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[bioontology-support] Using biomedical ontology feature in REDCap

O'Neill, Monica Monica.O'Neill at calvarymater.org.au
Sun Feb 11 16:20:58 PST 2018


Thank you John for getting back to me so quickly.

Our browser is indeed behind a firewall. My issue is that I cannot find the specific URL that my IT department has to whitelist. My IT department conducted many tests to monitor traffic and where exactly the firewall was blocking access, but couldn’t find anything. They suggested I get in contact with someone like yourself, who may know exactly what URL address redcap is trying to access when you first try to enable the bioontology feature in redcap.

Does that make more sense? Unfortunately I am not from an IT background so I can’t be more specific.

Much appreciated – I look forward to using your ontologies!

Monica O'Neill
Data Manager |Clinical Cancer Research Network
Email: monica.o'neill at calvarymater.org.au<mailto:monica.o'neill at calvarymater.org.au>
Please note I work a 7 day fortnight

Monday, Tuesday and Wednesday
Calvary Mater Newcastle
Due to hot-desking arrangements, please contact via email

Every second Friday
John Hunter Hospital
Tel 02 4923 6397 | Fax 02 4921 4274

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Tuesday, 6 February 2018 5:30 AM
To: O'Neill, Monica
Cc: support at bioontology.org; Alberto.varas at hnehealth.nsw.gov.au
Subject: Re: [bioontology-support] Using biomedical ontology feature in REDCap

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
Due to hot-desking arrangements, please contact via email

Thursday and Friday
John Hunter Hospital
Tel 02 4923 6397 | Fax 02 4921 4274

This message is intended for the addressee and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender, and are not necessarily the views of the Calvary Mater Newcastle or NSW Health. _______________________________________________
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