GraphDB Workbench 无法从 Protégé 加载 .owl ontology 文件

Question

我用 Protege 创建了一个 ontology，保存为 .owl 文件。

当我尝试通过 Workbench Import -> RDF -> 将其加载到 GraphDB (8.9.0) 时上传RDF文件（支持的RDF格式为.ttl .rdf .rj .n3 .nt .nq .trig .trix .brf .owl .jsonld，以及它们的.gz版本和. zip 存档） 我收到错误消息：

RDF Parse Error: Content is not allowed in prolog. [line 1, column 1].

完整日志：

01:00:37.877 [import-task-Accounting-1] ERROR o.e.r.rio.helpers.ParseErrorLogger - [Rio fatal] Content is not allowed in prolog. (1, 1)
01:00:37.879 [import-task-Accounting-1] ERROR c.o.f.impex.FileImportRunnableTask - RDF Parse Error 
org.eclipse.rdf4j.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1]
    at org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:442)
    at org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.reportFatalError(AbstractRDFParser.java:783)
    at org.eclipse.rdf4j.rio.rdfxml.RDFXMLParser.reportFatalError(RDFXMLParser.java:1176)
    at org.eclipse.rdf4j.rio.rdfxml.RDFXMLParser.fatalError(RDFXMLParser.java:1315)
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:180)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400)
    at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327)
    at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1472)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:994)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
    at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:841)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:770)
    at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
    at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
    at org.eclipse.rdf4j.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:265)
    at org.eclipse.rdf4j.rio.rdfxml.RDFXMLParser.parse(RDFXMLParser.java:207)
    at org.eclipse.rdf4j.repository.util.RDFLoader.loadInputStreamOrReader(RDFLoader.java:286)
    at org.eclipse.rdf4j.repository.util.RDFLoader.load(RDFLoader.java:197)
    at org.eclipse.rdf4j.repository.base.AbstractRepositoryConnection.add(AbstractRepositoryConnection.java:329)
    at com.ontotext.trree.monitorRepository.MonitorRepositoryConnection.add(MonitorRepositoryConnection.java:177)
    at com.ontotext.trree.parallel.ParallelRDFLoader.add(ParallelRDFLoader.java:125)
    at com.ontotext.trree.parallel.ParallelRDFLoader.add(ParallelRDFLoader.java:54)
    at com.ontotext.forest.impex.ParallelAwareImporter.lambda$add(ParallelAwareImporter.java:107)
    at com.ontotext.forest.impex.ParallelAwareImporter.wrapInBeginCommit(ParallelAwareImporter.java:128)
    at com.ontotext.forest.impex.ParallelAwareImporter.add(ParallelAwareImporter.java:89)
    at com.ontotext.forest.impex.FileImportRunnableTask.load(FileImportRunnableTask.java:36)
    at com.ontotext.forest.impex.ImportRunnableTask.run(ImportRunnableTask.java:82)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: org.xml.sax.SAXParseException: Content is not allowed in prolog.
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:203)
    at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:177)
    ... 29 common frames omitted

任何 help/advice/hint 将不胜感激。

Answer 1

我的猜测是文件以 BOM 字符 U+FEFF 开头：第 1 行错误，列 1.This 是零宽度 space 有时用于将文件标记为在一些 Unicode 表示，UTF-8、UTF-16LE、UTF-16BE。你能分享文件的第一行吗？您可以尝试删除文件开头的标签，或者使用 Encoding(Tab) > Encode in UTF-8:selected.

将文件保存在 Notepad++ 中

Answer 2

问题是 GraphDB 假定 .owl 文件是用 XML 编写的，因此尝试这样解析它们。但是，正如OWL Conformance (2.2 Tool Conformance)中提到的：

A conformant OWL 2 tool may also accept ontology documents using other serializations, for example Turtle ...

事实上，OWL ontology 定义可以有 5 种不同的有效格式：函数式、RDF/XML、OWL/XML、Turtle 和曼彻斯特语法。 Protégé 决定对其 .owl 文件使用 Turtle 语法，因此 GraphDB 在尝试将它们解析为 XML.

时会出错

解决方法：只需将文件扩展名从 .owl 更改为 .ttl，GraphDB 将很乐意加载它。

GraphDB Workbench 无法从 Protégé 加载 .owl ontology 文件

GraphDB Workbench fails to load .owl ontology file from Protégé

ontology

protege

graphdb