of that entry, you?d be able to ensure that no modifications are made for the duration of your study. To add an entry for an older version of CTCAE in BioPortal, you would need to create an account [2], then navigate to the Tools -> Ontology Browser page, and click the Submit New Ontology button.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nlm.nih.gov_research_umls_knowledge-5Fsources_metathesaurus_&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=O6dFQHEpJW9nMxkywjx7sUUR8ZT2h4NSohkny0LhWaA&s=FflCQa6uObbIK_Q80_Vmq_OpE7dBm0qB5QyUblgH-X0&e=>
[2] https://bioportal.bioontology.org/accounts/new<https://urldefense.proofpoint.com/v2/url?u=https-3A__bioportal.bioontology.org_accounts_new&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=WgUuXEZxxnXFMyW7y9PgsrcZI3Wdrk7U4ztbdTbhVmo&m=O6dFQHEpJW9nMxkywjx7sUUR8ZT2h4NSohkny0LhWaA&s=K1H9YPFo3cHYkoWRuMeRWmyK_GwbAqL85f3R9i7MG1Y&e=>

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

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

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


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From support at bioontology.org  Thu May 17 04:25:39 2018
From: support at bioontology.org (support at bioontology.org)
Date: Thu, 17 May 2018 04:25:39 -0700
Subject: [bioontology-support] [BioPortal] Feedback from Paulina Wiejak
Message-ID: <5afd66b314fba_6c613fbbf6c47178943a4@ncbo-prd-app-08.stanford.edu.mail>

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From vendetti at stanford.edu  Thu May 17 11:25:33 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 17 May 2018 18:25:33 +0000
Subject: [bioontology-support] [BioPortal] Feedback from Paulina Wiejak
In-Reply-To: <5afd66b314fba_6c613fbbf6c47178943a4@ncbo-prd-app-08.stanford.edu.mail>
References: <5afd66b314fba_6c613fbbf6c47178943a4@ncbo-prd-app-08.stanford.edu.mail>
Message-ID: <4E2CA453-1EBC-41CA-A004-6CE9FEBBAEF2@stanford.edu>

Thanks for letting us know Paulina. It appears that this ontology was moved from Google Code to GitHub. I updated the links on the ontology summary page: http://bioportal.bioontology.org/ontologies/MFOEM.

Kind regards,
Jennifer



On May 17, 2018, at 4:25 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Paulina Wiejak

Email: paulinawiejak91 at gmail.com<mailto:paulinawiejak91 at gmail.com>

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

Feedback:

Hi! I just wanted to report that this link http://emotion-ontology.googlecode.com/ is not working. The error that shows is: "The requested URL / was not found on this server. That?s all we know."

Sincerely,
Paulina Wiejak

_______________________________________________
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From support at bioontology.org  Fri May 18 06:56:21 2018
From: support at bioontology.org (support at bioontology.org)
Date: Fri, 18 May 2018 06:56:21 -0700
Subject: [bioontology-support] [BioPortal] Feedback from kushida
Message-ID: <5afedb8594977_44a23fc5cc3a7ed49243c@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Fri May 18 11:25:08 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Fri, 18 May 2018 18:25:08 +0000
Subject: [bioontology-support] [BioPortal] Feedback from kushida
In-Reply-To: <5afedb8594977_44a23fc5cc3a7ed49243c@ncbo-prd-app-09.stanford.edu.mail>
References: <5afedb8594977_44a23fc5cc3a7ed49243c@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <0B6C4DD7-7103-414A-9AA4-7075D72AC046@stanford.edu>

Hello Tatsuya,


On May 18, 2018, at 6:56 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: kushida

Email: kushida at biosciencedbc.jp<mailto:kushida at biosciencedbc.jp>

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

Feedback:

To whom it may concern,
I updated my ontology "Interlinking Ontology for Biological Concepts (ICBO)" (http://purl.bioontology.org/ontology/IOBC). I want to make this ontology "public", however I don't know how to set "public?.

I looked at the ontology summary page for IOBC and it?s set to public visibility. I assume you figured out how to do this?



And I also want to delete previous data except for the latest data (ver.1.0.0). Could you teach me the procedures?



We don?t offer a way to do this via the BioPortal user interface. I went ahead and deleted the older submissions on your behalf. The only remaining entry is the latest (version 1.0.0).

