THIS IS A TEST INSTANCE. ALL YOUR CHANGES WILL BE LOST!!!!
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h2. Overview of NE Contexts
{note}As of cTAKES 2.5, NE Contexts is no longer a part of the default pipeline. Instead the newer [assertion|cTAKES 3.0 - Assertion] annotator is used to identify general attributes of EntityMentions (but not attributes specific to a single type of named entity such as the dosage attribute of a medication){note}
The context annotator provides a mechanism for examining the context of existing annotations, finding events of interest in the context, and acting on those events in some way. The negation and status annotators both take advantage of this infrastructure by examining the context of named entities (e.g. disorders and findings) to see if they should be considered as negated (e.g. "no chest pain") or if their status should be modified (e.g. "myocardial infarction" should have status "history of").
In fact, the "negation annotator" is really just the context annotator configured to deal with negations. Similarly, the "status annotator" is the context annotator configured to identify the status of named entities.
{tip}To better understand the context annotator code you should start by reading the Javadocs for the class |
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Overview of NE Contexts
| Note |
|---|
As of cTAKES 2.5, NE Contexts is no longer a part of the default pipeline. Instead the newer assertion annotator is used to identify general attributes of EntityMentions (but not attributes specific to a single type of named entity such as the dosage attribute of a medication) |
The context annotator provides a mechanism for examining the context of existing annotations, finding events of interest in the context, and acting on those events in some way. The negation and status annotators both take advantage of this infrastructure by examining the context of named entities (e.g. disorders and findings) to see if they should be considered as negated (e.g. "no chest pain") or if their status should be modified (e.g. "myocardial infarction" should have status "history of").
In fact, the "negation annotator" is really just the context annotator configured to deal with negations. Similarly, the "status annotator" is the context annotator configured to identify the status of named entities.
| Tip |
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To better understand the context annotator code you should start by reading the Javadocs for the class edu.mayo.bmi.uima.context.ContextAnnotator.java. It provides a conceptual overview of how the code works. {tip} h2. Negation annotator The negation detection annotator is a |
Negation annotator
The negation detection annotator is a pattern-based
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(no
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MaxEnt
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models
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required/used)
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approach
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that
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uses
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finite
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state
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machines
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and
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is
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roughly
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based
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on
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the
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popular
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...
...
...
...
...
...
...
...
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introduced
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by
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...
...
...
...
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What follows is an explanation of how negation is performed using the context annotator.
NegationAnnotator.xml
We will start by examining the descriptor file desc/NegationAnnotator.xml.
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It
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calls
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edu.mayo.bmi.uima.context.ContextAnnotator,
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instead
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of
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a
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"NegationAnnotator".
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In
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fact,
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there
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is
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no
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"negation
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annotator"
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analysis
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engine.
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We
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simply
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configure
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the
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ContextAnnotator
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for
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the
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task.
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Next
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we
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will
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discuss
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each
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of
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the
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parameter
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settings
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in
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turn:
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- MaxLeftScopeSize
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- =
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- 10
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- -
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- The
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- maximum
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- number
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- of
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- annotations
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- that
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- will
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- make
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- up
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- the
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- left-hand
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- side
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- context
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- is
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- ten.
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- Increase
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- or
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- decrease
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- this
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- parameter
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- setting
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- to
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- increase
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- or
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- decrease
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- the
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- left
...
- hand
...
- side
...
- context.
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- MaxRightScopeSize
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- =
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- 10
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- -
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- The
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- maximum
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- number
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- of
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- annotations
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- that
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- will
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- make
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- up
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- the
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- right-hand
...
- side
...
- context
...
- is
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- ten.
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- Increase
...
- or
...
- decrease
...
- this
...
- parameter
...
- setting
...
- to
...
- increase
...
- or
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- decrease
...
- the
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- right-hand
...
- side
...
- context.
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- ScopeOrder
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- =
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- LEFT,
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- RIGHT
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- -
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- The
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- context
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- annotator
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- will
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- look
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- for
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- signs
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- of
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- negation
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- on
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- the
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- left-hand
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- side
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- of
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- a
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- named
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- entity
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- first
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- and
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- then
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- the
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- right-hand
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- side.
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- ContextAnalyzerClass
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- =
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- edu.mayo.bmi.uima.context.negation.NegationContextAnalyzer
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- -
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- The
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- context
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- analyzer
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- looks
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- at
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- the
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- context
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- (e.g.
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- the
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- 10
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- words
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- on
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- the
...
- left
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- or
...
- right
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- of
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- the
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- named
...
