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[bioontology-support] Using biomedical ontology feature in REDCap

John Graybeal jgraybeal at stanford.edu
Thu Feb 15 18:12:04 PST 2018


It makes more sense, but the IT people should have all the information they need from the BioPortal side of things. If you follow the directions I previously gave from something outside the firewall (a browser on your cell phone, or your home machine) you should be able to verify that the API to BIoPortal works.

With that information, you can go to your IT department and say "This is the domain name I am trying to access from my here. It works on my home system. If you whitelist it, I should be able to access it from here."  They can look up the IP address from the domain name, and whitelist that, and you can verify that your browser now works for you. (If they can't figure out how to make it possible for your browser to access BioPortal, I am not sure how to help—no one has ever had that particular problem in my experience. I'll double-check with our DevOps person to make sure, but this is something that your IT department has to have the ability to address.)

That will not necessariy fix RedCAP. It seems that RedCAP is likely not able to access BioPortal at all, but I have no way to examine why that might be in your environment. You could try to contact the REDcap people to find out what *their* system actually accesses—I have no idea how the RedCAP code accesses BioPortal, and perhaps they are accessing another system first before accessing BioPortal, and that system needs to be whitelisted.  I am sorry I can't help you with that particular situation.

John


On Feb 11, 2018, at 4:20 PM, O'Neill, Monica <Monica.O'Neill at calvarymater.org.au<mailto:Monica.O'Neill at calvarymater.org.au>> wrote:

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<mailto:support at bioontology.org>; Alberto.varas at hnehealth.nsw.gov.au<mailto: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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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.

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