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[bioontology-support] Owl issue

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Nov 10 11:26:48 PST 2015


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 stanford.edu<http://stanford.edu>).

Best,
Jennifer

[1] http://www.metadatacenter.org/



On Nov 10, 2015, at 6:15 AM, Brendan Wright <bwright at rsna.org<mailto:bwright at rsna.org>> 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 stanford.edu<mailto:ray.fergerson at stanford.edu>
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.






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