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obo-behavior / behavior-ontology

Neuro Behaviour Ontology: an ontology for human and animal behaviour processes and behaviour phenotypes
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Importing NBO into ECOCORE #43

Closed pbuttigieg closed 5 years ago

pbuttigieg commented 6 years ago

Dear NBO team,

We've created an ontology for core ecological entities (ECOCORE) over at this repo.

We'll need ethology semantics and will be importing NBO. We'll likely have some requests for NBO - are you able to address these in the near-term? If not, we'll create some classes in ECOCORE and mark them as "to be surrendered to NBO" or similar, in anticipation of new class creation here.

Looking forward to developing!

reality commented 6 years ago

Hi, please let us know what terms you'd like added, and we'll get to them within 1-2 weeks :)

pbuttigieg commented 5 years ago

Hi @reality,

We're active again at ECOCORE and have refreshed our imports for our release process. However, we're getting a parse error on NBO (output below).

Any insight? Is there some sort of encoding error? The other ontologies we import through our OSK Makefile seem to work fine.

2018-07-29 20:09:55,550 ERROR (CommandRunner:4068) could not parse:http://purl.obolibrary.org/obo/nbo.owl
org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://purl.obolibrary.org/obo/nbo.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:
1) RDFXMLParser
2) OWLXMLParser
3) OWLFunctionalSyntaxOWLParser
4) TurtleOntologyParser
5) KRSS2OWLParser
6) ManchesterOWLSyntaxOntologyParser
7) OBOFormatOWLAPIParser

Detailed logs:
--------------------------------------------------------------------------------
Parser: RDFXMLParser
org.xml.sax.SAXParseException; systemId: http://purl.obolibrary.org/obo/nbo.owl; lineNumber: 549314; columnNumber: 47; Premature end of file.

--------------------------------------------------------------------------------
Parser: OWLXMLParser
Attribute not found: IRI (Line 53)

--------------------------------------------------------------------------------
Parser: OWLFunctionalSyntaxOWLParser
Encountered " <ERROR> "< "" at line 1, column 1.
Was expecting:
    "Ontology" ...
     (Line 0)

--------------------------------------------------------------------------------
Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:

--------------------------------------------------------------------------------
Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" "<?xml version=\"1.0\"?> "" at line 1, column 1.
Was expecting:
    <EOF>

--------------------------------------------------------------------------------
Parser: ManchesterOWLSyntaxOntologyParser
Encountered '<?xml version="1.0"?>' at line 1 column 1.  Expected either 'Ontology:' or 'Prefix:' (Line 1)

--------------------------------------------------------------------------------
Parser: OBOFormatOWLAPIParser
LINENO: 1 - Could not find tag separator ':' in line.
LINE: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">

        at uk.ac.manchester.cs.owl.owlapi.ParsableOWLOntologyFactory.loadOWLOntology(ParsableOWLOntologyFactory.java:242)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:867)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:778)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:735)
        at owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:172)
        at owltools.io.ParserWrapper.parseOWL(ParserWrapper.java:159)
        at owltools.io.ParserWrapper.parse(ParserWrapper.java:141)
        at owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4056)
        at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:76)
        at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:68)
        at owltools.cli.CommandLineInterface.main(CommandLineInterface.java:12)
Makefile:42: recipe for target 'mirror/nbo.owl' failed
make: *** [mirror/nbo.owl] Error 1
pbuttigieg commented 5 years ago

Hi again,

Mysteriously, we were able to fix this by running the import target again. Not sure what happened or if it's really an issue.

reality commented 5 years ago

Looks like it was probably a temporary failure to download the ontology? Please re-open the issue if it continues to be a problem!