ctakes temporal

This module is dedicated to processing electronic medical records for meaningful events, temporal expressions, and their relations on a timeline.

Temporal relations are of prime importance in biomedicine as they are intrinsically linked to diseases, signs and symptoms, and treatments. The identification of temporal relations in medical text has drawn growing attention because of its potential to dramatically increase the understanding of many medical phenomena such as disease progression, longitudinal effects of medications, and a patient's clinical course, and its many clinical applications such as question answering[1, 2], clinical outcomes prediction[3], and the recognition of temporal patterns and timelines[4, 5].

Key components

Event annotator
A Begin-Inside-Outside (BIO) style sequence annotator for clinically meaningful events, i.e. anything that would show up on a detailed timeline of the patient’s care or life.

Temporal expression annotators
A series of BIO style sequence annotators that employed forward and backward search algorithms and multiple learning methods (Support Vector Machine (SVM), Conditional Random Field (CRV) ) for annotating temporal expressions which would provide concrete temporal references throughout the document or section, e.g. “today”, “24 hours ago”, “postoperative”. More details can be found in [6].

DocTimeRel annotator
For every event, there is an SVM-based annotator that can automatically reason the temporal relation between the target event and the document creation time (DCT). This module provided a basic and stable temporal solution that can position all events into coarse temporal bins, e.g. “before the DCT”, “after the DCT”, or “overlap the DCT”. This annotator has proved helpful in solving real clinical temporal-sensitive tasks for multiple institutions [5].

Temporal relation (TLINK) annotators
SVM-based annotators for detecting within-sentence Event-Time relations and Event-Event relations. For i2b2 datasets there are also cross sentence Event-Time and Event-Event relation annotators. Multiple techniques have been implemented, including narrative container-based annotation concept [7], tree kernels [8] for syntactic similarity measurement, multi-layered temporal modeling [9], event expansion [10], and deep neural network methods [11, 12].

Evaluation

The SVM-based temporal relation annotators achieve an F-score of 0.589 which outperform the best system of Clinical TempEval 2016 [13], whose F-score was 0.573. State-of-the-art results for event-time relations have been achieved with our neural network approaches.

All the above annotators were trained and tested on colon cancer notes from the THYME data set [14].

References

1. Das, A.K. and M.A. Musen. A comparison of the temporal expressiveness of three database query methods. in Annual Symposium on Computer Applications in Medical Care. 1995. IEEE COMPUTER SOCIETY PRESS. 2. Kahn, M.G., L.M. Fagan, and S. Tu, Extensions to the time-oriented database model to support temporal reasoning in medical expert systems. Methods of information in medicine, 1990. 30(1): p. 4-14. 3. Schmidt, R., S. Ropele, C. Enzinger, et al., White matter lesion progression, brain atrophy, and cognitive decline: the Austrian stroke prevention study. Annals of neurology, 2005. 58(4): p. 610-616. 4. Zhou, L. and G. Hripcsak, Temporal reasoning with medical data—a review with emphasis on medical natural language processing. Journal of biomedical informatics, 2007. 40(2): p. 183-202. 5. Lin, C., E.W. Karlson, D. Dligach, et al., Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. Journal of the American Medical Informatics Association, 2014: p. amiajnl-2014-002642. 6. Miller, T.A., S. Bethard, D. Dligach, et al., Extracting Time Expressions from Clinical Text, in Proceedings of BioNLP 15. 2015. 7. Miller, T.A., S. Bethard, D. Dligach, et al., Discovering narrative containers in clinical text, in ACL 2013. 2013: Sofia, Bulgaria. p. 18. 8. Lin, C., T. Miller, A. Kho, et al., Descending-Path Convolution Kernel for Syntactic Structures, in Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics (ACL). 2014: Baltimore, Maryland, USA. p. 81-86. 9. Lin, C., D. Dligach, T.A. Miller, et al., Multilayered temporal modeling for the clinical domain. J Am Med Inform Assoc, 2016. 23(2): p. 387-95. 10. Lin, C., T. Miller, D. Dligach, et al., Improving Temporal Relation Extraction with Training Instance Augmentation. BioNLP 2016, 2016: p. 108. 11. Dligach, D., T. Miller, C. Lin, et al., Neural temporal relation extraction., in European Chapter of the Association for Computational Linguistics (EACL 2017). 2017: Valencia, Spain. 12. Hartzell, E. and C. Lin. Enhancing Clinical Temporal Relation Discovery with Syntactic Embeddings from GloVe. in International Conference on Intelligent Biology and Medicine (ICIBM 2016). 2016. Houston, Texas, USA. 13. Bethard, S., G. Savova, W.-T. Chen, et al., Semeval-2016 task 12: Clinical tempeval. Proceedings of SemEval, 2016: p. 1052-1062. 14. Styler IV, W.F., S. Bethard, S. Finan, et al., Temporal annotation in the clinical domain. Transactions of the Association for Computational Linguistics, 2014. 2: p. 143-154.

