You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@ctakes.apache.org by bu...@apache.org on 2012/11/16 00:03:37 UTC
svn commit: r838549 - in /websites/staging/ctakes/trunk/content: ./
ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.html
Author: buildbot
Date: Thu Nov 15 23:03:37 2012
New Revision: 838549
Log:
Staging update by buildbot for ctakes
Added:
websites/staging/ctakes/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.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 23:03:37 2012
@@ -1 +1 @@
-1410089
+1410092
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 (added)
+++ 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" "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>cTAKES 2.6 Drug Named Entity Recognition</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-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="http://ohnlp.sourceforge.net/cTAKES/#binary_install">Chapter 1 in the cTAKES documentation on
+SourceForge</a>. Install the
+Binary Release, <a href="http://ohnlp.sourceforge.net/cTAKES/#compile_from_source">Chapter 2 in the cTAKES documentation on
+SourceForge</a>.
+<a href="http://ohnlp.sourceforge.net/cTAKES/#compile_in_eclipse">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 <cTAKES_HOME>/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 <cTAKES_HOME>/.</p>
+<ul>
+<li>DrugMentionAnnotator</li>
+<li>DrugLookupWindowAnnotator</li>
+</ul>
+<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 <String/Single-valued/Required></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>DrugLookupWindowAnnotation.</p>
+<p>destDrugObjClass <String/Single-valued/Required></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 <String/Multi-valued/Required></p>
+<p>(Default Values = 'getBegin|setBegin, getEnd|setEnd')</p>
+<p>Binds data from source to destination.</p>
+<p>sectionOverrideSet <String/Multi-valued/Optional></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 <cTAKES_HOME>/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 <String/Single-valued/Optional></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
+cTAKESdesc/drugnerdesc/collection_processing_engine/DrugNER_PlainText_CPE.xml
+provides an XML-specification of a collection processing engine (CPE).</p>
+<p>To run the CPE</p>
+<ul>
+<li>Start UIMA CPE GUI.</li>
+</ul>
+<p><strong>java -cp</strong> <strong><em><classpath></em></strong> <strong>org.apache.uima.tools.cpm.CpmFrame</strong></p>
+<ul>
+<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>
+</ul>
+<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 © 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>
+