svn commit: r1410451 - /incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Side-Effect.mdtext

[bl...@apache.org]

Author: bleeker
Date: Fri Nov 16 16:43:45 2012
New Revision: 1410451

URL: http://svn.apache.org/viewvc?rev=1410451&view=rev
Log:
CMS commit to ctakes by bleeker

Added:
    incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Side-Effect.mdtext   (with props)

Added: incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Side-Effect.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Side-Effect.mdtext?rev=1410451&view=auto
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+Title:     cTAKES 2.6 Side Effect
+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 - Side Effect
+
+## Overview of Side Effect
+
+The side effect extraction system extracts physician-asserted drug side
+effects from clinical notes. Alternatively the system can extract sentences
+that possibly contain both side effects and causative drugs, which cover
+higher number of side effect occurrences but needs human validation to extract
+individual causative drugs and side effects.
+
+## Analysis engines (Annotator) Descriptors
+
+### SideEffectAggregateTAE.xml
+
+An aggregated engine defines a pipeline used by side effect extraction on
+plain text with Mayo format section tags.
+
+### SideEffectAggregate_CDA_TAE.xml
+
+An aggregated engine defines a pipeline used by side effect extraction on CDA
+documents.
+
+### SideEffectSentenceAggregateTAE.xml
+
+An aggregated engine defines a pipeline used by side effect sentence
+extraction on plain text with Mayo format section tags.
+
+### SideEffectSentenceAggregate_CDA_TAE.xml
+
+An aggregated engine defines a pipeline used by side effect sentence
+extraction on CDA documents.
+
+### SideEffectAnnotator.xml
+
+This annotator uses pattern matching rules to identify side effect and
+causative drug.
+
+**Parameters**
+
+  * sectionToIgnore  
+sections to ignore for side effect extraction (a default one uses Mayo Clinic
+section convention)
+
+The following parameters are side effect indication keywords in pattern
+matching rules. Users may use their own keywords:
+
+  * hasPatternOfDrugCauseVerbPse
+  * hasPatternOfPseDueToDrug
+  * hasPatternOfDrugDueToPse
+  * hasPatternOfDiscontDrugBecausePse
+  * sideEffectWord
+  * hasPatternOfNotePseWithDrug
+  * hasPatternOfDrugMadePse
+  * hasPatternOfPseAfterDrug
+
+**Resources**  
+sideEffectDic: - A:: dictionary file that contains the drug and known side
+effect used for the dictionary lookup rule. The default file includes sample
+cases
+
+### SESentenceClassifierAnnotator.xml
+
+An annotator to extract sentences that contains side effect and causative
+drugs.
+
+**Parameters**  
+PathOfModel - A machine learning model of side effect sentence classification
+
+### PSESentenceAnnotator.xml
+
+This annotator extracts spans of sentences that contain potential side effects
+(i.e., signs/symptoms and diseases/disorders) and drugs and add them to the
+type PSESentence. Note that certain sections (in clinical notes) defined in
+parameter, SectionsToIgnore are ignored.
+
+**Parameters**  
+SectionToIgnore: sections not to be considered for this annotation (a default
+one uses Mayo Clinic section convention)
+
+### SESentenceFeatureAnnotator.xml
+
+This annotator extracts features for side effect sentence classification and
+add them to the type PSESentenceFeature.
+
+**Parameters**  
+MetaKeywordsFile:
+
+A file of keywords used for side effect sentence classification
+
+### LookupWindowAnnotator_sideEffect.xml
+
+A customized lookup window annotator for side effect extraction to properly
+catch potential side effect candidates.
+
+### DictionaryLookupAnnotator_sideEffect.xml
+
+A customized dictionary lookup annotator for side effect extraction.
+
+**Resources**  
+LookupDescriptorFile: a lookup descriptor file used for this project
+
+SnomedIndexReader: custom resource specifier
+
+RxnormIndexReader: custom resource specifier
+
+OrangeBookIndexReader: custom resource specifier
+
+CsvSEFile: a file for supplemental named entities. A user may use this file to
+add extra named entities that are not in a dictionary (the format should be
+first_word|full_named_entity|typeID(e.g., drug=1, disease/disorder=2,
+signs/symptoms=3, etc.). The default file includes sample cases.
+
+## CAS Consumers
+
+  * SideEffectCasConsumer  
+Write side effects and causative drugs to the file in the format of: documentN
+ame|sideEffect|beginOffset|endOffset|drug|beginOffset|endOffset|sentence
+
+  * SideEffectSentenceCasConsumer  
+Write side effects sentences to the file in the format of:
+document_name|side_effect_sentence|beginOffset|endOffset
+
+## Collection Processing Engine (CPE)
+
+### SideEffect_CDA_CPE.xml
+
+A CPE for both side effect and side effect sentence extraction on CDA
+documents.
+
+### SideEffectSentenceCPE.xml
+
+A CPE for both side effect and side effect sentence extraction on plain text
+with Mayo format section tags.
+
+**Resources**  
+libsvm-2.91.jar: The support vector machine (SVM) classification tool used to
+side effect sentence classification.
+
+## Type System - SideEffectTypeSystem.xml
+
+Types used in this project. Click JCasGen to generate necessary types.
+
+## How to
+
+  * Run side effect extraction  
+Use SideEffectCPE.xml for plain text with Mayo section tags or
+SideEffect_CDA_CPE.xml for CDA documents
+
+  * Run both side effect and side effect sentence extraction  
+Use SideEffectSentenceCPE.xml for plain text with Mayo section tags or
+SideEffectSentence_CDA_CPE.xml for CDA documents
+
+INFO Input file can be either plain text with Mayo format section tags or CDA
+documents (if you use a CDA format, take out SimpleSegmentWithTagsAnnotator in
+the TAE workflow)
+
+  * Customize side effect extraction rules  
+The method, getSideEffectsWithPrioritizedRule() in SideEffectAnnotator.java
+contains the list of rules used for side effect extraction. A user can modify
+existing rules or create new rules.
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