cTAKES 2.5 - Assertion

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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.

Tip
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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:

polarity (integer values of -1 and +1)
uncertainty (integer value 0 or 1)
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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cTAKES 2.5 - Assertion

Overview of Assertion

Negation, uncertainty, and conditional attribute annotator

Generic attribute annotator

Subject attribute annotator