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Subject svn commit: r838549 - in /websites/staging/ctakes/trunk/content: ./ ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.html
Date Thu, 15 Nov 2012 23:03:37 GMT
Author: buildbot
Date: Thu Nov 15 23:03:37 2012
New Revision: 838549

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 23:03:37 2012
@@ -1 +1 @@

Added: websites/staging/ctakes/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.html
--- websites/staging/ctakes/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.html
+++ websites/staging/ctakes/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.html
Thu Nov 15 23:03:37 2012
@@ -0,0 +1,206 @@
+<!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">
+<title>cTAKES 2.6 Drug Named Entity Recognition</title>
+<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-26-drug-named-entity-recognition-optional">cTAKES 2.6 - Drug Named
Entity Recognition (optional)</h1>
+<h2 id="overview-of-drug-named-entity-recognition-optional">Overview of Drug Named
Entity Recognition (optional)</h2>
+<p>The Drug NER (Drug Named Entity Recognition), also referred to as Medication
+Annotator, processes flat files or CDA (plain text wrapped with Clinical
+Document Architecture) documents to identify drug NEs and related attributes
+such as dosage, strength, route, etc. The annotator extracts data from both
+lists as well as narrative text.</p>
+<p><img alt="" src="/images/icons/emoticons/information.png" /></p>
+<p>Refer to <a href="">Chapter
1 in the cTAKES documentation on
+SourceForge</a>. Install the
+Binary Release, <a href="">Chapter
2 in the cTAKES documentation on
+<a href="">Compile from Source
(cTAKES documentation on
+SourceForge</a>, or
+refer to Section 2.2, "Compile in Eclipse" for detailed install and setup
+information pertaining to all the cTAKES components. Other 'optional'
+components need not be installed for Drug NER to work. For additional
+documentation pertaining to this pipeline see &lt;cTAKES_HOME&gt;/Drug NER/README.</p>
+<h2 id="analysis-engines-annotators">Analysis engines (annotators)</h2>
+<h3 id="drugaggregatecdaprocessorxml">DrugAggregateCDAProcessor.xml</h3>
+<p>The file cTAKESdesc/drugnerdesc/analysis_engine/DrugAggregateCDAProcessor.xml
+provides a working example of the Medication Annotator. This aggregate
+includes DrugLookupWindow, DrugMention Annotator and various annotators form
+cTAKES release all of whom can be found in projects at &lt;cTAKES_HOME&gt;/.</p>
+<p><img alt="" src="/images/icons/emoticons/information.png" /></p>
+<p>DrugAggregateCDAProcessor.xml is also provided to process CDA documents. The
+aggregate flow will contain the annotator version CdaCasInitializer.xml which
+will process the document as a Clinic Document Architecture (CDA) wrapped
+file. Additionally, the Sofa Mappings are enabled for the plaintext output
+view, which is intended to handle mapping the DTD properties to properties
+used by the pipeline (e.g. Patient and date meta-data).</p>
+<h3 id="druglookupwindowannotatorxml">DrugLookupWindowAnnotator.xml</h3>
+<p>This annotator is similar to
+cTAKESdesc/cdpdesc/analysis_engine/LookupWindowAnnotator.xml with
+customizations. The original LookupWindowAnnotator is an Aggregate which
+includes NP2LookupWindow and MaxLookupWindows annotators. DrugLookupWindow
+aggregate adds DrugCNP2LookupWindow annotator to the original set of
+annotators in the flow.</p>
+<p><strong>Parameters</strong><br />
+srcDrugObjClass &lt;String/Single-valued/Required&gt;</p>
+<p>(Default Value = 'edu.mayo.bmi.uima.chunker.type.NP')</p>
+<p>Identifies the Chunk type that needs to be used to generate</p>
+<p>destDrugObjClass &lt;String/Single-valued/Required&gt;</p>
+<p>(Default Value = 'edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation')</p>
+<p>Identifies the destination type that the Chunk type defined by srcDrugObjClass
+is the source of.</p>
+<p>dataDrugBindMap &lt;String/Multi-valued/Required&gt;</p>
+<p>(Default Values = 'getBegin|setBegin, getEnd|setEnd')</p>
+<p>Binds data from source to destination.</p>
+<p>sectionOverrideSet &lt;String/Multi-valued/Optional&gt;</p>
+<p>(Default Values = 'getBegin|setBegin, getEnd|setEnd')</p>
+<p>Identifies the sections which as a whole should be treated as a lookup window.</p>
+<h3 id="drugcnp2lookupwindowxml">DrugCNP2LookupWindow.xml</h3>
+<p>This annotator generates new DrugLookupWindow annotations for the sections
+whose seaction ids are specified in the parameter sectionOverrideSet. The
+default for out of the box configuration does not contain any section ids
+specified. Please read &lt;cTAKES_HOME&gt;/drugner/README for more information on
+recommended usage.</p>
+<h3 id="dictionarylookupannotatorxml">DictionaryLookupAnnotator.xml</h3>
+<p>This descriptor is similar to the one in cTAKESdesc/lookup/analysis_engine.
