Annotation Engines

Annotation Engines

Name	Description
AbstractPatientConsumer	Abstract Engine to take action on a patient level instead of document level.
AbstractPatientConsumer	Abstract Engine to take action on a patient level instead of document level.
AbstractPatientConsumer	Abstract Engine to take action on a patient level instead of document level.
Admission Time Annotator	Adds Temporal Relations for Events with respect to the time of Patient Admission.
Assertion Engine	Adds Negation, Uncertainty, Conditional and Subject to annotations.
Assertion Engine (FIT)	Adds Negation, Uncertainty, Conditional and Subject to annotations.
Backward Timex Annotator	Annotates absolute time / date Temporal expressions.
CasedAnnotationFinder	Finds all-uppercase or normal terms in text.
Causal Relation Annotator	Annotates Causal relations in sentences.
CCDA Sectionizer	Annotates Document Sections by detecting Section Headers using Regular Expressions provided in a File.
CDA View Sectionizer	Transforms CDA text into plain text, inserts hyphens into words, stores the resulting text in a new View and creates Sections.
Chunker	Annotator that generates chunks of any kind as specified by the chunker model and the chunk creator.
ClearNLP POS Tagger	Adds Parts of Speech to Annotations.
ClearNLP Semantic Role Labeler	Adds Semantic Roles Relations.
ClearTK Conditional Annotator	Determines whether or not Identified Annotations are conditional.
ClearTK Conditional Annotator	Determines whether or not Identified Annotations are conditional.
ClearTK DocTime Creator	Creates an annotation for document creation time.
ClearTK Event Creator	Creates ClearTK Events from cTAKES Events.
ClearTK Thyme Linker	Maps old THYME project relations to a binary text relation representation.
Concept Converter	Creates a simple Concept for each Identified Annotation.
Constituency Parser	Adds Terminal Treebank Nodes, necessary for Coreference Markables.
Constituency Timex Filter	Creates Timex annotations.
Context Annotator	Collects context for focus annotations for use by context consuming annotators.
Context Dependent Annotator	Finds tokens based upon context. Time, Date, Roman numeral, Fraction, Range, Measurement, Person title.
Context Modality Annotator	Sets Modality based upon context.
Coreference (Cluster Rank)	Coreference annotator using mention-synchronous paradigm.
Coreference (Clusters)	Coreference annotator using mention-synchronous paradigm.
Date Annotator	Annotates Dates based upon whether or not text can be normalized to a date.
Degree of Annotator	Annotates Degree Of relations.
Degree of Annotator 1	Annotates Degree Of relations in sentences containing a single entity mention of a valid degree_of type and a single modifier.
Degree of Annotator 2	Annotates Degree Of relations between two shortest-distance entities in sentences with multiple modifiers.
Degree of Annotator 3	Annotates Degree Of relations between two shortest-distance entities in sentences as long as there is no intervening modifier.
Degree of Annotator 4	Annotates Degree Of relations between two entities whenever they are enclosed within the same noun phrase.
Dictionary Lookup (Default)	Annotates clinically-relevant terms. Terms must match dictionary entries exactly.
Dictionary Lookup (Old)	Annotates clinically-relevant terms. This is an older, slower dictionary lookup implementation.
Dictionary Lookup (Overlap)	Annotates clinically-relevant terms. Terms can overlap dictionary entries.
Discharge Time Annotator	Adds Temporal Relations for Events with respect to the time of Patient Discharge.
DocTimeApproximator	Sets the document time based upon the latest normalized date earlier than now.
DocTimeRel Annotator	Annotates event relativity to document creation time.
DocTimeRel ClearTK Annotator	Annotates event relativity to document creation time.
Drug Mention Annotator	Creates modifier annotations needed to handle the drug mentions.
E-E BIO TLinker	Creates Event - Event TLinks from Begin, Inner, Outer.
E-E CNN TLinker	Creates Event - Event TLinks with Convolutional Neural Network.