Kind regards,
Jennifer

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From kushida at biosciencedbc.jp  Fri May 18 11:58:29 2018
From: kushida at biosciencedbc.jp (Tatsuya Kushida)
Date: Sat, 19 May 2018 03:58:29 +0900
Subject: [bioontology-support] [BioPortal] Feedback from kushida
In-Reply-To: <0B6C4DD7-7103-414A-9AA4-7075D72AC046@stanford.edu>
References: <5afedb8594977_44a23fc5cc3a7ed49243c@ncbo-prd-app-09.stanford.edu.mail>
 <0B6C4DD7-7103-414A-9AA4-7075D72AC046@stanford.edu>
Message-ID: <CAJuGyWnYmxxJM7eVQ+JufjjFJ27prBL36JgvJPv09MFxz58p_Q@mail.gmail.com>

Dear Jennifer,

Thank you so much for your prompt response.
Due to your efforts, all of the problems were resolved!

Best regards,
Tatsuya

2018-05-19 3:25 GMT+09:00 Jennifer Leigh Vendetti <vendetti at stanford.edu>:
> Hello Tatsuya,
>
>
> On May 18, 2018, at 6:56 AM, support at bioontology.org wrote:
>
> Name: kushida
>
> Email: kushida at biosciencedbc.jp
>
> Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FIOBC%2Fedit
>
>
> Feedback:
>
> To whom it may concern,
> I updated my ontology "Interlinking Ontology for Biological Concepts (ICBO)"
> (http://purl.bioontology.org/ontology/IOBC). I want to make this ontology
> "public", however I don't know how to set "public?.
>
>
> I looked at the ontology summary page for IOBC and it?s set to public
> visibility. I assume you figured out how to do this?
>
>
> And I also want to delete previous data except for the latest data
> (ver.1.0.0). Could you teach me the procedures?
>
>
>
>
> We don?t offer a way to do this via the BioPortal user interface. I went
> ahead and deleted the older submissions on your behalf. The only remaining
> entry is the latest (version 1.0.0).
>
> Kind regards,
> Jennifer
>

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

From FW3U at hscmail.mcc.virginia.edu  Mon May 21 12:44:19 2018
From: FW3U at hscmail.mcc.virginia.edu (Khan, Fauzia W *HS)
Date: Mon, 21 May 2018 19:44:19 +0000
Subject: [bioontology-support] University of Virginia - REDCap Data
	Management System Issue
Message-ID: <0d02cfff3b41459dac0804128febac3a@HSTSEXCHA2.hscs.virginia.edu>

Good Afternoon,

I am emailing because I am having some issues with setting up Ontologies on a new server for our REDCap system. We are currently using Ontologies as expected in our existing system. During testing of our new server, I noticed it doesn't work. I have generated a new token but still not luck. Please advise, our go-live is next week!

Thank you,

Fauzia Khan, MMCi
Application Systems Analyst/Programmer
REDCap Admin, Clinical Business Intelligence
University of Virginia
Stacey Hall, 1105 West Main Street
Charlottesville, VA 22903
434.982.4108 | Office
fw3u at hscmail.mcc.virginia.edu<mailto:fw3u at hscmail.mcc.virginia.edu>



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From vendetti at stanford.edu  Mon May 21 14:18:57 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Mon, 21 May 2018 21:18:57 +0000
Subject: [bioontology-support] University of Virginia - REDCap
	Data	Management System Issue
In-Reply-To: <0d02cfff3b41459dac0804128febac3a@HSTSEXCHA2.hscs.virginia.edu>
References: <0d02cfff3b41459dac0804128febac3a@HSTSEXCHA2.hscs.virginia.edu>
Message-ID: <7D640A99-7C34-4053-AB55-ED3CD7E6C7DE@stanford.edu>

Hello Fauzia,

You?ve reached the support list for the Bioportal REST API [1] and BioPortal application [2]. We have no knowledge of the REDCap software.

I assume your application is accessing ontology data via our REST API? To test your API key, simply open a browser window and enter any of the sample URLs we provide in our REST API documentation, e.g.:

http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F410607006<http://data.bioontology.org/ontologies/SNOMEDCT/classes/http://purl.bioontology.org/ontology/SNOMEDCT/410607006>?apikey=your_api_key_goes_here

If there?s an issue with your API key, the browser will display an error. If the call was successful, you?ll see JSON results displayed in the browser.

