svn commit: r1410075 - /incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Clinical-Documents-Pipeline.mdtext

[bl...@apache.org]

Author: bleeker
Date: Thu Nov 15 22:37:44 2012
New Revision: 1410075

URL: http://svn.apache.org/viewvc?rev=1410075&view=rev
Log:
CMS commit to ctakes by bleeker

Added:
    incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Clinical-Documents-Pipeline.mdtext   (with props)

Added: incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Clinical-Documents-Pipeline.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Clinical-Documents-Pipeline.mdtext?rev=1410075&view=auto
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--- incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Clinical-Documents-Pipeline.mdtext (added)
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+Title:     cTAKES 2.6 Clinical Documents Pipeline
+Notice:    Licensed to the Apache Software Foundation (ASF) under one
+           or more contributor license agreements.  See the NOTICE file
+           distributed with this work for additional information
+           regarding copyright ownership.  The ASF licenses this file
+           to you under the Apache License, Version 2.0 (the
+           "License"); you may not use this file except in compliance
+           with the License.  You may obtain a copy of the License at
+           .
+             http://www.apache.org/licenses/LICENSE-2.0
+           .
+           Unless required by applicable law or agreed to in writing,
+           software distributed under the License is distributed on an
+           "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+           KIND, either express or implied.  See the License for the
+           specific language governing permissions and limitations
+           under the License.
+
+# cTAKES 2.6 - Clinical Documents Pipeline
+
+
+## Overview of Clinical Documents Pipeline
+
+This project is the top-level, main project for processing a clinical document
+through the entire cTAKES pipeline, including sentence detection, part of
+speech tagging [POS](http://ohnlp.sourceforge.net/cTAKES/#cd_pos_tagger),
+[chunking](http://ohnlp.sourceforge.net/cTAKES/#cd_chunker), named entity
+recognition, context detection, and negation detection. Refer to [context in
+the cTAKES documentation on
+SourceForge](http://ohnlp.sourceforge.net/cTAKES/#cd_necontexts).
+
+The pipeline can process two types of documents
+
+  * plain text files
+  * Clinical Document Architecture (CDA) XML files that conform to the DTD provided
+
+## Analysis engines (annotators)
+
+### AggregateCdaProcessor.xml for CDA documents conforming to the provided DTD
+
+The file desc/analysis_engine/AggregateCdaProcessor.xml is the aggregate
+analysis engine to use to run the entire pipeline, including the
+CdaCasInitialzer analysis engine, which reads CDA documents that conform to
+the DTD provided, and create Segment annotations based on the sections within
+the CDA document.
+
+**Parameters**
+
+**ChunkerCreatorClass**  
+the full class name of an implementation of the interface
+edu.mayo.bmi.uima.chunker.ChunkerCreator
+
+### AggregatePlaintextProcessor.xml for plain text documents
+
+The file desc/analysis_engine/AggregatePlaintextProcessor.xml is the aggregate
+analysis engine to use to run the entire pipeline, including the
+SimpleSegmentAnnotator analysis engine, which creates a Segment annotation
+that wraps the entire plain text document. Other annotators in the pipeline
+require at least one Segment annotation.
+
+**Parameters**  
+SegmentID the identifier or name to assign to the Segment annotation
+ChunkerCreatorClass the full class name of an implementation of the interface
+edu.mayo.bmi.uima.chunker.ChunkerCreator
+
+![](/images/icons/emoticons/information.png)
+
+The ChunkCreatorClass parameter of both annotators is set to
+edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator so that each phrase type gets
+its own type of annotation, rather than having all chunks be of type Chunk.
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