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[bioontology-support] [BioPortal] Feedback from afarhat

David Booth david at dbooth.org
Tue May 8 14:49:04 PDT 2018


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