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From blee...@apache.org
Subject svn commit: r1410092 - /incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.mdtext
Date Thu, 15 Nov 2012 23:03:33 GMT
Author: bleeker
Date: Thu Nov 15 23:03:32 2012
New Revision: 1410092

URL: http://svn.apache.org/viewvc?rev=1410092&view=rev
Log:
CMS commit to ctakes by bleeker

Added:
    incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.mdtext
  (with props)

Added: incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.mdtext?rev=1410092&view=auto
==============================================================================
--- incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.mdtext
(added)
+++ incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Drug-Named-Entity-Recognition.mdtext
Thu Nov 15 23:03:32 2012
@@ -0,0 +1,170 @@
+Title:     cTAKES 2.6 Drug Named Entity Recognition
+Notice:    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.
+
+# cTAKES 2.6 - Drug Named Entity Recognition (optional)
+
+## Overview of Drug Named Entity Recognition (optional)
+
+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.
+
+![](/images/icons/emoticons/information.png)
+
+Refer to [Chapter 1 in the cTAKES documentation on
+SourceForge](http://ohnlp.sourceforge.net/cTAKES/#binary_install). Install the
+Binary Release, [Chapter 2 in the cTAKES documentation on
+SourceForge](http://ohnlp.sourceforge.net/cTAKES/#compile_from_source).
+[Compile from Source (cTAKES documentation on
+SourceForge](http://ohnlp.sourceforge.net/cTAKES/#compile_in_eclipse), 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.
+
+## Analysis engines (annotators)
+
+### DrugAggregateCDAProcessor.xml
+
+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>/.
+
+  * DrugMentionAnnotator
+  * DrugLookupWindowAnnotator
+
+![](/images/icons/emoticons/information.png)
+
+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).
+
+### DrugLookupWindowAnnotator.xml
+
+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.
+
+**Parameters**  
+srcDrugObjClass <String/Single-valued/Required>
+
+(Default Value = 'edu.mayo.bmi.uima.chunker.type.NP')
+
+Identifies the Chunk type that needs to be used to generate
+
+DrugLookupWindowAnnotation.
+
+destDrugObjClass <String/Single-valued/Required>
+
+(Default Value = 'edu.mayo.bmi.uima.lookup.type.DrugLookupWindowAnnotation')
+
+Identifies the destination type that the Chunk type defined by srcDrugObjClass
+is the source of.
+
+dataDrugBindMap <String/Multi-valued/Required>
+
+(Default Values = 'getBegin|setBegin, getEnd|setEnd')
+
+Binds data from source to destination.
+
+sectionOverrideSet <String/Multi-valued/Optional>
+
+(Default Values = 'getBegin|setBegin, getEnd|setEnd')
+
+Identifies the sections which as a whole should be treated as a lookup window.
+
+### DrugCNP2LookupWindow.xml
+
+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.
+
+### DictionaryLookupAnnotator.xml
+
+This descriptor is similar to the one in cTAKESdesc/lookup/analysis_engine.
+Refer to [Dictionary Lookup](/display/VKC/cTAKES+2.6+-+Dictionary+Lookup)
+
+### DrugMentionAnnotator.xml
+
+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.
+
+**Parameters**  
+medicationRelatedSection <String/Single-valued/Optional>
+
+(Defaule Value = 'SIMPLE_SEGMENT')
+
+IDs of sections generated by your Segment Annotator where drug mentions appear
+in a list format.
+
+### StatusAnnotator.xml
+
+This descriptor is similar to the one with the same name in
+cTAKESdesc/necontextdesc/analysis_engine. Refer to [NE
+Contexts](/pages/viewpage.action?pageId=75014306) for a description.
+
+### NegationAnnotator.xml
+
+This descriptor is similar to the one with the same name in
+cTAKESdesc/necontextdesc/analysis_engine. Refer to [NE
+Contexts](/pages/viewpage.action?pageId=75014306) for a description.
+
+### DrugNER_PlainText_CPE.xml
+
+The file
+cTAKESdesc/drugnerdesc/collection_processing_engine/DrugNER_PlainText_CPE.xml
+provides an XML-specification of a collection processing engine (CPE).
+
+To run the CPE
+
+  * Start UIMA CPE GUI.
+
+**java -cp** **_<classpath>_** **org.apache.uima.tools.cpm.CpmFrame**
+
+  * Open this file.
+  * Set the parameters for the collection reader to point to a local collection of files
that you want part-of-speech tagged.
+  * Set the parameters for the DrugMentionAnnotator as appropriate for your environment.
+  * Set the output directory of the XCAS Writer CAS Consumer.
+
+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.
+
+A sample plian text document has been provided for convenience that can be
+used as input document for the process described above.
+
+![](/images/icons/emoticons/information.png)
+
+The steps described under DrugNER_PlainText_CPE.xml can be used to process the
+sample document provided to validate Drug NER pipeline.
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