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[bioontology-support] [BioPortal] Feedback from chen.yang at

Chen Yang Chen.Yang at
Fri Aug 24 07:49:03 PDT 2018

Hi Michael,
I modified my ontology and uploaded again (e.g. 00073 --> ne00073). It seemed ok after uploading on 22/08, however, it is finally marked as error rdf today.

From: Michael Dorf [mailto:mdorf at]
Sent: 21 August 2018 23:44
To: support at
Cc: Chen Yang <Chen.Yang at>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at

Hi Chen,

I’ve gotten some more insight on why your ontology isn’t processing correctly in BioPortal. is both an Annotation and a Class in the NEST OWL file. (You can see this in Protege, if you know the little purple things are Annotations and the little orange circles are Classes.) When an OWL file is converted to RDF/XML, it is necessary to convert the properties (which Annotations are) to QNames. The QName is the last fragment of the URI, so in the case above, the QName is evaluated to 00057.
Unfortunately, in addition to QNames not being able to include colons (#16<> problem), QNames also can not start with a digit. So the resulting transformation produces an RDF/XML which can not be parsed.
The full QNames spec can be found here:

You can reproduce this issue if you open NEST.owl in Protege and then attempt to save it as RDF/XML Syntax. The resulting error in Protege log is:

2018-08-21 14:38:03.927 [AWT-EventQueue-0] ERROR OWLEditorKit    An error occurred whilst saving the
at java.util.concurrent.ThreadPoolExecutor$ ~[na:1.8.0_40]
at ~[na:1.8.0_40]
Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):

The easiest solution to this issue is to add a letter in front of the QName for the annotations.

Hope this helped clarify the issue.



On Aug 20, 2018, at 3:45 PM, Michael Dorf <mdorf at<mailto:mdorf at>> wrote:

Hi Chen,

Thanks for contacting us. I’ve looked at your ontology, and it did fail to process in BioPortal. It seems that the underlying issue is:

Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):

I’ve created an issue in our Github tracker that details our progress on working to resolve it:

There is a similar issue in our system with an identical error, but I haven’t found the exact solution in the tracker history.

I need to consult on this further with my colleagues, one of which, unfortunately, is on vacation until August 30th. I’ll try to keep you posted on what further I find out.



Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at<mailto:mdorf at>
O: 650-723-0357
M: 650-995-4374

On Aug 20, 2018, at 3:13 AM, support at<mailto:support at> wrote:

Name: chen.yang at<mailto:chen.yang at>
Email: chen.yang at<mailto:chen.yang at>

I submitted the newest version of NEST ontology. I tested it before uploading, no error was detected. However, it is marked as error rdf in BioPortal.

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