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Subject svn commit: r838493 - in /websites/staging/ctakes/trunk/content: ./ ctakes/2.6.0/component-use-guide-2.6.html
Date Thu, 15 Nov 2012 21:36:53 GMT
Author: buildbot
Date: Thu Nov 15 21:36:53 2012
New Revision: 838493

Staging update by buildbot for ctakes

    websites/staging/ctakes/trunk/content/   (props changed)

Propchange: websites/staging/ctakes/trunk/content/
--- cms:source-revision (original)
+++ cms:source-revision Thu Nov 15 21:36:53 2012
@@ -1 +1 @@

Added: websites/staging/ctakes/trunk/content/ctakes/2.6.0/component-use-guide-2.6.html
--- websites/staging/ctakes/trunk/content/ctakes/2.6.0/component-use-guide-2.6.html (added)
+++ websites/staging/ctakes/trunk/content/ctakes/2.6.0/component-use-guide-2.6.html Thu Nov
15 21:36:53 2012
@@ -0,0 +1,170 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "">
+    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
+ 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.
+<link href="/ctakes/css/ctakes.css" rel="stylesheet" type="text/css">
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+ <div class="banner">
+      <div id="bannerleft">
+		<a href=""><img src=""
alt="The Apache Software Foundation" border="0"/></a>
+	<br/>
+			<img alt="cTAKES logo" src="/ctakes/images/ctakes_logo.jpg" border="0"/>
+      </div>  
+    <div id="bannerright">	
+	      <img id="asf-logo" alt="Apache Incubator" src=""
+	  </div>
+ </div>  
+  <div id="clear"></div>
+  <div id="sidenav">
+    <h1 id="general">General</h1>
+<li><a href="/ctakes/index.html">About</a></li>
+<li><a href="/ctakes/gettingstarted.html">Getting Started</a></li>
+<li><a href="/ctakes/downloads.html">Downloads</a></li>
+<li><a href="/ctakes/glossary.html">Glossary</a></li>
+<h1 id="community">Community</h1>
+<li><a href="/ctakes/get-involved.html">Get Involved</a></li>
+<li><a href="">Bug Tracker</a></li>
+<li><a href="/ctakes/mailing-lists.html">Mailing Lists</a></li>
+<li><a href="/ctakes/people.html">People</a></li>
+<li><a href="">Incubator page</a></li>
+<li><a href="/ctakes/license.html">License</a></li>
+<li><a href="/ctakes/history.html">History</a></li>
+<li><a href="/ctakes/community-faqs.html">Community FAQs</a></li>
+<h1 id="users">Users</h1>
+<li><a href="/ctakes/userguide.html">User Guide</a></li>
+<li><a href="/ctakes/user-faqs.html">User FAQs</a></li>
+<h1 id="developers">Developers</h1>
+<li><a href="/ctakes/developerguide.html">Developer Guide</a></li>
+<li><a href="/ctakes/developer-faqs.html">Developer FAQs</a></li>
+<h1 id="ppmc">PPMC</h1>
+<li><a href="/ctakes/ppmc-faqs.html">PPMC FAQs</a></li>
+<li><a href="/ctakes/ctakes-release-guide.html">Release Guide</a> <br
+<h1 id="asf">ASF</h1>
+<li><a href="">Apache Software Foundation</a></li>
+<li><a href="">Thanks</a></li>
+<li><a href="">Become a Sponsor</a></li>
+  </div>
+  <div id="contenta">
+    <h1 id="ctakes-25-component-use-guide">cTAKES 2.5 Component Use Guide</h1>
+<p>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
+<p>cTAKES provides two variants of the original cTAKES pipeline which discovers
+Named Entities and assigns attributes to them:</p>
+<li>for processing plain text notes: cTAKESdesc/cdpdesc/analysis_engine/AggregatePlaintextProcessor.xml</li>
+<li>for processing Clinical Document Architecture (CDA) formatted notes: cTAKESdesc/cdpdesc/analysis_engine/AggregateCdaProcessor.xml</li>
+<p>Both variants use the same set of components except that the Document
+Preprocessor is not used for plain text.</p>
+<p><strong>Note</strong>: cTAKES is not designed to be thread safe and
has not been tested for thread
+<p>These are the components within cTAKES:</p>