Annotation Engines
Output Writers
Utilities
Piper Files

---

Annotation Engines

Admission Time Annotator

Adds Temporal Relations for Events with respect to the time of Patient Admission.

Source class: EventAdmissionTimeAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Timex, Identified Annotation
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

Backward Timex Annotator

Annotates absolute time / date Temporal expressions.

Source class: BackwardsTimeAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalEntityAnnotator_ImplBase
Dependencies: Section, Sentence, Base Token
Products: Timex

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
TimexView	View to write timexes to (used for ensemble methods)	String	No

ClearTK DocTime Creator

Creates an annotation for document creation time.

Source class: ClearTKDocumentCreationTimeAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase

No available configuration parameters.

ClearTK Event Creator

Creates ClearTK Events from cTAKES Events.

Source class: EventToClearTKEventAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase
Dependencies: Event

No available configuration parameters.

ClearTK Thyme Linker

Maps old THYME project relations to a binary text relation representation.

Source class: ClearTKLinkToTHYMELinkAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase
Products: Temporal Relation

No available configuration parameters.

Constituency Timex Filter

Creates Timex annotations.

Source class: ConstituencyBasedTimeAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalEntityAnnotator_ImplBase
Dependencies: Section, Base Token, Timex

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
TimexView	View to write timexes to (used for ensemble methods)	String	No

Context Modality Annotator

Sets Modality based upon context.

Source class: ContextualModalityAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Identified Annotation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

Discharge Time Annotator

Adds Temporal Relations for Events with respect to the time of Patient Discharge.

Source class: EventDischargeTimeAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Timex, Identified Annotation
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

DocTimeApproximator

Sets the document time based upon the latest normalized date earlier than now.

Source class: DocTimeApproximator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase
Usables: Timex, Identified Annotation

No available configuration parameters.

DocTimeRel Annotator

Annotates event relativity to document creation time.

Source class: DocTimeRelAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Sentence, Identified Annotation, Event

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbView		String	No

DocTimeRel ClearTK Annotator

Annotates event relativity to document creation time.

Source class: ClearTKDocTimeRelAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase
Dependencies: Identified Annotation, Event

No available configuration parameters.

E-E BIO TLinker

Creates Event - Event TLinks from Begin, Inner, Outer.

Source class: EventEventTokenAndBIOBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-E CNN TLinker

Creates Event - Event TLinks with Convolutional Neural Network.

Source class: EventEventCNNAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-E CRF TLinker

Creates Event - Event TLinks with Conditional Random Field.

Source class: EventEventCRFRelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalSequenceAnnotator_ImplBase
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the SequenceClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. SequenceJarClassifierFactory
dataWriterFactoryClassName	provides the full name of the SequenceDataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultSequenceDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
TimexView	View to write timexes to (used for ensemble methods)	String	No

E-E Consecutive Sentence TLinker

Creates Event - Event TLinks between consecutive sentences.

Source class: ConsecutiveSentencesEventEventRelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

E-E Cross- Sentence TLinker

Creates Event - Event TLinks across sentences.

Source class: CrossSentenceTemporalRelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase
Dependencies: Event, Timex
Products: Temporal Relation

No available configuration parameters.

