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[bioontology-support] [BioPortal] Feedback from afarhat

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue May 8 10:38:09 PDT 2018


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

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