THIS IS A TEST INSTANCE. ALL YOUR CHANGES WILL BE LOST!!!!
Create custom pipelines to extract more information than is available through the Default Clinical Pipeline. Special Analysis Engines are in various cTAKES modules. Analysis Engines can be removed or added to pipelines to obtain desired results.
There are four methods available to create custom pipelines.
- XML Descriptor files are the original method used to create pipelines in Apache UIMA™. Though self-descriptive, they are verbose and error prone.
- uimaFIT™ enables creation of pipelines through Java code. This greatly simplifies unit testing and experimentation.
The PipelineBuilder class in ctakes-core is a facade for uimaFIT™ factories and objects.
- Piper files are a modern equivalent of the XML descriptor files. Piper files list basic commands and parameters in a flat format.
| Command | Parameter 1 | Parameters 2-n | Description |
|---|---|---|---|
| package | package path | Add to known packages. Shortens load and add specifications. | |
| load | Piper file path | Load external piper file. | |
| set | name=value | <name=value ...> | Add global parameter values. |
| cli | name=char | <name=char ...> | Add global parameter values based upon command-line character option values. |
| reader | CR name | <name=value ...> | Set the collection reader for pipeline input data. |
| readFiles | input directory | Set the collection reader for pipeline input data to the files in directory tree reader. | |
| add | AE or CC name | <name=value ...> | Add AE/CC to pipeline. |
| addDescription | AE or CC name | <value ...> | Add AE/CC to pipeline using its .createDescription method. |
| addLogged | AE or CC name | <name=value ...> | Add AE/CC to pipeline with Start/Finish logging. |
| addLast | AE or CC name | <name=value ...> | Add AE/CC to the end of pipeline. Useful if the pipeline is meant to be extended. |
| writeXmis | output directory | Add XMI writer to the pipeline. | |
| // or # or ! | comment text | Line Comment. |
Table 1. Standard Piper commands.
A complete pipeline can be created using a reader (or readFiles) and add commands.
Step-by-step guide
- Create an empty text file. The standard file extension for piper files is .piper .
- If applicable, start with a load of an available piper file. See Table 2 for standard piper files in cTAKES.
| Piper file | Module | Description | Contains |
|---|---|---|---|
| DefaultTokenizerPipeline.piper | core | Complete Tokenizer pipeline. | SimpleSegmentAnnotator SentenceDetector TokenizerAnnotatorPTB |
| ChunkerSubPipe.piper | chunker | Chunker partial pipeline. | Chunker ChunkAdjuster (NP,NP 1) ChunkAdjuster (NP,NP,NP 2) |
| AssertionSubPipe.piper | assertion | Entity attribute partial pipeline. | ClearNLPDependencyParserAE ClearNLPSemanticRoleLabelerAE ConceptConverterAnalysisEngine AssertionAnalysisEngineFit GenericAttributeAnalysisEngine SubjectAttributeAnalysisEngine |
| AttributeCleartkSubPipe.piper | assertion | Entity attribute partial pipeline. | ClearNLPDependencyParserAE ClearNLPSemanticRoleLabelerAE PolarityCleartkAnalysisEngine UncertaintyCleartkAnalysisEngine HistoryCleartkAnalysisEngine ConditionalCleartkAnalysisEngine GenericCleartkAnalysisEngine SubjectCleartkAnalysisEngine |
| DefaultFastPipeline.piper | clinical-pipeline | Complete Clinical pipeline. | DefaultTokenizerPipeline.piper ContextDependentTokenizerAnnotator POSTagger ChunkerSubPipe.piper DefaultJCasTermAnnotator AttributeCleartkSubPipe.piper |
Table 2. Available standard piper files in cTAKES.
Diagram 1. Piper files used in the cTAKES default Clinical Pipeline. Upper left is DefaultFastPipeline.piper
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