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[protege-owl] Adding deprecated anotation causes Error while parsing ontology created in Protege4.0.2 with OWLAPI when reopening ontology

Karin Michel karin.michel.ebsi at gmail.com
Wed Apr 21 06:12:03 PDT 2010


Yes, I tried in Protege 4.1 and it works. It not a owl problem but it seems
to be a conflict with skos which doesn't support deprecated sub-annotations
yet. As I read later. And since OWL2 is only partly supported in Protege
4.0.2 it might be the reason why there are errors in the parser.

In fact, I will create a separate ontology in pure owl2 to track deprecated
items outside my main thesaurus for which I need skos. This is the way I
think to manage things for now.

Thanks for your help.

Karin
On Tue, Apr 20, 2010 at 2:58 PM, Timothy Redmond <tredmond at stanford.edu>wrote:

>
> Have you tried in Protege 4.1?  If it fails there could you send the
> ontology (out of line if you are worried about intellectual property)?  It
> is less likely to be fixed in Protege 4.0 but I could take a peek at that
> also if you send the file.
>
> -Timothy
>
>
>
> On 04/20/2010 08:52 AM, Karin Michel wrote:
>
>   Hi,
>
> I'm using Protege4.0.2 because I need to use the SKOS plugin, everything
> was working well until I used the deprecated annotation available in
> built-in SKOS anotations
>
> Since, I can't load my file file I get the following errors :
> RDFXMLParser
> org.coode.owl.rdfxml.parser.OWLRDFXMLParserMalformedNodeException: missing
> owl:object triple.
> OWLFunctionalSyntaxOWLParser
> org.coode.owl.functionalparser.ParseException: Encountered "<" at line 1,
> column 1.
> Was expecting one of:
>     "Ontology" ...
>     "Namespace" ...
>      (Line 0)
> etc.
> I read following message which speaks of similar problem :
> https://mailman.stanford.edu/pipermail/protege-owl/2009-August/012010.html
> But it doesn't help me.
>
> I tried to uninstall/reunistall Protege 4.0.2. same problem. I can load
> without any problem another ontology or the same file from a backup but when
> I tried to continue editing it, I got the same error once I use the
> «deprecated» anotation field .
>
> Any idea of what the problem could be ?
>
> Thanks
>
> Karin
> Taxonomist at SNC-Lavalin
>
>
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