- entity)
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- and
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- determines
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- if
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- the
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- named
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- entity
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- should
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- be
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- negated.
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- If
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- it
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- should,
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- then
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- the
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- negation
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- context
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- analyzer
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- will
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- generate
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- a
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- context
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- hit
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- to
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- be
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- consumed
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- by
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- the
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- context
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- hit
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- consumer
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- (see
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- ContextHitConsumerClass.)
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- ContextHitConsumerClass
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- =
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- edu.mayo.bmi.uima.context.negation.NegationContextHitConsumer
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- -
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- The
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- context
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- hit
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- consumer
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- handles
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- context
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- hits
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- generated
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- by
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- the
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- context
...
- analyzer.
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- In
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- this
...
- case,
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- the
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- negation
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- context
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- hit
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- consumer
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- simply
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- sets
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- the
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- certainty
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- of
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- a
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- named
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- entity
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- to
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- -1
...
- which
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- indicates
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- that
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- it
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- has
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- been
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- negated.
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- WindowAnnotationClass
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- =
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- edu.mayo.bmi.uima.core.type.textspan.Sentence
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- -
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- When
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- the
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- context
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- annotator
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- collects
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- the
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- context
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- annotations
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- for
...
- a
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- named
...
- entity,
...
- it
...
- will
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- not
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- look
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- beyond
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- the
...
- boundaries
...
- of
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- the
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- sentence
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- that
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- the
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- named
...
- entity
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- is
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- found
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- in.
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- FocusAnnotationClass
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- =
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- edu.mayo.bmi.uima.core.type.textsem.IdentifiedAnnotation
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- -
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- The
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- negation
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- annotator
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- is
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- concerned
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- with
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- negating
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- named
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- entities
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- and
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- thus
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- the
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- focus
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- annotation
...
- type
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- (the
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- annotations
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- for
...
- which
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- a
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- context
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- is
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- generated
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- and
...
- examined)
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- specifies
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- the
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- parent
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- of
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- EventMention
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- and
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- of
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- EntityMention
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- classes.
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- ContextAnnotationClass
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- =
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- edu.mayo.bmi.uima.common.type.BaseToken
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- -
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- The
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- context
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- of
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- the
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- named
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- entities
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- is
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- a
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- list
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- of
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- tokens.
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- This
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- is
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- what
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- the
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- context
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- analyzer
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- is
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- going
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- to
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- examine.
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So,
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the
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work
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of
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negating
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a
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named
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entity
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is
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done
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by:
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- finding
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- negations
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- by
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- the
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- NegationContextAnalyzer
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- updating
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- the
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- status
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- of
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- NamedEntities
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- by
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- the
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- NegationContextHitConsumer
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The
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former
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is
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a
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pretty
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lightweight
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wrapper
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around
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another
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class
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which
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has
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all
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of
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the
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negation
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pattern
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finding
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logic,
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edu.mayo.bmi.fsm.machine.NegationFSM.
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If
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you
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want
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to
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update
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the
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pattern
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matching
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of
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negation
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detection,
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then
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you
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would
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do
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it
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in
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that
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class.
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Updating
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Negex
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patterns
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Updating
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the
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negation
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detection
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patterns
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will
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involve
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either:
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- trial
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- and
...
- error
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- experimentation.
...
- or
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- understanding
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- how
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- the
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- NegationFSM
...
- works
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The
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rules,
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patterns,
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words
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that
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identify
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negation
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are
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hard-coded
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into
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the
...
class
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edu.mayo.bmi.fsm.machine.NegationFSM
...
which
...
is
...
found
...
in
...
the
...
core
...
project.
...
We
...
would
...
suggest
...
starting
...
off
...
with
...
the
...
trial-and-error
...
approach.
...
For
...
example,
...
if
...
you
...
wanted
...
to
...
add
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"impossible"
...
to
...
the
...
lexicon
...
of
...
negation
...
words,
...
then
...
you
...
could
...
try
...
adding
...
it
...
to
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the
...
_negAdjectivesSet
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and
...
test
...
the
...
behavior.
...
Status
...
annotator
...
The
...
way
...
the
...
status
...
annotator
...
works
...
mirrors
...
very
...
closely
...
how
...
the
...
negation
...
annotator
...
works.
...
You
...
are
...
encouraged
...
to
...
read the above section, "Negation
...
annotator"
...
,
...
examine
...
the
...
parameter
...
settings
...
given
...
for
...
desc/StatusAnnotator.xml,
...
and
...
look
...
at
...
edu.mayo.bmi.fsm.machine.StatusIndicatorFSM.