+<li><a href="2.6.0/ctakes-2.6-Assertion">cTAKES 2.6 - Assertion</a></li>
+<li><a href="2.6.0/ctakes-2.6-Chunk-Adjuster">cTAKES 2.6 - Chunk Adjuster</a></li>
+<li><a href="2.6.0/ctakes-2.6-Chunker">cTAKES 2.6 - Chunker</a></li>
+<li><a href="2.6.0/ctakes-2.6-Clinical-Documents-Pipeline">cTAKES 2.6 - Clinical
Documents Pipeline</a></li>
+<li><a href="2.6.0/ctakes-2.6-Constituency-Parser">cTAKES 2.6 - Constituency
Parser (optional)</a></li>
+<li><a href="2.6.0/ctakes-2.6-Context-Dependent-Tokenizer">cTAKES 2.6 - Context
Dependent Tokenizer</a></li>
+<li><a href="2.6.0/ctakes-2.6-Core">cTAKES 2.6 - Core</a></li>
+<li><a href="2.6.0/ctakes-2.6-Dependency-Parser-and-Semantic-Role-Labeler">cTAKES
2.6 - Dependency Parser and Semantic Role Labeler</a></li>
+<li><a href="2.6.0/ctakes-2.6-Dictionary-Lookup">cTAKES 2.6 - Dictionary Lookup</a></li>
+<li><a href="2.6.0/ctakes-2.6-Document-Preprocessor">cTAKES 2.6 - Document Preprocessor</a></li>
+<li><a href="2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition">cTAKES 2.6 - Drug
Named Entity Recognition (optional)</a></li>
+<li><a href="2.6.0/ctakes-2.6-LVG">cTAKES 2.6 - LVG</a></li>
+<li><a href="2.6.0/ctakes-2.6-NE-Contexts">cTAKES 2.6 - NE Contexts (optional
as of 2.5)</a></li>
+<li><a href="2.6.0/ctakes-2.6-PAD-Term-Spotter">cTAKES 2.6 - PAD Term Spotter
+<li><a href="2.6.0/ctakes-2.6-POS-Tagger">cTAKES 2.6 - POS Tagger</a></li>
+<li><a href="2.6.0/ctakes-2.6-Side-Effect">cTAKES 2.6 - Side Effect (optional)</a></li>
+<li><a href="2.6.0/ctakes-2.6-Smoking-Status">cTAKES 2.6 - Smoking status (optional)</a></li>
+<h2 id="component-dependencies">Component Dependencies</h2>
+<p>This diagram shows which components rely on the output of another component.
+Following the diagram is a textual description.</p>
+<p><img alt="Diagram showing cTAKES dependencies" src="images/cTAKES_dependencies.jpg"
+<li>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.</li>
+<li>The output of Core is used by several components, including <ul>
+<li>Context Dependent Tokenizer</li>
+<li>Part of Speech Tagger</li>
+<li>The output of the Part of Speech Tagger is used by the Chunker</li>
+<li>The outputs of the Chunker and of LVG are used by Dictionary Lookup <ul>
+<li>LVG is not strictly required by the Dictionary Lookup but better results are achieved
if LVG is used.</li>
+<li>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.</li>
+<p>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.<br />
+Note that prior to cTAKES 2.5, the output of Dictionary Lookup was used by NE
+Contexts instead.</p>
+<p>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 </p>
+<li>PAD Term Spotter</li>
+<li>Clinical Documents Pipeline</li>
+<li>Drug NER</li>
+<li>If the Drug NER pipeline was used, the output of the Context Dependent Tokenizer
is used by the Drug NER component.</li>
+<li>If the Side Effect pipeline was used, the output of Drug NER is used by the Side
Effect component</li>
+<li>If the Constituency Parser or Coref-resolver pipeline was used, the output of Clinical
Documents Pipeline is used by the Constituency Parser</li>
+<li>If the Coref-resolver pipeline was used, the output of the Constituency Parser
is used by the Co-ref resolver.</li>
+<li>If the Smoking Status pipeline was used, the output of the Clinical Documents Pipeline
is used by the Smoking Status component.</li>
+  </div>
+ <div id="footera">
+    <div id="copyrighta">
+      <p>Copyright &#169; 2011 The Apache Software Foundation, Licensed under the
<a href="">Apache License, Version 2.0</a>.<br/>Apache
and the Apache feather logo are trademarks of The Apache Software Foundation.</p>
+    </div>
+ </div>

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