E-E Gold TLinker

Creates Event - Event TLinks from the Gold View.

Source class: EventEventRelationGoldContainerAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

E-E I2B2 TLinker

Creates Event - Event TLinks with I2B2 model.

Source class: EventEventI2B2RelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

E-E POS TLinker

Creates Event - Event TLinks with Parts of Speech.

Source class: EventEventPosBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-E POS and Token TLinker

Creates Event - Event TLinks from Part of Speech and Token Type.

Source class: EventEventTokenAndPosBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-E Position TLinker

Creates Event - Event TLinks with position.

Source class: EventEventPositionBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-E Seed TLinker

Creates Event - Event TLinks from Seeds.

Source class: EventEventRelationSeedBasedAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

E-E TLinker

Creates Event - Event TLinks.

Source class: EventEventRelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No
ProbView		String	No

E-E Token TLinker

Creates Event - Event TLinks from Token type.

Source class: EventEventTokenBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-T BIO TLinker

Creates Event - Time TLinks from Begin, Inner, Outer.

Source class: EventTimeTokenAndBIOBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-T Baseline Scorer

Prints Event - Time Scores ...

Source class: F1BaselineEventTimeRelationAnnotator
Source package: org.apache.ctakes.temporal.ae.baselines
Parent class: org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
Dependencies: Sentence, Event, Timex

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

E-T CNN TLinker

Creates Event - Time TLinks with Convolutional Neural Network.

Source class: EventTimeCNNAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-T Consecutive Sentence TLinker

Creates Event - Time TLinks between consecutive sentences.

Source class: ConsecutiveSentencesEventTimeRelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

E-T I2B2 TLinker

Creates Event - Time TLinks with I2B2 model.

Source class: EventTimeI2B2RelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

E-T Neural TLinker

Use Neural Network to link temporal events and times. Read the named entity regex - concept id map from the db.

Source class: NeuralEventTimeSelfRelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator
Dependencies: Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No
ProbView		String	No

E-T POS TLinker

Creates Event - Time TLinks with Parts of Speech.

Source class: EventTimePosBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-T POS and Token TLinker

Creates Event - Time TLinks from Part of Speech and Token Type.

Source class: EventTimeTokenAndPosBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-T Position TLinker

Creates Event - Event TLinks with position.

Source class: EventTimePositionBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

E-T Precision TLinker

Creates Event - Time relations.

Source class: PrecisionBaselineEventTimeRelationAnnotator
Source package: org.apache.ctakes.temporal.ae.baselines
Parent class: org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
Dependencies: Sentence, Identified Annotation, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

E-T Self TLinker

Creates Event - Time TLinks.

Source class: EventTimeSelfRelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalRelationExtractorAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No
ProbView		String	No

E-T TLinker

Creates Event - Time TLinks.

Source class: EventTimeRelationAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

E-T Token TLinker

Creates Event - Time TLinks from Token type.

Source class: EventTimeTokenBasedAnnotator
Source package: org.apache.ctakes.temporal.nn.ae
Parent class: org.cleartk.ml.CleartkAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

Event Annotator

Annotates Temporal Events.

Source class: EventAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalEntityAnnotator_ImplBase
Dependencies: Section, Sentence, Chunk, Identified Annotation
Products: Event

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
FeatureSelectionURI	provides a URI where the feature selection data will be written	URI	No
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
NumOfNeighborForSMOTE	the number of neighbors used for minority instances for SMOTE algorithm	Float	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	Float	No
WhetherToDoFeatureSelection	the Chi-squared threshold at which features should be removed	Float	No

Meta Time Annotator

...

Source class: MetaTimeAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalSequenceAnnotator_ImplBase
Dependencies: Section, Sentence, Base Token, Timex

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the SequenceClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. SequenceJarClassifierFactory
dataWriterFactoryClassName	provides the full name of the SequenceDataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultSequenceDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

NE Predicate Annotator

Creates Events from Identified Annotations and Predicates.

Source class: NEPredicateEventAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalEntityAnnotator_ImplBase
Dependencies: Identified Annotation
Products: Event

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No

SimpleMedDatesFinder

Finds start and stop dates for medication events.

