Annotation Engines - apache/ctakes GitHub Wiki

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.
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