Kind regards,
Jennifer

[1] http://data.bioontology.org/documentation
[2] http://bioportal.bioontology.org/



On May 21, 2018, at 12:44 PM, Khan, Fauzia W *HS <FW3U at hscmail.mcc.virginia.edu<mailto:FW3U at hscmail.mcc.virginia.edu>> wrote:

Good Afternoon,

I am emailing because I am having some issues with setting up Ontologies on a new server for our REDCap system. We are currently using Ontologies as expected in our existing system. During testing of our new server, I noticed it doesn?t work. I have generated a new token but still not luck. Please advise, our go-live is next week!

Thank you,

Fauzia Khan, MMCi
Application Systems Analyst/Programmer
REDCap Admin, Clinical Business Intelligence
University of Virginia
Stacey Hall, 1105 West Main Street
Charlottesville, VA 22903
434.982.4108 | Office
fw3u at hscmail.mcc.virginia.edu<mailto:fw3u at hscmail.mcc.virginia.edu>



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From awagner24 at wustl.edu  Wed May 23 15:07:14 2018
From: awagner24 at wustl.edu (Wagner, Alex)
Date: Wed, 23 May 2018 22:07:14 +0000
Subject: [bioontology-support] non-obsolete deprecated term
Message-ID: <6F7DDEA2-1B3C-4E6D-9D63-1D7DD9078EC2@wustl.edu>

Hello,

I queried data.bioontology.org<http://data.bioontology.org> for "CNS Cancer":

http://data.bioontology.org/search?q="CNS%20Cancer"<http://data.bioontology.org/search?q=%22CNS%20Cancer%22>

and the first result in the collection is "embryonal cancer of CNS", DOID:1665. This is a deprecated disease ontology identifier, and the best response for this query would be "central nervous system cancer", DOID:3620. The aforementioned result is marked as obsolete: false. Just letting you know in case this is unexpected behavior.

Best,
Alex

--
Alex H. Wagner, Ph.D.
Postdoctoral Research Scholar
McDonnell Genome Institute
Washington University School of Medicine
Campus Box 8501
4444 Forest Park Ave
St. Louis, MO, 63108
P: (480) ALEX-PHD
E: awagner24 at wustl.edu<mailto:awagner24 at wustl.edu>
W: alexwagner.info<http://alexwagner.info/>




________________________________
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From irmgard.teschke at osthus.com  Thu May 24 00:55:20 2018
From: irmgard.teschke at osthus.com (Irmgard Teschke)
Date: Thu, 24 May 2018 07:55:20 +0000
Subject: [bioontology-support] Question about reproducing Bioportal mapping
	and class metrics
Message-ID: <6330f0387a72442dbc4bdbf168deeecc@osthus.com>

Dear Bioontology Support,

I have downloaded some ontologies and a few mappings from the Bioportal REST API and have been trying (unsuccessfully) to reproduce the class and mappings metrics for these ontologies and mapping pairs. I must be missing something and was hoping that someone might be able to point me in the right direction.

I will try to explain my problem with the example of the ontologies ORDO<https://bioportal.bioontology.org/ontologies/ORDO?p=summary> (Orphanet Rare Disease Ontology) and MP<https://bioportal.bioontology.org/ontologies/MP?p=summary> (Mammalian Phenotype Ontology).

To count number of classes in the ontology I used a sparql query (Table below, lefthand column), the result of which (no. classes) is given on the right for the ontologies ORDO and MP. The Bioportal result (see ORDO<https://bioportal.bioontology.org/ontologies/ORDO?p=summary>  and MP<https://bioportal.bioontology.org/ontologies/MP?p=summary>) is given in the 2nd and 3rd column of the table below.

My Query

ORDO

MP

PREFIX owl: <http://www.w3.org/2002/07/owl#>

SELECT (count( ?s) as ?no_mappings)

FROM <http://xyzmapping.com/ORDO>

WHERE {?s a owl:Class .
Filter (! isblank(?s))
}

13,666 classes

12,795 classes

Bioportal

13,666 classes

13,556 classes



As you can see, my number is the same as the bioportal no. classes for ORDO, but not for MP. I wonder why?