Source class: SimpleMedDatesFinder
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase
Dependencies: Identified Annotation
Products: Temporal Relation

Parameter	Description	Class	Required	Default
CuiList	path to a file containing a list of cuis of interest. If none is specified then all cuis are viable.	String	No
LookupWindow	Type of Lookup window to use. Default is Paragraph.	String	No	org.apache.ctakes.typesystem.type.textspan. Paragraph
SectionList	Path to a file containing a list of sections of interest. If none is specified then all sections are viable.	String	No

Thread safe Backward Timex Annotator

Annotates absolute time / date Temporal expressions.

Source class: ThreadSafeBackTimeAnnotator
Source package: org.apache.ctakes.temporal.concurrent
Parent class: org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator
Dependencies: Section, Sentence, Base Token
Products: Timex

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
TimexView	View to write timexes to (used for ensemble methods)	String	No

Thread safe DocTimeRel Annotator

Annotates event relativity to document creation time.

Source class: ThreadSafeDocTimeRelAnnotator
Source package: org.apache.ctakes.temporal.concurrent
Parent class: org.apache.ctakes.temporal.ae.DocTimeRelAnnotator
Dependencies: Sentence, Identified Annotation, Event

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbView		String	No

Thread safe E-E TLinker

Creates Event - Event TLinks.

Source class: ThreadSafeEventEventRelAnnotator
Source package: org.apache.ctakes.temporal.concurrent
Parent class: org.apache.ctakes.temporal.ae.EventEventRelationAnnotator
Dependencies: Section, Sentence, Event
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No
ProbView		String	No

Thread safe E-T TLinker

Creates Event - Time TLinks.

Source class: ThreadSafeEventTimeRelAnnotator
Source package: org.apache.ctakes.temporal.concurrent
Parent class: org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator
Dependencies: Section, Sentence, Event, Timex
Products: Temporal Relation

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	double	No

Thread safe Event Annotator

Annotates Temporal Events.

Source class: ThreadSafeEventAnnotator
Source package: org.apache.ctakes.temporal.concurrent
Parent class: org.apache.ctakes.temporal.ae.EventAnnotator
Dependencies: Section, Sentence, Chunk, Identified Annotation
Products: Event

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
FeatureSelectionURI	provides a URI where the feature selection data will be written	URI	No
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
NumOfNeighborForSMOTE	the number of neighbors used for minority instances for SMOTE algorithm	Float	No
ProbabilityOfKeepingANegativeExample	probability that a negative example should be retained for training	Float	No
WhetherToDoFeatureSelection	the Chi-squared threshold at which features should be removed	Float	No

Time Annotator

...

Source class: TimeAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalEntityAnnotator_ImplBase
Dependencies: Section, Sentence, Base Token
Products: Timex

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the ClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. JarClassifierFactory
dataWriterFactoryClassName	provides the full name of the DataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultDataWriterFactory
FeatureSelectionURI	provides a URI where the feature selection data will be written	URI	No
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
NumOfNeighborForSMOTE	the number of neighbors used for minority instances for SMOTE algorithm	Float	No
TimexView	View to write timexes to (used for ensemble methods)	String	No
WhetherToDoFeatureSelection	the Chi-squared threshold at which features should be removed	Float	No

---

Output Writers

Event Time Anafora Writer

Writes Temporal Events and Times in Anafora format.

Source class: EventTimeAnaforaWriter
Source package: org.apache.ctakes.temporal.cc
Parent class: org.apache.ctakes.core.cc.AbstractJCasFileWriter
Usables: Document Id Prefix, Base Token

Parameter	Description	Class	Required	Default
OutputDirectory	Directory for all output files.	File	Yes
FileExtension	The extension for the written files. Default is .EventTime.ctakes.completed.xml	String	No	.EventTime.ctakes.completed.xml
OnlyTemporalEvents	Only use temporal events, not those created by dictionary lookup. Default is yes.	String	No	yes
SubDirectory	SubDirectory for files.	String	No

SimpleMedDatesPrinter

Finds start and stop dates for medication events.

