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analysis_engines
concept_mapper_pipelines
simple_uima_example
.gitignore
README.md

README.md

uima_sample

some basic, simple, uima pipelines and analysis engines cribbed from both UIMA and uimaFIT tutorials. Some requires code from here: http://sourceforge.net/projects/bionlp-uima/files/ccp-nlp/v3.1/

Contents:

  • simple_uima_example (standalone)

    • ProteinAnnotator.java
    • ProteinReporter.java
    • ProteinPipeline.java
    • ...and others. Start with these.
  • analysis_engines

    • AnalysisEngineTest.java
    • Debug_AE.java
    • LingPipeSentenceDetector_AE.java
    • LingPipeSentenceDetectorAeTest.java
    • ClassMentionX.java An extension of the generated ClassMention class with a static function that might have been a member of ClassMention or ClassMentionX if it weren't for the fact you can't do type conversion as easily in Java or that UIMA is in control of what objects get created in the JCas.
  • concept_mapper_pipelines

    • BaseUimaFitPipeline.java This one is the basic RoomNumberAnnotator code from the UIMA tutorial. It adds a pipeline, driven here by uimaFIT.:w RoomNumber.java RoomNumberAnnotator.java

    • ProteinPipeline.java This is basically a type system modification over the RoomNumberAnnotator. The maven pom includes steps to generate and include for compilation the type system classes. It adds usage of the CASDumpWriter from uimafit. Protein.java ProteinAnnotator.java

    • ParameterExamplePipeline.java (TBD) We need a subtle modification to show parameters uimaFIT-style.

    • ConceptMapperPipeline.java This set includes work from a number of people showing how to create a ConceptMapper Dictionary from an OBO file, then run CM in a pipeline to create RDF output. It uses xml files to describe the UIMA Analysis Engines. See: https://groups.google.com/forum/?fromgroups#!topic/uimafit-users/BiCdfJrwGBE

  • lucene_pipelines

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