E-E Consecutive Sentence TLinker	Creates Event - Event TLinks between consecutive sentences.
E-E CRF TLinker	Creates Event - Event TLinks with Conditional Random Field.
E-E Cross- Sentence TLinker	Creates Event - Event TLinks across sentences.
E-E Gold TLinker	Creates Event - Event TLinks from the Gold View.
E-E I2B2 TLinker	Creates Event - Event TLinks with I2B2 model.
E-E POS and Token TLinker	Creates Event - Event TLinks from Part of Speech and Token Type.
E-E POS TLinker	Creates Event - Event TLinks with Parts of Speech.
E-E Position TLinker	Creates Event - Event TLinks with position.
E-E Seed TLinker	Creates Event - Event TLinks from Seeds.
E-E TLinker	Creates Event - Event TLinks.
E-E Token TLinker	Creates Event - Event TLinks from Token type.
E-T Baseline Scorer	Prints Event - Time Scores ...
E-T BIO TLinker	Creates Event - Time TLinks from Begin, Inner, Outer.
E-T CNN TLinker	Creates Event - Time TLinks with Convolutional Neural Network.
E-T Consecutive Sentence TLinker	Creates Event - Time TLinks between consecutive sentences.
E-T I2B2 TLinker	Creates Event - Time TLinks with I2B2 model.
E-T Neural TLinker	Use Neural Network to link temporal events and times. Read the named entity regex - concept id map from the db.
E-T POS and Token TLinker	Creates Event - Time TLinks from Part of Speech and Token Type.
E-T POS TLinker	Creates Event - Time TLinks with Parts of Speech.
E-T Position TLinker	Creates Event - Event TLinks with position.
E-T Precision TLinker	Creates Event - Time relations.
E-T Self TLinker	Creates Event - Time TLinks.
E-T TLinker	Creates Event - Time TLinks.
E-T Token TLinker	Creates Event - Time TLinks from Token type.
End of Line Sentence Splitter	Re-annotates Sentences based upon short lines, preventing a Sentence from spanning over an intentional line break.
Event Annotator	Annotates Temporal Events.
Event Coreference Annotator	Annotates Event Coreferences.
Extraction Prepper	Assigns IDs and Canonical text to Identified Annotations.
Generic Status Annotator	Annotates the Generic status for Identified Annotations.
Generic Status ClearTK Annotator	Annotates the Generic status for Identified Annotations.
Generic Status ClearTK Annotator	Annotates the Generic status for Identified Annotations.
History of ClearTK Annotator	Annotate History of property.
History of ClearTK Annotator	Annotate History of property.
LabValueFinder	Associates Lab Mentions with values.
List Annotator	Annotates formatted List Sections by detecting them using Regular Expressions provided in an input File.
List Entry Negator	Checks List Entries for negation, which may be exhibited differently from unstructured negation.
List Paragraph Fixer	Re-annotates Paragraphs based upon existing Lists, preventing a Paragraph from spanning more than one List.
List Sentence Splitter	Re-annotates Sentences based upon existing List Entries, preventing a Sentence from spanning more than one List Entry.
Location of Annotator	Annotates Location Of relations.
Location of Annotator	Annotates Location Of relations.
Location of Annotator 1	Annotates Location Of relations in sentences containing exactly two entities (where the entities are of the correct types).
Location of Annotator 2	Annotates Location Of relations in sentences containing with multiple anatomical sites.
Location of Annotator 3	Links each anatomical site with the closest entity of a type that's suitable for location_of, as long as there is no intervening anatomical site.
Location of Annotator 4	Annotates Location Of relations between two entities whenever they are enclosed within the same noun phrase.
LVG Annotator	Adds canonical form of words.
LVG Basetoken Annotator	Adds canonical form of Base Tokens.
Manages / Treats Annotator	Annotates Manages / Treats relations.
Manifestation of Annotator	Annotates Manifestation Of relations.
Markable Annotator (Deterministic)	Annotates Markables for use by Coreference Annotators.