Source class: SimpleMedDatesPrinter
Source package: org.apache.ctakes.temporal.cc
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase
Dependencies: Identified Annotation

No available configuration parameters.

---

Utilities

Anafora XML Reader (DeepPhe)

Reads annotations from DeepPhe schema Anafora XML files in a directory.

Source class: DeepPheAnaforaXMLReader
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase
Products: Identified Annotation

Parameter	Description	Class	Required	Default
anaforaDirectory	root directory of the Anafora-annotated files, with one subdirectory for each annotated file	File	Yes
anaforaSuffixes	list of suffixes that might be added to a file name to identify the Anafora XML annotations file; only the first suffix corresponding to a file will be used	String[]	No

I2B2 XML Reader (THYME)

Reads annotations from THYME schema I2B2 XML files in a directory.

Source class: I2B2TemporalXMLReader
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.uima.fit.component.JCasAnnotator_ImplBase
Products: Event, Temporal Relation

Parameter	Description	Class	Required	Default
PARAM_INPUT_DIR	Directory containing i2b2 files to read	File	Yes
PARAM_MAP_THYME	Whether to map i2b2 relations/properties/types to THYME types	boolean	No

Knowtator XML Reader (THYME)

Reads annotations from THYME schema Knowtator XML files in a directory.

Source class: THYMEKnowtatorXMLReader
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.core.ae.SHARPKnowtatorXMLReader
Products: Identified Annotation, Event, Timex, Location Relation, Degree Relation, Temporal Relation

Parameter	Description	Class	Required	Default
knowtatorXMLDirectory		File	Yes
SetDefaults	whether or not to set default attribute values if no annotation is present	boolean	Yes
TextDirectory	directory containing the text files (if DocumentIDs are just filenames); defaults to assuming that DocumentIDs are full file paths	File	No

Timex Annotator

Annotates absolute time / date Temporal expressions into a View.

Source class: CRFTimeAnnotator
Source package: org.apache.ctakes.temporal.ae
Parent class: org.apache.ctakes.temporal.ae.TemporalSequenceAnnotator_ImplBase
Dependencies: Section, Sentence, Base Token
Products: Timex

Parameter	Description	Class	Required	Default
classifierFactoryClassName	provides the full name of the SequenceClassifierFactory class to be used.	String	No	org.cleartk.ml.jar. SequenceJarClassifierFactory
dataWriterFactoryClassName	provides the full name of the SequenceDataWriterFactory class to be used.	String	No	org.cleartk.ml.jar. DefaultSequenceDataWriterFactory
isTraining	determines whether this annotator is writing training data or using a classifier to annotate. Normally inferred automatically based on whether or not a DataWriterFactory class has been set.	Boolean	No
TimexView	View to write timexes to (used for ensemble methods)	String	No

---

Piper Files

Default Relation Temporal Pipeline

Clinical Pipeline with degree-of, location-of, events, times, temporal and event-doc creation time relations.

Default Relation Temporal Pipeline

$\textcolor{gray}{\textsf{// Clinical Pipeline with degree-of, location-of, events, times, temporal and event-doc creation time relations. }}$

$\textcolor{gray}{\textsf{// Clinical Pipeline with degree-of and location-of relations. }}$
$\textcolor{magenta}{\textbf{load}}$ DefaultRelationPipeline

$\textcolor{gray}{\textsf{// events, times, event-event, event-time and event-doc creation time relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TemporalSubPipe

Default Temporal Pipeline

Clinical Pipeline with events, times, event-event and event-time relations plus event-document creation time relations.

Default Temporal Pipeline

$\textcolor{gray}{\textsf{// Clinical Pipeline with events, times, event-event and event-time relations plus event-document creation time relations. }}$

$\textcolor{gray}{\textsf{// Clinical Pipeline. }}$
$\textcolor{magenta}{\textbf{load}}$ DefaultFastPipeline

$\textcolor{gray}{\textsf{// events, times, event-event, event-time and event-doc creation time relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TemporalSubPipe

Sectioned Relation Temporal Pipeline

Clinical Pipeline with sections, paragraphs, lists, degree-of, location-of, events, times, temporal and event-doc creation time relations.

