OWL Parsing From EFO

问题:

I have been trying endlessly to parse the Experimental Factor Ontology (EFO) file, but I am not able to parse it. The file I have opens fine in Protege, but I cannot seem to get it to load in Java. I have looked at a few sets of example code, and I am copying them seemingly exactly, but I do not understand why parsing fails. Here is my code:

System.setProperty("entityExpansionLimit","100000000");
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
URI uri = URI.create("file:~/efo.owl");
IRI iri = IRI.create(uri);
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(iri);

And here are the errors I get:

Could not load ontology: Problem parsing 
file:/~/efo.owl
Could not parse ontology.  Either a suitable parser could not be found, or 
parsing failed.  See parser logs below for explanation.
The following parsers were tried:

Thank you, I know some similar posts have been made, but I have been unable to figure it out and am quite desperate! I can provide the stack trace if necessary, but it is quite long as there is a trace for each parser.

回答1:

File URI need to be absolute for OWLAPI to parse them, but as you have a local file you can just create a File instance and pass that to IRI.create().

Alternatively pass the File instance to OWLOntologyManager::loadOntologyFromOntologyDocument()

回答2:

There must be something wrong with the local, downloaded file. Loading the ontology directly from the ontology IRI worked.