Furthermore, here<https://bioportal.bioontology.org/ontologies/ORDO?p=mappings> I checked the number of mappings from ORDO to MP and found that there should be 128 mappings. However, when I download/parse the json through the rest API, I only get 69 mappings. I have confirmed my number (69) also by actually counting the number of mapping pairs given in the REST API for this pair (the REST API source for the mapping I downloaded and also counted by hand is http://data.bioontology.org/mappings?ontologies=ORDO,MP&apikey=xyz). I have similar discrepancies for all ontologies and mappings that I have downloaded to date. Any ideas about why this could be?

Any help would be much appreciated!!!


Mit freundlichen Gr??en / Kind Regards

Irmgard Teschke
________________________________________________
OSTHUS GmbH
Eisenbahnweg 9 - 11
Eingang TH 6
52068 Aachen
T    +49 241-94314-xxx
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From vendetti at stanford.edu  Thu May 24 15:53:38 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Thu, 24 May 2018 22:53:38 +0000
Subject: [bioontology-support] Question about reproducing Bioportal
 mapping	and class metrics
In-Reply-To: <6330f0387a72442dbc4bdbf168deeecc@osthus.com>
References: <6330f0387a72442dbc4bdbf168deeecc@osthus.com>
Message-ID: <72C409C7-B551-4F7D-9848-72EB5860098C@stanford.edu>

Hello Irmgard,


On May 24, 2018, at 12:55 AM, Irmgard Teschke <irmgard.teschke at osthus.com<mailto:irmgard.teschke at osthus.com>> wrote:

Dear Bioontology Support,

I have downloaded some ontologies and a few mappings from the Bioportal REST API and have been trying (unsuccessfully) to reproduce the class and mappings metrics for these ontologies and mapping pairs. I must be missing something and was hoping that someone might be able to point me in the right direction.

I will try to explain my problem with the example of the ontologies ORDO<https://bioportal.bioontology.org/ontologies/ORDO?p=summary> (Orphanet Rare Disease Ontology) and MP<https://bioportal.bioontology.org/ontologies/MP?p=summary> (Mammalian Phenotype Ontology).

To count number of classes in the ontology I used a sparql query (Table below, lefthand column), the result of which (no. classes) is given on the right for the ontologies ORDO and MP. The Bioportal result (see ORDO<https://bioportal.bioontology.org/ontologies/ORDO?p=summary>  and MP<https://bioportal.bioontology.org/ontologies/MP?p=summary>) is given in the 2nd and 3rd column of the table below.


What are you executing the SPARQL query against? At the moment, we don?t have an open SPARQL endpoint that serves current ontology data. Is this something you?ve set up locally?




My Query

ORDO

MP

PREFIX owl: <http://www.w3.org/2002/07/owl#>

SELECT (count( ?s) as ?no_mappings)

FROM <http://xyzmapping.com/ORDO>

WHERE {?s a owl:Class .
Filter (! isblank(?s))
}

13,666 classes

12,795 classes

Bioportal

13,666 classes

13,556 classes



As you can see, my number is the same as the bioportal no. classes for ORDO, but not for MP. I wonder why?


We don?t use SPARQL to generate class, property, or individual metrics. When end users submit ontologies to BioPortal, we first consume the ontology source files with the OWL API [1]. We use OWL API functions to calculate metrics for classes, properties, and individuals. You can see that code here:

https://github.com/ncbo/owlapi_wrapper/blob/master/src/main/java/org/stanford/ncbo/oapiwrapper/OntologyMetrics.java#L45




Furthermore, here<https://bioportal.bioontology.org/ontologies/ORDO?p=mappings> I checked the number of mappings from ORDO to MP and found that there should be 128 mappings. However, when I download/parse the json through the rest API, I only get 69 mappings. I have confirmed my number (69) also by actually counting the number of mapping pairs given in the REST API for this pair (the REST API source for the mapping I downloaded and also counted by hand is http://data.bioontology.org/mappings?ontologies=ORDO,MP&apikey=xyz). I have similar discrepancies for all ontologies and mappings that I have downloaded to date. Any ideas about why this could be?


There?s a known issue in the BioPortal user interface with displaying duplicate mappings. We have an issue in our tracker here:

https://github.com/ncbo/bioportal-project/issues/69

Apologies that we haven?t had an opportunity to troubleshoot this yet.