Sectioned Relation Temporal Pipeline

$\textcolor{gray}{\textsf{// Clinical Pipeline with sections, paragraphs, lists, degree-of, location-of, events, times, temporal and event-doc creation time relations. }}$

$\textcolor{gray}{\textsf{// Clinical Pipeline with section, paragraph and list detection with degree-of and location-of relations. }}$
$\textcolor{magenta}{\textbf{load}}$ SectionedRelationPipeline

$\textcolor{gray}{\textsf{// events, times, event-event, event-time and event-doc creation time relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TemporalSubPipe

Sectioned Temporal Pipeline

Clinical Pipeline with sections, paragraphs, lists, events, times, temporal and event-doc creation time relations.

Sectioned Temporal Pipeline

$\textcolor{gray}{\textsf{// Clinical Pipeline with sections, paragraphs, lists, events, times, temporal and event-doc creation time relations. }}$

$\textcolor{gray}{\textsf{// Clinical Pipeline with section, paragraph and list detection. }}$
$\textcolor{magenta}{\textbf{load}}$ SectionedFastPipeline

$\textcolor{gray}{\textsf{// events, times, event-event, event-time and event-doc creation time relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TemporalSubPipe

Temporal Sub Pipe

Commands and parameters to create a temporal processing sub-pipeline.

Temporal Sub Pipe

$\textcolor{gray}{\textsf{// Commands and parameters to create a temporal processing sub-pipeline. }}$
$\textcolor{gray}{\textsf{// This is not a full pipeline. }}$

$\textcolor{gray}{\textsf{// 'Generic' Events. Use addDescription and let the EventAnnotator set itself up with defaults. }}$
$\textcolor{green}{\textbf{addDescription}}$ EventAnnotator

$\textcolor{gray}{\textsf{// Times. Use addLogged to log start and finish of processing. There aren't default models, so set specifically }}$
$\textcolor{green}{\textbf{add}}$ BackwardsTimeAnnotator $\textcolor{purple}{\textbf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/temporal/models/timeannotator/model.jar}}$

$\textcolor{gray}{\textsf{// DocTimeRel: the relation bin for Events to the Document Creation Time. }}$
$\textcolor{green}{\textbf{add}}$ DocTimeRelAnnotator $\textcolor{purple}{\textbf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/temporal/models/doctimerel/model.jar}}$

$\textcolor{gray}{\textsf{// Event - Time binary relations. }}$
$\textcolor{green}{\textbf{add}}$ EventTimeRelationAnnotator $\textcolor{purple}{\textbf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/temporal/models/eventtime/model.jar}}$

$\textcolor{gray}{\textsf{// Event - Event binary relations. }}$
$\textcolor{green}{\textbf{add}}$ EventEventRelationAnnotator $\textcolor{purple}{\textbf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/temporal/models/eventevent/model.jar}}$

$\textcolor{gray}{\textsf{// Need to improve. Generic Events (head words) should be replaced by overlapping subclasses with relations adjusted. }}$
$\textcolor{gray}{\textsf{//add FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator }}$

Ts Default Relation Temporal Pipeline

Thread Safe Clinical Pipeline with degree-of and location-of relations, events, times, temporal abd event-doc creation time relations.

Ts Default Relation Temporal Pipeline

$\textcolor{gray}{\textsf{// Thread Safe Clinical Pipeline with degree-of and location-of relations, events, times, temporal abd event-doc creation time relations. }}$

$\textcolor{gray}{\textsf{// Thread safe Clinical Pipeline with degree-of and location-of relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TsDefaultRelationPipeline

$\textcolor{gray}{\textsf{// Thread safe events, times, event-event, event-time and event-doc creation time relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TsTemporalSubPipe

Ts Default Temporal Pipeline

Thread Safe Default Clinical Pipeline with events, times, event-event and event-time relations plus event-document creation time relations

Ts Default Temporal Pipeline

$\textcolor{gray}{\textsf{// Thread Safe Default Clinical Pipeline with events, times, event-event and event-time relations plus event-document creation time relations }}$

$\textcolor{gray}{\textsf{// Thread safe Clinical Pipeline. }}$
$\textcolor{magenta}{\textbf{load}}$ TsDefaultFastPipeline

$\textcolor{gray}{\textsf{// Thread safe events, times, event-event, event-time and event-doc creation time relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TsTemporalSubPipe

Ts Sectioned Relation Temporal Pipeline

Thread safe Clinical Pipeline with sections, paragraphs, lists, degree-of, location-of, events, times, temporal and event-doc creation time relations.

