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[bioontology-support] [BioPortal] Feedback from afarhat

John Graybeal jgraybeal at stanford.edu
Tue May 8 16:31:49 PDT 2018


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