标签: ctakes

我试图弄清楚如何从Java运行临床文档管道.我有一套临床文件作为纯文本.我想解析这些文档并提取文档doc_ID中的列表,有频率为freq的CUI.我花了几天时间安装cTAKES并寻找解决方案.我将其缩小到ClinicalPipelineWithUmls.java,在那里进行测试并使用AnaylisisEngineDescription运行SimplePipeline.这是代码的一部分:

String documentText = "Text of document to test goes here, such as the following. No edema, some soreness, denies pain.";
InputStream inStream = InputStreamCollectionReader.convertToByteArrayInputStream(documentText);
CollectionReader collectionReader = InputStreamCollectionReader.getCollectionReader(inStream);
AnalysisEngineDescription pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createAnalysisEngineDescription(
            "desc/analysis_engine/AggregatePlaintextUMLSProcessor");
AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
            XWriter.class,
            XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
            AssertionConst.evalOutputDir,
            XWriter.PARAM_XML_SCHEME_NAME,
            XWriter.XMI,
            XWriter.PARAM_FILE_NAMER_CLASS_NAME,
            CtakesFileNamer.class.getName());
SimplePipeline.runPipeline(collectionReader, pipelineIncludingUmlsDictionaries, xWriter);
System.out.println("Done at " + new Date());

问题是找不到"InputStreamCollectionReader".我搜索它但到目前为止没有成功!你能给我一个提示或显示一些指示吗？谢谢你的帮助!

如何将新数据库添加到cTAKES管道以执行查找？如何指定要查找的列以及如何使用返回的匹配对文本进行注释？我已经浏览了DictionaryLookupAnnotatorDB.xml和LookupDesc_Db.xml文件.但是,我无法理解"lookupField","metaField","maxPermutationLevel"和"exclusionTags"等术语的含义.如果我添加新数据库,我需要正确配置此xml文件.请指导我这些问题.

我想知道如何从命令行使用Apache cTAKES.

例如:

• 我有一个文件note.txt,其中包含一些文字,如"患者血糖升高,但检查证实没有糖尿病.病人的父亲患有成人糖尿病."
• 我想使用提供的分析引擎 \apache-ctakes-3.2.2-bin\apache-ctakes-3.2.2\desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml

如何使用命令行获取分析引擎的输出(即注释)(即不使用UIMA CAS Visual Debugger或Collection Processing Engine等图形用户界面)？我更喜欢使用提供的JAR文件而不是编译代码.

问题很简单,但我无法在cTAKES的README或Confluence中找到这些信息 .

我在加载开源应用程序时遇到问题

我已经按照这些步骤

Perform a fresh checkout from SVN
1. Start IntelliJ IDEa.

2.In the "Quick Start" menu, select "Check out from Version Control".
This will display a drop-down box.

3.In the drop-down box, select "Subversion". 
This will open a "Checkout from Subversion" dialog.

4.In the "Checkout from Subversion" dialog, click the "+" button in the top left to add a new Repository. 
This will open a "New Repository Location" dialog.

5.In the "New Repository Location" dialog, enter the svn checkout …