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From build...@apache.org
Subject svn commit: r840733 - in /websites/staging/ctakes/trunk/content: ./ ctakes/components.html ctakes/sitemap.html
Date Tue, 04 Dec 2012 15:54:29 GMT
Author: buildbot
Date: Tue Dec  4 15:54:28 2012
New Revision: 840733

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 Tue Dec  4 15:54:28 2012
@@ -1 +1 @@

Added: websites/staging/ctakes/trunk/content/ctakes/components.html
--- websites/staging/ctakes/trunk/content/ctakes/components.html (added)
+++ websites/staging/ctakes/trunk/content/ctakes/components.html Tue Dec  4 15:54:28 2012
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+    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>Apache cTAKES components</title>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+ <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"
+	  </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="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>
+<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>
+<li><a href="/ctakes/3.0.0/developer-guide-3.0.html">Source Code</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="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>
+  </div>
+  <div id="contenta">
+    <h1 id="apache-ctakes-components">Apache cTAKES Components</h1>
+<h3 id="sentence-boundary-detection">Sentence boundary detection</h3>
+<p>Apache OpenNLP technology with a model trained on manually annotated clinical data
+(see Savova et al, 2010)</p>
+<h3 id="tokenization">Tokenization</h3>
+<p>(rule-based) (see Savova et al, 2010)</p>
+<h3 id="morphologic-normalization-national-library-of-medicines-lexical-variant-generation-tool">Morphologic
normalization (National Library of Medicine's Lexical Variant Generation tool</h3>
+<h3 id="pos-tagging">POS tagging</h3>
+<p>Apache OpenNLP technology with a model trained on manually annotated clinical data)
(see Savova et al, 2010; upcoming 2013 publication</p>
+<h3 id="shallow-parsing">Shallow parsing</h3>
+<p>(Apache OpenNLP technology with a model trained on manually annotated clinical data)
(see Savova et al, 2010)</p>
+<h3 id="named-entity-recognition-see-savova-et-al-2010">Named Entity Recognition (see
Savova et al, 2010)</h3>
+<li>Dictionary mapping (lookup algorithm)</li>
+<li>Semantic typing is based on these UMLS semantic types: diseases/disorders, signs/symptoms,
anatomical sites, procedures, medications</li>
+<h3 id="assertion-module">Assertion module</h3>
+<p>Discovers negation, degree of certainty and the subject/experiencer of the clinical
event (upcoming 2013 publication)</p>
+<h3 id="dependency-parser">Dependency parser</h3>
+<p>Detects dependency relations between words (machine learning with a model trained
on manually annotated clinical data) (see Choi and Palmer, 2011a; Choi and Palmer, 2011b;
upcoming 2013 publication)</p>
+<h3 id="constituency-parser">Constituency parser</h3>
+<p>Apache OpenNLP technology with a model trained on manually annotated clinical data
(see Zheng et al, 2011)</p>
+<h3 id="semantic-role-labeler">Semantic Role Labeler</h3>
+<p>Assigns the predicate-argument structure of the sentence (who did what to whom when
and where) (see Choi and Palmer, 2011a; Choi and Palmer, 2011b; upcoming 2013 publication)</p>
+<h3 id="co-reference-resolver">Co-reference resolver</h3>
+<p>Resolves co-referring entities. (machine learning with a model trained on manually
annotated clinical data) (see Zheng et al, 2011)</p>
+<h3 id="relation-extractor">Relation extractor</h3>
+<p>discovers such attributes as the location and the severity of a clinical condition
(machine learning with a model trained on manually annotated clinical data) (upcoming 2013
+<h3 id="drug-profile-module">Drug Profile module</h3>
+<p>discovers drug-specific attributes such as dosage, duration, form, frequency, route,
strength (see Sohn et al, 2010; Savova et al, 2011)</p>
+<h3 id="smoking-status-classifier">Smoking status classifier</h3>
+<p>past smoker, current smoker, non-smoker, smoker, unknown (see Savova et al, 2008)</p>
+<h1 id="select-publications">Select Publications:</h1>
+<p>Choi J, Palmer M. Getting the most out of Transition-based Dependency Parsing. 46th
Annual Meeting of the Association for Computational Linguistics: Human Language Technologies,.
Portland, OR.: ACL-HLT 2011a , 2011.</p>
+<p>Choi J, Palmer M. Transition-based Semantic Role Labeling Using Predicate Argument
Clustering. RELMS 2011: Relational Models of Semantics, held in conjunction with ACL-HLT 2011.
Portland, OR, 2011b.</p>
+<p>Savova G, Olson J, Murphy S, Cafourek V, Couch F, Goetz M, Ingle J, Suman V, Chute
C and Weinshilboum R. 2011. The electronic medical record and drug response research: automated
discovery of drug treatment patterns for endocrine therapy of breast cancer. Journal of American
Medical Informatics Association.</p>
+<p>Savova GK, Masanz JJ, Ogren PV, Zheng J, Sohn S, Kipper-Schuler KC, and Chute CG.
Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component
evaluation and applications. Journal of the American Medical Informatics Association : JAMIA
+<p>Savova G, Ogren P, Duffy P, Buntrock J and Chute C. 2008. Mayo Clinic System for
patient smoking status classification. J Am Med Inform Assoc. 2008; 15(1):25-8. PMID: 17947622</p>
+<p>Sohn S, Murphy SP, Masanz JJ, Kocher JP, Savova GK. Classification of medication
status change in clinical narratives. AMIA Annual Symposium proceedings / AMIA Symposium.
AMIA Symposium 2010;2010:762-6.</p>
+<p>Zheng J, Chapman W, Miller T, Lin C, Crowley R and Savova G. 2012. A system for
coreference resolution for the clinical narrative. Journal of the American Medical Informatics
Association. doi:10.1136/amiajnl-2011-000599</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>

Modified: websites/staging/ctakes/trunk/content/ctakes/sitemap.html
--- websites/staging/ctakes/trunk/content/ctakes/sitemap.html (original)
+++ websites/staging/ctakes/trunk/content/ctakes/sitemap.html Tue Dec  4 15:54:28 2012
@@ -86,6 +86,7 @@
   <div id="contenta">
 <li><a href="/ctakes/community-faqs.html">Community FAQs</a></li>
+<li><a href="/ctakes/components.html">Apache cTAKES components</a></li>
 <li><a href="/ctakes/ctakes-release-guide.html">Release Guide</a></li>
 <li><a href="/ctakes/developer-faqs.html">Developer FAQs</a></li>
 <li><a href="/ctakes/developerguide.html">Apache cTAKES - Building and Running

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