I found it's indeed a bug of OWL-API that was reported at the end of 2011. 
http://sourceforge.net/tracker/?func=detail&aid=3440117&group_id=90989&atid=595534
 


I think the easiest work around for me will be exporting everything to RDF/XML 
as long as the issue remains.




> 
> 
> Hello,
> 
> I have a set of ontologies heavily importing each other (generated by TBC). I 
> used to have them published as RDF/XML, and made them available via the 
> purl.org service at their URIs. Everything was fine, for example I was able 
> to load them with an ontology documentation tool 
> (http://www.essepuntato.it/lode/) and also services such as 
> http://owl.cs.manchester.ac.uk/converter/ were able to process the files (and 
> also dereference the imports successfully).
> 
> However, then I stored all files as turtle (with TBC) which is great because 
> it better supports version control (especially in combination with the sorted 
> printer). Now the services mentioned above  (they seem to use the OWLAPI 
> turtle parser) do not accept my files anymore. After doing some testing it 
> turned out that everything works fine as long as I do not use prefixes for 
> the ontology itself AND for the imports statements (Example below shows this 
> for using a prefix for the ontology resource only, but the same problem I 
> have with the imports). Are there any such restrictions on using prefixes I'm 
> not ware of, or is the OWL-API parser here wrong? 
> 
> Any help appreciated. I would not like to change everything back to  RDF/XML, 
> or should I prefer RDF/XML for publishing anyway for some reason I 
> overlooked? 
> 
> Best regards
> Jan
> 
> 
> 
> WORKS also in TTL:
> ######################################
> # Saved by TopBraid on Thu Jan 19 10:16:44 CET 2012
> # baseURI: http://purl.org/viso/test/
> 
> @prefix owl:     <http://www.w3.org/2002/07/owl#> .
> @prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> @prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
> @prefix test:    <http://purl.org/viso/test/> .
> @prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .
> 
> <http://purl.org/viso/test/>
>       rdf:type owl:Ontology ;
>       owl:versionInfo "Created with TopBraid Composer"^^xsd:string .
> 
> test:Thing_1
>       rdf:type owl:Class ;
>       rdfs:subClassOf owl:Thing .
> 
> 
> DOES NOT WORK in TTL
> ######################################
> # Saved by TopBraid on Thu Jan 19 10:16:44 CET 2012
> # baseURI: http://purl.org/viso/test/
> 
> @prefix owl:     <http://www.w3.org/2002/07/owl#> .
> @prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
> @prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
> @prefix test:    <http://purl.org/viso/test/> .
> @prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .
> 
> test:
>       rdf:type owl:Ontology ;
>       owl:versionInfo "Created with TopBraid Composer"^^xsd:string .
> 
> test:Thing_1
>       rdf:type owl:Class ;
>       rdfs:subClassOf owl:Thing .
> 
> 
> 
> 
> --
> Dipl. Medien-Inf. Jan Polowinski
> Research Assistant
> 
> Technische Universität Dresden
> Department of Computer Science
> Software- and Multimedia-Technology
> 01062 Dresden
> 
> Phone: +49 351 463 38608
> Mobil: +49 176 80158257
> E-Mail: [email protected]
> 

--
Dipl. Medien-Inf. Jan Polowinski
Research Assistant

Technische Universität Dresden
Department of Computer Science
Software- and Multimedia-Technology
01062 Dresden

Phone: +49 351 463 38608
Mobil: +49 176 80158257
E-Mail: [email protected]

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