Kind regards,
Jennifer


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From support at bioontology.org  Mon May 28 07:06:59 2018
From: support at bioontology.org (support at bioontology.org)
Date: Mon, 28 May 2018 07:06:59 -0700
Subject: [bioontology-support] [BioPortal] Feedback from tsrsilva
Message-ID: <5b0c0d0358062_f473fa9fe09c24c7148@ncbo-prd-app-09.stanford.edu.mail>

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From vendetti at stanford.edu  Tue May 29 11:21:55 2018
From: vendetti at stanford.edu (Jennifer Leigh Vendetti)
Date: Tue, 29 May 2018 18:21:55 +0000
Subject: [bioontology-support] [BioPortal] Feedback from tsrsilva
In-Reply-To: <5b0c0d0358062_f473fa9fe09c24c7148@ncbo-prd-app-09.stanford.edu.mail>
References: <5b0c0d0358062_f473fa9fe09c24c7148@ncbo-prd-app-09.stanford.edu.mail>
Message-ID: <15E71D62-80D1-4434-864F-D5108D789B83@stanford.edu>

Hello Thiago,

There?s a known issue in BioPortal where the visualizations don?t work over HTTPS [1]. If you change the protocol identifier in the address bar of your browser from ?https? to ?http?, the visualizations work.

We?re using a 3rd party tool for these visualizations, and have not had the resources to address this issue as of yet.

Kind regards,
Jennifer

[1] https://github.com/ncbo/biomixer/issues/2



On May 28, 2018, at 7:06 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: tsrsilva

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

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FPATO%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fpurl.obolibrary.org<http://252Fpurl.obolibrary.org>%252Fobo%252FPATO_0002295

Feedback:

Greetings

My name is Thiago Silva, and my e-mail is tsranzanidasilva at gmail.com<mailto:tsranzanidasilva at gmail.com>.

I'm having this error when I try to visualize concepts, relationships between concepts and mappings in any ontology. The visualization tool doesn't load any concept and the visualization screen remains blank.

The steps to replicate the error are the following:
- Load any ontology (e.g. PATO).
- Choose a class.
- Choose the "Visualization" tab.

Thank you

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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 SPM9R at hscmail.mcc.virginia.edu  Wed May 30 13:21:31 2018
From: SPM9R at hscmail.mcc.virginia.edu (Mullane, Sean *HS)
Date: Wed, 30 May 2018 20:21:31 +0000
Subject: [bioontology-support] API limits
Message-ID: <cbc8c2b97d94407c80087e8860d105fd@HSTSEXCHB3.hscs.virginia.edu>

Hello,

Can you tell me what, if any, limits there are on the BioPortal API in terms of requests/sec or requests/day or other rate limits as applicable?

Thanks,
Sean Mullane
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From jgraybeal at stanford.edu  Thu May 31 21:27:06 2018
From: jgraybeal at stanford.edu (John Graybeal)
Date: Fri, 1 Jun 2018 04:27:06 +0000
Subject: [bioontology-support] API limits
In-Reply-To: <cbc8c2b97d94407c80087e8860d105fd@HSTSEXCHB3.hscs.virginia.edu>
References: <cbc8c2b97d94407c80087e8860d105fd@HSTSEXCHB3.hscs.virginia.edu>
Message-ID: <23C322EE-45CF-45F2-96C2-960E20A33AFA@stanford.edu>

Hi Sean, thanks for the question.

The default (and current) limit for requests is 15 requests/second. (This is set in https://github.com/ncbo/ontologies_api/blob/6bb08dab3d4ed01daa3a7f0fc34c36e702987e92/config/config.rb, and the code that handles it is https://github.com/ncbo/ontologies_api/blob/master/config/rack_attack.rb. The final settings can be overwritten in https://github.com/ncbo/bioportal_config/blob/master/ontologies_api/config/environments/production.rb but this one is not.)

Please be aware that there are queries that will overload the system when run at anything approaching 15 requests/second. Downloading large ontologies via API by walking their pages, getting ontology recommendations on large bodies of text, and searching within large branches are 3 examples of operations that can overload BioPortal.

We encourage anyone considering repeated requests to avoid parallelizing their requests, instead waiting for one to complete before issuing the next. (Considering that a number of other people may also be making expensive requests at the same time.)

John


On May 30, 2018, at 1:21 PM, Mullane, Sean *HS <SPM9R at hscmail.mcc.virginia.edu<mailto:SPM9R at hscmail.mcc.virginia.edu>> wrote:

Hello,

Can you tell me what, if any, limits there are on the BioPortal API in terms of requests/sec or requests/day or other rate limits as applicable?

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

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


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