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[bioontology-support] Owl issue

Jennifer Leigh Vendetti vendetti at
Tue Nov 10 11:29:23 PST 2015

Sorry - I just noticed that you already included the source files below, which answers a few of the questions I posed to you just now.  Perhaps I need a second cup of coffee.  :)

I’m going to try to meet up with a member of the Protege team and see if we can get the conversion to work and load the OWL file into the Protege application w/out getting any parsing errors.  If we can do that, I think it would also work in BioPortal.

I’ll report back as soon as I have a chance to get to this.


On Nov 10, 2015, at 11:26 AM, Jennifer Vendetti <vendetti at<mailto:vendetti at>> wrote:

Hi Brendan,

Firstly I wanted to mention that Ray is no longer at Stanford.  John Graybeal is the new Technical Program Manager for the BioPortal team (and also the CEDAR project at BMIR [1]).

Secondly, we did notice that the latest two versions of RADLEX failed to parse.  Both the BioPortal software and the Protege Desktop application report the same error:

"org.xml.sax.SAXParseException; systemId: file:radlex.owl; lineNumber: 10898; columnNumber: 35; XML document structures must start and end within the same entity.”

I noticed in your email below you describe a process that sounds to me like this ontology is developed in an older version of Protege?  (PPRJ files were abandoned after the Protege 3.x series).  Is this a Frames ontology that you are converting to OWL?  Are you using Protege to do this?

Thanks in advance for providing us with these additional details.  It would also be helpful if you could send me all of the files that you mention below.  You can post them to the support list, or if you prefer, you can send them directly to me (vendetti at<>).



On Nov 10, 2015, at 6:15 AM, Brendan Wright <bwright at<mailto:bwright at>> wrote:

Hi I am looking for some help with loading my owl file into bioportal radlex as outlined below.  I tried emailing Ray but haven’t heard back so any help you can give me would be much appreciated.  Please feel free to email myself or Robert Boden if you have questions.

From: Brendan Wright
Sent: Thursday, November 05, 2015 1:14 PM
To: ray.fergerson at<mailto:ray.fergerson at>
Subject: Owl issue

Hi Ray we are trying to load a new version of radlex into bioportal but are having an issue with the owl file.
Attached is a zip of the files.
in step1 is the src pprj files, they work fine.
In step2 you will see the flattened pprj files they seems to work fine as well.
In step three we convert to owl file but the file will not open in Protégé without an error. I’m unsure as to how to proceed.
It errors as well when we tried to load it into bioportal.

Any advice on how we can test /debug these issues w/o your help would be much appreciated.<>
Brendan Wright
Web Developer Tier 2
IT: Development

Oak Brook 2nd Floor North 229F

bwright at<mailto:bwright at>

Radiological Society of North America
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