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From build...@apache.org
Subject svn commit: r838524 - in /websites/staging/ctakes/trunk/content: ./ ctakes/2.6.0/ctakes-2.6-Assertion.html
Date Thu, 15 Nov 2012 22:26:12 GMT
Author: buildbot
Date: Thu Nov 15 22:26:12 2012
New Revision: 838524

Log:
Staging update by buildbot for ctakes

Added:
    websites/staging/ctakes/trunk/content/ctakes/2.6.0/ctakes-2.6-Assertion.html
Modified:
    websites/staging/ctakes/trunk/content/   (props changed)

Propchange: websites/staging/ctakes/trunk/content/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Thu Nov 15 22:26:12 2012
@@ -1 +1 @@
-1410056
+1410066

Added: websites/staging/ctakes/trunk/content/ctakes/2.6.0/ctakes-2.6-Assertion.html
==============================================================================
--- websites/staging/ctakes/trunk/content/ctakes/2.6.0/ctakes-2.6-Assertion.html (added)
+++ websites/staging/ctakes/trunk/content/ctakes/2.6.0/ctakes-2.6-Assertion.html Thu Nov 15
22:26:12 2012
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<!--
+ 
+    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.
+-->
+
+<link href="/ctakes/css/ctakes.css" rel="stylesheet" type="text/css">
+
+<title></title>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+
+</head>
+ 
+<body>
+ <div class="banner">
+      <div id="bannerleft">
+		<a href="http://www.apache.org/"><img src="http://www.apache.org/images/asf_logo_wide.gif"
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="http://incubator.apache.org/images/egg-logo.png"
border="0"/></a>			
+	  </div>
+ </div>  
+  <div id="clear"></div>
+
+
+  <div id="sidenav">
+    <h1 id="general">General</h1>
+<ul>
+<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>
+</ul>
+<h1 id="community">Community</h1>
+<ul>
+<li><a href="/ctakes/get-involved.html">Get Involved</a></li>
+<li><a href="https://issues.apache.org/jira/browse/ctakes">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="http://incubator.apache.org/projects/ctakes.html">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>
+</ul>
+<h1 id="users">Users</h1>
+<ul>
+<li><a href="/ctakes/userguide.html">User Guide</a></li>
+<li><a href="/ctakes/user-faqs.html">User FAQs</a></li>
+</ul>
+<h1 id="developers">Developers</h1>
+<ul>
+<li><a href="/ctakes/developerguide.html">Developer Guide</a></li>
+<li><a href="/ctakes/developer-faqs.html">Developer FAQs</a></li>
+</ul>
+<h1 id="ppmc">PPMC</h1>
+<ul>
+<li><a href="/ctakes/ppmc-faqs.html">PPMC FAQs</a></li>
+<li><a href="/ctakes/ctakes-release-guide.html">Release Guide</a> <br
/>
+</li>
+</ul>
+<h1 id="asf">ASF</h1>
+<ul>
+<li><a href="http://www.apache.org">Apache Software Foundation</a></li>
+<li><a href="http://www.apache.org/foundation/thanks.html">Thanks</a></li>
+<li><a href="http://www.apache.org/foundation/sponsorship.html">Become a Sponsor</a></li>
+</ul>
+  </div>
+  <div id="contenta">
+    <h1 id="ctakes-25-assertion">cTAKES 2.5 - Assertion</h1>
+<p><strong>Contents of this Page</strong></p>
+<ul>
+<li>Overview of Assertion</li>
+<li>Negation, uncertainty, and conditional attribute annotator</li>
+<li>Generic attribute annotator</li>
+<li>Subject attribute annotator</li>
+</ul>
+<h2 id="overview-of-assertion">Overview of Assertion</h2>
+<p>The assertion annotator provides a mechanism for examining and documenting the
+real-world implications for annotations in text.  For example, one might
+assume that a mention of "diabetes" in text implies that patient has diabetes.
+However, the assertion module will consider whether a named entity or event is
+<em>negated</em>, <em>uncertain</em>, or <em>conditional</em>.
 Additionally, the <em>subject</em> of the
+statement may be someone other than the patient (e.g., the patient's father,
+for "father has hx of diabetes"), or the use of a term might be <em>generic</em>
+(e.g., "gave pt a diabetes brochure").  Each of these attributes illustrate
+how the "assertion" value of a named entity might be marked.</p>
+<p><img alt="" src="/images/icons/emoticons/check.png" /></p>
+<p><strong>Tip</strong><br />
+</p>
+<p>The assertion module and the NE Contexts annotator have overlapping
+functionality, and only one should be used at a time.</p>
+<p>The default means of running the assertion annotator is to use an aggregate
+analysis engine that includes
+assertion/desc/AssertionMiniPipelineAnalysisEngine.xml. This is itself an
+aggregate analysis engine, consisting of the components listed below.</p>
+<h2 id="negation-uncertainty-and-conditional-attribute-annotator">Negation, uncertainty,
and conditional attribute annotator</h2>
+<p>The conceptConverterAnalysisEngine and the AssertionAnalysisEngine work
+together within the assertionMiniPipelineAnalysisEngine, and the pair of these
+two together may be included explicitly on their own.</p>
+<p>This pair of annotators depends on the following modules being run prior to
+invocation of this annotator:</p>
+<ul>
+<li>tokenizer</li>
+<li>sentence detector</li>
+<li>dictionary lookup</li>
+</ul>
+<p>We use the following types as input</p>
+<ul>
+<li>Sentence</li>
+<li>UmlsConcept</li>
+<li>OntologyConcept</li>
+<li>EntityMention</li>
+<li>EventMention</li>
+<li>BaseToken</li>
+</ul>
+<p>Then as output we modify attributes on EntityMention and EventMention.  The
+three attributes that we modify are:</p>
+<ol>
+<li>polarity (integer values of -1 and +1)</li>
+<li>uncertainty (integer value 0 or 1)</li>
+<li>conditional (a boolean value of true or false).</li>
+</ol>
+<h2 id="generic-attribute-annotator">Generic attribute annotator</h2>
+<p>The generic attribute annotator can be included individually from
+assertiondesc/GenericAttributeAnalysisEngine.xml or as part of the
+AssertionMiniPipelineAnalysisEngine.  It relies on the output of the
+tokenizer, sentence detector, dependency parser, and semantic role labeler to
+find whether each IdentifiedAnnotation is generic, then sets the
+IdentifiedAnnotation:generic feature accordingly.</p>
+<p>The possible values are specified by the prefix NE_GENERIC_ in
+edu.mayo.bmi.uima.core.type.constants.CONST.</p>
+<h2 id="subject-attribute-annotator">Subject attribute annotator</h2>
+<p>The subject attribute annotator can be included individually from
+assertiondesc/SubjectAttributeAnalysisEngine.xml or as part of the
+AssertionMiniPipelineAnalysisEngine.  It relies on the output of the
+tokenizer, sentence detector, dependency parser, and semantic role labeler to
+find the subject of each IdentifiedAnnotation, then sets the
+IdentifiedAnnotation:subject feature accordingly.The possible values are
+specified by the prefix ATTR_SUBJECT_ in
+edu.mayo.bmi.uima.core.type.constants.CONST.</p>
+  </div>
+ 
+ <div id="footera">
+    <div id="copyrighta">
+      <p>Copyright &#169; 2011 The Apache Software Foundation, Licensed under the
<a href="http://www.apache.org/licenses/LICENSE-2.0">Apache License, Version 2.0</a>.<br/>Apache
and the Apache feather logo are trademarks of The Apache Software Foundation.</p>
+    </div>
+ </div>
+ 
+</body>
+</html>
+



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