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From blee...@apache.org
Subject svn commit: r1410066 - /incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Assertion.mdtext
Date Thu, 15 Nov 2012 22:26:08 GMT
Author: bleeker
Date: Thu Nov 15 22:26:07 2012
New Revision: 1410066

URL: http://svn.apache.org/viewvc?rev=1410066&view=rev
Log:
CMS commit to ctakes by bleeker

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

Added: incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Assertion.mdtext
URL: http://svn.apache.org/viewvc/incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Assertion.mdtext?rev=1410066&view=auto
==============================================================================
--- incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Assertion.mdtext (added)
+++ incubator/ctakes/site/trunk/content/ctakes/2.6.0/ctakes-2.6-Assertion.mdtext Thu Nov 15
22:26:07 2012
@@ -0,0 +1,102 @@
+Title:
+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 2.5 - Assertion
+
+**Contents of this Page**
+
+  * Overview of Assertion
+  * Negation, uncertainty, and conditional attribute annotator
+  * Generic attribute annotator
+  * Subject attribute annotator
+
+## Overview of Assertion
+
+The assertion annotator provides a mechanism for examining and documenting the
+real-world implications for annotations in text.  For example, one might
+assume that a mention of "diabetes" in text implies that patient has diabetes.
+However, the assertion module will consider whether a named entity or event is
+_negated_, _uncertain_, or _conditional_.  Additionally, the _subject_ of the
+statement may be someone other than the patient (e.g., the patient's father,
+for "father has hx of diabetes"), or the use of a term might be _generic_
+(e.g., "gave pt a diabetes brochure").  Each of these attributes illustrate
+how the "assertion" value of a named entity might be marked.
+
+![](/images/icons/emoticons/check.png)
+
+**Tip**  
+
+The assertion module and the NE Contexts annotator have overlapping
+functionality, and only one should be used at a time.
+
+The default means of running the assertion annotator is to use an aggregate
+analysis engine that includes
+assertion/desc/AssertionMiniPipelineAnalysisEngine.xml. This is itself an
+aggregate analysis engine, consisting of the components listed below.
+
+## Negation, uncertainty, and conditional attribute annotator
+
+The conceptConverterAnalysisEngine and the AssertionAnalysisEngine work
+together within the assertionMiniPipelineAnalysisEngine, and the pair of these
+two together may be included explicitly on their own.
+
+This pair of annotators depends on the following modules being run prior to
+invocation of this annotator:
+
+  * tokenizer
+  * sentence detector
+  * dictionary lookup
+
+We use the following types as input
+
+  * Sentence
+  * UmlsConcept
+  * OntologyConcept
+  * EntityMention
+  * EventMention
+  * BaseToken
+
+Then as output we modify attributes on EntityMention and EventMention.  The
+three attributes that we modify are:
+
+  1. polarity (integer values of -1 and +1)
+  2. uncertainty (integer value 0 or 1)
+  3. conditional (a boolean value of true or false).
+
+## Generic attribute annotator
+
+The generic attribute annotator can be included individually from
+assertiondesc/GenericAttributeAnalysisEngine.xml or as part of the
+AssertionMiniPipelineAnalysisEngine.  It relies on the output of the
+tokenizer, sentence detector, dependency parser, and semantic role labeler to
+find whether each IdentifiedAnnotation is generic, then sets the
+IdentifiedAnnotation:generic feature accordingly.
+
+The possible values are specified by the prefix NE_GENERIC_ in
+edu.mayo.bmi.uima.core.type.constants.CONST.
+
+## Subject attribute annotator
+
+The subject attribute annotator can be included individually from
+assertiondesc/SubjectAttributeAnalysisEngine.xml or as part of the
+AssertionMiniPipelineAnalysisEngine.  It relies on the output of the
+tokenizer, sentence detector, dependency parser, and semantic role labeler to
+find the subject of each IdentifiedAnnotation, then sets the
+IdentifiedAnnotation:subject feature accordingly.The possible values are
+specified by the prefix ATTR_SUBJECT_ in
+edu.mayo.bmi.uima.core.type.constants.CONST.
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