Ts Sectioned Relation Temporal Pipeline

$\textcolor{gray}{\textsf{// Thread safe Clinical Pipeline with sections, paragraphs, lists, degree-of, location-of, events, times, temporal and event-doc creation time relations. }}$


$\textcolor{gray}{\textsf{// Clinical Pipeline with section, paragraph and list detection with degree-of and location-of relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TsSectionedRelationPipeline

$\textcolor{gray}{\textsf{// Thread safe events, times, event-event, event-time and event-doc creation time relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TsTemporalSubPipe

Ts Sectioned Temporal Pipeline

Thread safe Clinical Pipeline with sections, paragraphs, lists, events, times, temporal and event-doc creation time relations.

Ts Sectioned Temporal Pipeline

$\textcolor{gray}{\textsf{// Thread safe Clinical Pipeline with sections, paragraphs, lists, events, times, temporal and event-doc creation time relations. }}$


$\textcolor{gray}{\textsf{// Clinical Pipeline with section, paragraph and list detection. }}$
$\textcolor{magenta}{\textbf{load}}$ TsSectionedFastPipeline

$\textcolor{gray}{\textsf{// Thread safe events, times, event-event, event-time and event-doc creation time relations. }}$
$\textcolor{magenta}{\textbf{load}}$ TsTemporalSubPipe

Ts Temporal Sub Pipe

Commands and parameters to create a thread safe temporal processing sub-pipeline.

Ts Temporal Sub Pipe

$\textcolor{gray}{\textsf{// Commands and parameters to create a thread safe temporal processing sub-pipeline. }}$
$\textcolor{gray}{\textsf{// This is not a full pipeline. }}$

$\textcolor{gray}{\textsf{// 'Generic' Events. Use addDescription and let the EventAnnotator set itself up with defaults. }}$
$\textcolor{green}{\textbf{addDescription}}$ $\textcolor{blue}{\textsf{concurrent.ThreadSafeEventAnnotator}}$

$\textcolor{gray}{\textsf{// Times. Use addLogged to log start and finish of processing. There aren't default models, so set specifically }}$
$\textcolor{green}{\textbf{add}}$ $\textcolor{blue}{\textsf{concurrent.ThreadSafeBackTimeAnnotator}}$ $\textcolor{purple}{\textbf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/temporal/models/timeannotator/model.jar}}$

$\textcolor{gray}{\textsf{// DocTimeRel: the relation bin for Events to the Document Creation Time. }}$
$\textcolor{green}{\textbf{add}}$ $\textcolor{blue}{\textsf{concurrent.ThreadSafeDocTimeRelAnnotator}}$ $\textcolor{purple}{\textbf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/temporal/models/doctimerel/model.jar}}$

$\textcolor{gray}{\textsf{// Event - Time binary relations. }}$
$\textcolor{green}{\textbf{add}}$ $\textcolor{blue}{\textsf{concurrent.ThreadSafeEventTimeRelAnnotator}}$ $\textcolor{purple}{\textbf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/temporal/models/eventtime/model.jar}}$

$\textcolor{gray}{\textsf{// Event - Event binary relations. }}$
$\textcolor{green}{\textbf{add}}$ $\textcolor{blue}{\textsf{concurrent.ThreadSafeEventEventRelAnnotator}}$ $\textcolor{purple}{\textbf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/temporal/models/eventevent/model.jar}}$

$\textcolor{gray}{\textsf{// Need to improve. Generic Events (head words) should be replaced by overlapping subclasses with relations adjusted. }}$
$\textcolor{gray}{\textsf{//add FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator }}$