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[bioontology-support] Using biomedical ontology feature in REDCap

John Graybeal jgraybeal at stanford.edu
Mon Feb 5 10:30:08 PST 2018


Hi Monica,

Thanks for doing most of this investigation for us! I will confirm what you have already found, but can give you one more test you can perform.

If you look at the URL for any query from the http://data.bioontology.org/documentation, for example something like http://data.bioontology.org/search?q=melanoma, you can try it in your browser. Probably it won't work, assuming you haven't entered your API key in a query before. To do so, complete the query like so:
 http://data.bioontology.org/search?q=melanoma&apikey=YOUR_API_KEY_HERE

If that still doesn't work, your browser is probably also behind some firewall that has to be opened to allow access to BioPortal. But if it *does* work, then you have confirmed your API key works, and now you have to get the firewall opened that is in front of the REDCap machine.)

This step of 'whitelisting' the BioPortal site is something that your IT department has to do—we can not help with that, sorry. Please have your IT person contact us if he or she is having some difficulty.

John



On Feb 4, 2018, at 6:51 PM, O'Neill, Monica <Monica.O'Neill at calvarymater.org.au<mailto:Monica.O'Neill at calvarymater.org.au>> wrote:

Hello,

I am an administrator of REDCap for my institution. I am very keen to employ the biomedical ontology functionality within REDCap for use in our clinical trials, but I am having some technical issues.

When I copy-paste the API token from my account with NCBO (username: monicaoneill), REDCap tells me this is not a valid token. I searched the online REDCap community and found others experienced the same error (see image below), which turned out to be because of security settings at their institution. I contacted Yelena Fridgant to ask for more details but she was unable to assist any further other than remembering she asked her IT Department to “whitelist” the website.

I have been in contact with Alberto Varas (cc’d) from my institutions IT department, who made every attempt to figure out which URL specifically needed “whitelisting”. Are you able to help in this regard? I would be happy to provide you with more information if you need it, just let Alberto and myself know.

<image001.png>

Many thanks in advance,
Monica O'Neill
Data Manager |Clinical Cancer Research Network
monica.o'neill at calvarymater.org.au<mailto:monica.o'neill at calvarymater.org.au>

Monday, Tuesday and Wednesday
Calvary Mater Newcastle
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