svn commit: r1410028 - /incubator/ctakes/site/trunk/content/ctakes/2.6.0/component-use-guide-2.6.mdtext

[bl...@apache.org]

Author: bleeker
Date: Thu Nov 15 21:36:48 2012
New Revision: 1410028

URL: http://svn.apache.org/viewvc?rev=1410028&view=rev
Log:
CMS commit to ctakes by bleeker

Added:
    incubator/ctakes/site/trunk/content/ctakes/2.6.0/component-use-guide-2.6.mdtext   (with props)

Added: incubator/ctakes/site/trunk/content/ctakes/2.6.0/component-use-guide-2.6.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/2.6.0/component-use-guide-2.6.mdtext?rev=1410028&view=auto
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+Title:
+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 2.5 Component Use Guide
+
+cTAKES consists of a number of components. Each one has unique qualities and
+capabilities. Each component includes at least one annotator, some include
+more. You will want to assess each component's usefulness to you. UIMA
+provides the tooling for selecting which annotators are used together and the
+order in which annotators are run. Each section in this Guide covers one
+component.
+
+cTAKES provides two variants of the original cTAKES pipeline which discovers
+Named Entities and assigns attributes to them:
+
+  * for processing plain text notes: cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml
+  * for processing Clinical Document Architecture (CDA) formatted notes: cTAKESdesc/cdpdesc/analysis_engine/AggregateCdaProcessor.xml
+
+Both variants use the same set of components except that the Document
+Preprocessor is not used for plain text.
+
+**Note**: cTAKES is not designed to be thread safe and has not been tested for thread
+safety.
+
+These are the components within cTAKES:
+
+  * [cTAKES 2.6 - Assertion](2.6.0/ctakes-2.6-Assertion)
+  * [cTAKES 2.6 - Chunk Adjuster](2.6.0/ctakes-2.6-Chunk-Adjuster)
+  * [cTAKES 2.6 - Chunker](2.6.0/ctakes-2.6-Chunker)
+  * [cTAKES 2.6 - Clinical Documents Pipeline](2.6.0/ctakes-2.6-Clinical-Documents-Pipeline)
+  * [cTAKES 2.6 - Constituency Parser (optional)](2.6.0/ctakes-2.6-Constituency-Parser)
+  * [cTAKES 2.6 - Context Dependent Tokenizer](2.6.0/ctakes-2.6-Context-Dependent-Tokenizer)
+  * [cTAKES 2.6 - Core](2.6.0/ctakes-2.6-Core)
+  * [cTAKES 2.6 - Dependency Parser and Semantic Role Labeler](2.6.0/ctakes-2.6-Dependency-Parser-and-Semantic-Role-Labeler)
+  * [cTAKES 2.6 - Dictionary Lookup](2.6.0/ctakes-2.6-Dictionary-Lookup)
+  * [cTAKES 2.6 - Document Preprocessor](2.6.0/ctakes-2.6-Document-Preprocessor)
+  * [cTAKES 2.6 - Drug Named Entity Recognition (optional)](2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition)
+  * [cTAKES 2.6 - LVG](2.6.0/ctakes-2.6-LVG)
+  * [cTAKES 2.6 - NE Contexts (optional as of 2.5)](2.6.0/ctakes-2.6-NE-Contexts)
+  * [cTAKES 2.6 - PAD Term Spotter (optional)](2.6.0/ctakes-2.6-PAD-Term-Spotter)
+  * [cTAKES 2.6 - POS Tagger](2.6.0/ctakes-2.6-POS-Tagger)
+  * [cTAKES 2.6 - Side Effect (optional)](2.6.0/ctakes-2.6-Side-Effect)
+  * [cTAKES 2.6 - Smoking status (optional)](2.6.0/ctakes-2.6-Smoking-Status)
+
+##  Component Dependencies
+
+This diagram shows which components rely on the output of another component.
+Following the diagram is a textual description.
+
+![Diagram showing cTAKES dependencies](images/cTAKES_dependencies.jpg)
+
+  * If the input is a CDA document, the Document Preprocessor is needed at the start of the pipeline, and its output is used by Core.
+  * The output of Core is used by several components, including 
+    * Context Dependent Tokenizer
+    * Part of Speech Tagger
+    * LVG
+  * The output of the Part of Speech Tagger is used by the Chunker
+  * The outputs of the Chunker and of LVG are used by Dictionary Lookup 
+    * LVG is not strictly required by the Dictionary Lookup but better results are achieved if LVG is used.
+  * The output of Dictionary Lookup can be used without using LVG, the Semantic Role Labeler (which is part of the Dependency Parser) or the Assertion component, depending on which attributes are of interest.
+  * The output of Dictionary Lookup is typically used by LVG, the Semantic Role Labeler (which is part of the Dependency Parser) and the Assertion component.  
+Note that prior to cTAKES 2.5, the output of Dictionary Lookup was used by NE
+Contexts instead.
+
+  * Depending upon which pipeline was used, the output of the Assertion annotator (or the Dictionary Lookup directly) is then used by one of the following 
+    * PAD Term Spotter
+    * Clinical Documents Pipeline
+    * Drug NER
+  * If the Drug NER pipeline was used, the output of the Context Dependent Tokenizer is used by the Drug NER component.
+  * If the Side Effect pipeline was used, the output of Drug NER is used by the Side Effect component
+  * If the Constituency Parser or Coref-resolver pipeline was used, the output of Clinical Documents Pipeline is used by the Constituency Parser
+  * If the Coref-resolver pipeline was used, the output of the Constituency Parser is used by the Co-ref resolver.
+  * If the Smoking Status pipeline was used, the output of the Clinical Documents Pipeline is used by the Smoking Status component.
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