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[p4-feedback] Imports in Protege 4

Nick Drummond nick.drummond at cs.manchester.ac.uk
Mon Sep 22 06:27:33 PDT 2008


Hi,
The imports statement always contains the URI of the ontology (not its
location).
The strategy P4 uses to find imports is:

1) look into the directory that the ontology was loaded from
2) look into any ontology libraries that have been set up
3) look on the web at the URI of the ontology being imported

The ontology you import is located at [1] but is called [2]
So, p4 is failing to find any ontology at [2].

The easiest way to resolve this is:
a) if you are happy to use your own local version, copy the file at [1] to
the same folder as your main ontology OR
b) set up an ontology library (under the file menu) to point [2] to [1] OR
c) if you have control over the imported ontology get the people responsible
to move it to [2]

Nick

[1] http://ccdb.ucsd.edu/NIF/NIF-Cell4.owl
[2] http://ccdb.ucsd.edu/NIF/ <http://ccdb.ucsd.edu/NIF/NIF-Cell4.owl>

On Fri, Sep 19, 2008 at 7:44 PM, Sarah Maynard <smaynard at ncmir.ucsd.edu>wrote:

> I am having trouble successfully importing ontologies and opening
> ontologies that import other ontologies in Protege 4beta (build 110).
>
> The first problem I have is that saving a new ontology as OWL/XML doesn't
> seem to save the import correctly.  I have performed the following steps:
>
> I open Protege 4 beta (build 110) and create a new ontology.  I go to the
> "Active Ontology" tab and hit the "plus" on direct imports.  When I import
> an ontology from the web: http://ccdb.ucsd.edu/NIF/NIF-Cell4.owl the
> ontology loads successfully.  When I save the ontology as OWL/XML and reopen
> it, under the direct imports label in the Active Ontology tab, the imported
> ontology says "Not Loaded".  There are no obvious exceptions in the console
> output.  Looking at the text of the saved OWL/XML file, the import statement
> writes the URI of the imported owl file instead of the URL. I have pasted
> the full ontology below. It is also strange that Protege seems to write the
> import statement twice.
>
>
> The second problem I have is that saving a new ontology as RDF/XML doesn't
> seem to save the import correctly either.
>
> When I create a new ontology, I can import
> http://ccdb.ucsd.edu/NIF/NIF-Cell4.owl and the ontology loads fine.  But
> when I save the file as RDF/XML,and reopen the file up again, the ontology
> does not load the the import statement and again has the URI and not the
> URL.
>
> I am attaching both the OWL/XML and the RDF/XML versions of this ontology.
>
> What should I do about this issue?  Thank you.
>
> OWL/XML file:
> <?xml version="1.0"?>
>
> <!DOCTYPE Ontology [
>     <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
>     <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
>     <!ENTITY owl2xml "http://www.w3.org/2006/12/owl2-xml#" >
>     <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
>     <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
> ]>
>
> <Ontology xmlns="http://www.w3.org/2006/12/owl2-xml#"
>      xml:base="http://www.w3.org/2006/12/owl2-xml#"
>      xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
>      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>      xmlns:owl="http://www.w3.org/2002/07/owl#"
>      URI="
> http://www.semanticweb.org/ontologies/2008/8/Ontology1221770647156.owl">
>     <Imports
>         >http://ccdb.ucsd.edu/NIF/</Imports>
>     <Imports
>         >http://ccdb.ucsd.edu/NIF/</Imports>
> </Ontology>
>
> <!-- Generated by the OWL API (version 2.2.1.842)
> http://owlapi.sourceforge.net -->
>
> RDF/XML:
> <?xml version="1.0"?>
>
> <!DOCTYPE rdf:RDF [
>     <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
>     <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
>     <!ENTITY owl2xml "http://www.w3.org/2006/12/owl2-xml#" >
>     <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
>     <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
> ]>
>
> <rdf:RDF xmlns="
> http://www.semanticweb.org/ontologies/2008/8/Ontology1221771082921.owl#"
>      xml:base="
> http://www.semanticweb.org/ontologies/2008/8/Ontology1221771082921.owl"
>      xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
>      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
>      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>      xmlns:owl="http://www.w3.org/2002/07/owl#">
>     <owl:Ontology rdf:about="">
>         <owl:imports rdf:resource="http://ccdb.ucsd.edu/NIF/"/>
>     </owl:Ontology>
> </rdf:RDF>
>
> <!-- Generated by the OWL API (version 2.2.1.842)
> http://owlapi.sourceforge.net -->
>
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