Overview of Assertion
The assertion annotators 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, used in a generic way, or in the context of a person's history. 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"). Each of these attributes illustrate how the "assertion" value of a named entity might be marked.
The annotators set the value of their attribute using constants in org.apache.ctakes.typesystem.type.constants.CONST
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 annotators is to use an aggregate analysis engine that includes the assertion annotators of interest to you.
To use a single annotator such as the PolarityCleartkAnalysisEngine,
- if writing code using uimaFIT, use the class org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine
- if using XML descriptors, use the AE descriptor ctakes-assertion/desc/analysis_engine/PolarityCleartkAnalysisEngine.xml
- If using the Pipeline Fabricator GUI, include the annotator called "Negation Annotator (ClearTK)"
Negation attribute annotator
Modifies an attribute on EntityMention and EventMention.
polarity (1 or -1, -1=negated)
See org.apache.ctakes.typesystem.type.constants.CONST.NE_POLARITY_NEGATION_ABSENT and CONST.NE_POLARITY_NEGATION_PRESENT.
Uncertainty attribute annotator
Modifies an attribute on EntityMention and EventMention.
uncertainty (0 or 1, 1 = uncertain)
See CONST.NE_UNCERTAINTY_PRESENT and CONST.NE_UNCERTAINTY_ABSENT.
History attribute annotator
Modifies an attribute on EntityMention and EventMention:
historyOf (0 or 1, 1=history of).
See CONST.NE_HISTORY_OF_PRESENT and CONST.NE_HISTORY_OF_ABSENT
Generic attribute annotator
Modifies an attribute on EntityMention and EventMention:
generic (true or false).
See CONST.NE_GENERIC_TRUE and CONST.NE_GENERIC_FALSE
Subject attribute annotator
Modifies an attribute on EntityMention and EventMention:
subject ("patient", "other", and other values)
See the constants with the prefix ATTR_SUBJECT_* within class org.apache.ctakes.typesystem.type.constants.CONST