+Refer to <a href="/display/VKC/cTAKES+2.6+-+Dictionary+Lookup">Dictionary Lookup</a></p>
+<h3 id="drugmentionannotatorxml">DrugMentionAnnotator.xml</h3>
+<p>This annotator adds the ability to identify attributes of drug mentions such
+as Dosage, Frequency, Frequency Unit, Route and Strength from either plaintext
+or CDA documents. It also provides the ability to specify which sections of a
+note contain drugs in a list format versus drug mentions within the narrative
+of the note. This allows for customized processing done on different sections
+and generally improves the quality of the annotations. This project utilizes
+various cTAKES components and hence requires cTAKES to be installed prior to
+using this component.</p>
+<p><strong>Parameters</strong><br />
+medicationRelatedSection &lt;String/Single-valued/Optional&gt;</p>
+<p>(Defaule Value = 'SIMPLE_SEGMENT')</p>
+<p>IDs of sections generated by your Segment Annotator where drug mentions appear
+in a list format.</p>
+<h3 id="statusannotatorxml">StatusAnnotator.xml</h3>
+<p>This descriptor is similar to the one with the same name in
+cTAKESdesc/necontextdesc/analysis_engine. Refer to <a href="/pages/viewpage.action?pageId=75014306">NE
+Contexts</a> for a description.</p>
+<h3 id="negationannotatorxml">NegationAnnotator.xml</h3>
+<p>This descriptor is similar to the one with the same name in
+cTAKESdesc/necontextdesc/analysis_engine. Refer to <a href="/pages/viewpage.action?pageId=75014306">NE
+Contexts</a> for a description.</p>
+<h3 id="drugner_plaintext_cpexml">DrugNER_PlainText_CPE.xml</h3>
+<p>The file
+provides an XML-specification of a collection processing engine (CPE).</p>
+<p>To run the CPE</p>
+<li>Start UIMA CPE GUI.</li>
+<p><strong>java -cp</strong> <strong><em>&lt;classpath&gt;</em></strong>
+<li>Open this file.</li>
+<li>Set the parameters for the collection reader to point to a local collection of
files that you want part-of-speech tagged.</li>
+<li>Set the parameters for the DrugMentionAnnotator as appropriate for your environment.</li>
+<li>Set the output directory of the XCAS Writer CAS Consumer.</li>
+<p>The results of running the pipeline are written to the output directory as
+XCAS files. These files can be viewed in the CAS Visual Debugger.</p>
+<p>A sample plian text document has been provided for convenience that can be
+used as input document for the process described above.</p>
+<p><img alt="" src="/images/icons/emoticons/information.png" /></p>
+<p>The steps described under DrugNER_PlainText_CPE.xml can be used to process the
+sample document provided to validate Drug NER pipeline.</p>
+  </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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