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dissys / sbol-owl3

The ontology for the SBOL v3 specification
Apache License 2.0
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Unable to load the latest sbol OWL rdf file into Protege 5.5.0 #3

Open rpgoldman opened 3 years ago

rpgoldman commented 3 years ago

When I try, I get this error:

  ERROR  12:24:46  An error occurred whilst extracting the Ontology Id from the imported ontology: {}
java.lang.NullPointerException: null
    at org.protege.editor.owl.model.repository.MasterOntologyIDExtractor.getOntologyId(MasterOntologyIDExtractor.java:27) ~[protege-editor-owl.jar:na]
    at org.protege.editor.owl.ui.ontology.imports.wizard.page.AnticipateOntologyIdPage.checkImport(AnticipateOntologyIdPage.java:109) [protege-editor-owl.jar:na]
    at org.protege.editor.owl.ui.ontology.imports.wizard.page.AnticipateOntologyIdPage.lambda$new$0(AnticipateOntologyIdPage.java:44) [protege-editor-owl.jar:na]
    at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_121]

I am not sure, but I was wondering if this is related to the ontology header, which reads:

<owl:Ontology rdf:about="http://sbols.org/v3"/>

But when I look at the OWL docs I see this:

The line

<owl:Ontology rdf:about="">

states that this block describes the current ontology. More precisely, it states the current base URI identifies an instance of the class owl:Ontology. It is recommended that the base URI be defined using an xml:base attribute in the element at the beginning of the document.

When I replace what's in the file with what the documentation recommends, Protege seems happier, although there are still some other issues.

/cc @jakebeal

goksel commented 3 years ago

I can't replicate this issue. I downloaded Protege 5.5.0 (Mac) and it seems to be ok. Could you please test it with other ontologies too? Please use this repo: https://github.com/SynBioDex/sbol-owl3