无法用OWL API解析某些turtle格式文件

Question

我想从BioPortal阅读LNC/LOINC RDF/TURTLE版本的类，可以在http://BioPortal.bioontology.org/ontologies/LOINC/,最新提交。

我的解析代码就像

OWLOntologyManager ontologyManager = OWLManager.createOWLOntologyManager();
ontologyManager.loadOntologyFromOntologyDocument(new File("LOINC.ttl"));

   Exception in thread "main" org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/home/faessler/Coding/workspace/bioportal-ontology-tools/LOINC.ttl
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) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@3b9d6699
2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@2ad3a1bb
3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@120f38e6
4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@3ad394e6
6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
13) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@5b43e173
14) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
15) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@13cda7c9
16) org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxOWLParser@1da6ee17
17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@253c1256
18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
19) org.coode.owlapi.obo12.parser.OWLOBO12Parser@c827db
20) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d


Detailed logs:
--------------------------------------------------------------------------------

SNIP

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
    Stack trace:
org.openrdf.rio.UnsupportedRDFormatException: Did not recognise RDF format object Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl)        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:138)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:175)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:997)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:961)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:910)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:922)
        de.julielab.bioportal.ontologies.apps.Test.main(Test.java:43)
Did not recognise RDF format object Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl)        org.openrdf.rio.Rio.html" target="_blank">lambda$unsupportedFormat$0(Rio.java:630)
        java.util.Optional.orElseThrow(Optional.java:290)
        org.openrdf.rio.Rio.createParser(Rio.java:119)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:173)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:125)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:175)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:997)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:961)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:910)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:922)


--------------------------------------------------------------------------------

Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@5b43e173
    Stack trace:
org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered " <PN_CHARS> "- "" at line 3635316, column 64.
Was expecting:
    "." ...
            org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:60)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:175)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:997)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:961)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:910)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:922)
        de.julielab.bioportal.ontologies.apps.Test.main(Test.java:43)
Encountered " <PN_CHARS> "- "" at line 3635316, column 64.
Was expecting:
    "." ...
            org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.generateParseException(TurtleParser.java:1960)
        org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.jj_consume_token(TurtleParser.java:1829)
        org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseDocument(TurtleParser.java:111)
        org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:56)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:175)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:997)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:961)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:910)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:922)
        de.julielab.bioportal.ontologies.apps.Test.main(Test.java:43)



SNIP

    java.net.URL documentUrl = new File("LOINC.ttl").toURI().toURL();
    InputStream inputStream = documentUrl.openStream();
    RDFParser rdfParser = new TurtleParser();
    java.util.ArrayList myList = new ArrayList();
    StatementCollector collector = new StatementCollector(myList);
    rdfParser.setRDFHandler(collector);
    try {
        rdfParser.parse(inputStream, documentUrl.toString());
    } catch (IOException | RDFParseException | RDFHandlerException e) {
        e.printStackTrace();
    }

我不认为有语法错误，因为Protégé可以在没有抱怨的情况下打开文件（在日志中没有什么特别的地方）。我还尝试了缩短版本的文件，因为它是相当大的。使用大约一半的文件是有效的。但是我没有找到关于OWL-API长度限制的任何东西。又一次。门徒可以打开它。

Bioportal上的mesh.ttl和pdq.ttl文件也是如此。但是，ncbitaxon.ttl起作用。

OWL-API版本为5.0.5，使用Protege5.0beta for Mac成功打开该文件。

谢谢！

Answer 1

在owl api中没有明确的限制，除了可用内存和集合的大小--这被限制为整数可以假设的最大值。

这个解析器的详细日志是什么？

13)org.semanticweb.owlapi.rdf.turtle.parser.turtleontologyparser@5b43e173

还有，你使用的是owlapi和Protégé的哪个版本？

编辑：使用解析器的错误消息，我能够找到失败的行：

“”“3”“-乙酸酯；[cut]”“”^^xsd:string；

第二次编辑：这是一个bug；应该已正确分析了文字。请参阅相关的海龟规格。