Markable Creator (MiPACQ)	Annotates Markables using a word list.
Markable Salience Annotator	Annotates Markable Salience.
Meta Time Annotator	...
Modifier Extractor	Annotates Modifiers and Chunks.
Named Entity Annotator (RegEx)	Use regex to identify the Named Entities. Read the named entity regex - concept id map from the db.
NE Predicate Annotator	Creates Events from Identified Annotations and Predicates.
Negation Annotator (ClearTK)	Annotates negation property.
Negation Annotator (ClearTK)	Annotates negation property.
Negation Annotator (Feda)	Annotates negation property.
Negation Annotator (Negex)	Use negex to assign polarity to Named Entities.
Paragraph Annotator	Annotates Paragraphs by detecting them using Regular Expressions provided in an input File or by empty text lines.
Paragraph Sentence Splitter	Re-annotates Sentences based upon existing Paragraphs, preventing a Sentence from spanning more than one Paragraph.
Parser Evaluator	..
Part of Speech Tagger	Annotate Parts of Speech.
PbjReceiverAE	Annotation Engine wrapper for the PbjReceiver.
PcsClassifier	Uses SVM for smoking status classification.
Person Coreference Annotator	Annotates coreferences between person mentions.
Property Cue Finder	Reads assertion cue words from file and annotates them.
Prose Sentence Detector	Sentence detector that uses B I O for determination. Useful for documents in which newlines may not indicate sentence boundaries.
PTB Tokenizer	Annotates Document Penn TreeBank Tokens.
Regex Sectionizer	Annotates Document Sections by detecting Section Headers using Regular Expressions provided in a Bar-Separated-Value (BSV) File.
Sectionizer	Annotates Document Sections by detecting Section Headers in template.
Sentence Detector	Annotates Sentences based upon an OpenNLP model.
SimpleMedDatesFinder	Finds start and stop dates for medication events.
Single Sectionizer	Annotates Document as a single Section.
SVM Chain Creator (MiPACQ)	Creates Coreferences using a Simple Vector Machine.
Tag Sectionizer	Annotates Document Sections by detecting start and end Section Tags.
Thread safe Backward Timex Annotator	Annotates absolute time / date Temporal expressions.
Thread safe Chunker	Annotator that generates chunks of any kind as specified by the chunker model and the chunk creator.
Thread safe ClearNLP Semantic Role Labeler	Adds Semantic Roles Relations.
Thread safe Constituency Parser	Adds Terminal Treebank Nodes, necessary for Coreference Markables.
Thread safe Context Annotator	Collects context for focus annotations for use by context consuming annotators.
Thread safe Coreference (Clusters)	Coreference annotator using mention-synchronous paradigm.
Thread safe Degree of Annotator	Annotates Degree Of relations.
Thread safe Dictionary Lookup (Default)	Annotates clinically-relevant terms. Terms must match dictionary entries exactly.
Thread safe DocTimeRel Annotator	Annotates event relativity to document creation time.
Thread safe E-E TLinker	Creates Event - Event TLinks.
Thread safe E-T TLinker	Creates Event - Time TLinks.
Thread safe Event Annotator	Annotates Temporal Events.
Thread safe Markable Salience Annotator	Annotates Markable Salience.
Thread safe Modifier Extractor	Annotates Modifiers and Chunks.
Thread safe Part of Speech Tagger	Annotate Parts of Speech.
Thread Safe Sentence Detector	Annotates Sentences based upon an OpenNLP model.
Thread Safe Sentence Detector BIO	Thread safe sentence detector that uses B I O for determination. Useful for documents in which newlines may not indicate sentence boundaries.
Thread-Safe LVG	Annotates Lexical Variants for terms with attempted thread safety.
Time Annotator	...
Tokenizer	Annotates Document Tokens.
UMLS Dictionary Lookup (Old)	Annotates clinically-relevant terms. This is an older, slower dictionary lookup implementation.