我想阅读BioPortal的LNC / LOINC RDF / Turtle版本的类，可以在最新提交的http://bioportal.bioontology.org/ontologies/LOINC/找到。
我的解析代码就像
一样简单OWLOntologyManager ontologyManager = OWLManager.createOWLOntologyManager();
ontologyManager.loadOntologyFromOntologyDocument(new File("LOINC.ttl"));
但是，我得到一个错误，没有解析器能够解析本体（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可以正常加载文件，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();
}
贯穿始终。但是，我依赖OWL-API。
我认为没有语法错误，因为Protégé可以在不抱怨的情况下打开文件（日志中没有什么特别之处）。我也尝试过缩短版本的文件，因为它相当大。使用大约一半的文件工作。但我没有找到任何有关OWL-API长度限制的信息。然后再次。 Protégé可以打开它。
与BioPortal上的MESH.ttl和PDQ.ttl文件相同。然而，NCBITAXON.ttl可以工作。
OWL-API版本为5.0.5，Protege 5.0beta for Mac用于成功打开文件。
我非常感谢任何提示，因为现在我真的不知道这是什么问题。
谢谢！
答案 0 :(得分：0)
除了可用的内存和集合的大小之外，owl api没有明确的限制 - 这限制为整数可以假设的最大值。
此解析器的详细日志是什么？
13) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@5b43e173
这是owlapi本身的乌龟解析器，而不是Rio解析器。
另外，你使用的是哪个版本的owlapi和protégé？
EDiT：有了解析器的错误消息，我找到了失败的行：
<http://purl.bioontology.org/ontology/LNC/LRN2> """3'''-acetate; [cut]"""^^xsd:string ;
问题是三个引号：'''这些引号被解释为等同于"""，它是文字分隔符。较旧的OWLAPI在此中的规格表现不正确，但看起来这个文字格式不正确，因此它与较新的OWLAPI失败。 Protege Beta最多（我认为）版本15使用OWLAPI 3.5，它有一个较旧的解析器。
我不确定在解析器中是否可以纠正这个问题，或者在此阶段是否需要修复数据。我会在GitHub上提出一个问题。 https://github.com/owlcs/owlapi/issues/610
第二次编辑：这是一个错误;文字本应该被正确解析。请参阅the relevant Turtle specs。