我想阅读来自 BioPortal 的 LNC/LOINC RDF/Turtle 版本的课程,可以在http://bioportal.bioontology.org/ontologies/LOINC/找到,最新提交。
我的解析代码很简单
OWLOntologyManager ontologyManager = OWLManager.createOWLOntologyManager();
ontologyManager.loadOntologyFromOntologyDocument(new File("LOINC.ttl"));
但是,我收到关于没有解析器能够解析本体的错误(由于字符限制而缩短):
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$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
15) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@13cda7c9
16) org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxOWLParser@1da6ee17
17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@253c1256
18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
19) org.coode.owlapi.obo12.parser.OWLOBO12Parser@c827db
20) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d
Detailed logs:
--------------------------------------------------------------------------------
SNIP
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Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
Stack trace:
org.openrdf.rio.UnsupportedRDFormatException: Did not recognise RDF format object Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:138)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:175)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:997)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:961)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:910)
uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:922)
de.julielab.bioportal.ontologies.apps.Test.main(Test.java:43)
Did not recognise RDF format object Turtle (mimeTypes=text/turtle, application/x-turtle; ext=ttl) org.openrdf.rio.Rio.lambda$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
Protégé 可以很好地加载文件,甚至可以直接使用 TurtleParser,如
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();
}
纵贯。但是,我依赖于 OWL-API。
我不认为有语法错误,因为 Protégé 可以打开文件而不会抱怨(日志中没有什么特别的)。我还尝试了文件的缩短版本,因为它相当大。使用大约一半的文件可以工作。但是我没有找到任何关于 OWL-API 长度限制的信息。然后再次。Protégé 可以打开它。
BioPortal 上的 MESH.ttl 和 PDQ.ttl 文件也是如此。但是,NCBITAXON.ttl 有效。
OWL-API版本为5.0.5,使用Protege 5.0beta for Mac成功打开文件。
我会非常感谢任何提示,因为现在我真的不知道问题出在哪里。
谢谢!