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Sean Finan edited this page Sep 19, 2024 · 3 revisions

Utilities

Name Description
Anafora XML Reader (DeepPhe) Reads annotations from DeepPhe schema Anafora XML files in a directory.
Anafora XML Reader (Metastasis) Reads annotations from DeepPhe schema Anafora XML files in a directory.
Annotation Remover Removes annotations of a given type from the JCas.
ArtemisStarter Starts an Apache Artemis broker.
ArtemisStopper Stops an Apache Artemis broker.
Chunk Adjuster Annotator that uses a pattern and a rule about that pattern to adjust certain annotations.
ClearNLP Dependency Parser Analyses Sentence Structure, storing information in nodes.
ClearNLP Dependency Parser Analyses Sentence Structure, storing information in nodes.
CommandRunner Runs an external process.
Coreference Copier Copy relations from Gold viewCas to current
Coreference Score Writer Writes scores of system coreference chains compared to chains in a Gold View.
CtakesRunner Starts a new instance of cTAKES with the given piper parameters.
Deprecated Finished Logger use FinishedLogger in (sub) package log.
Document ID Printer Logs the Document ID to Log4j and Standard Output.
Drug Copier Copies data from an existing JCas into a new JCas.
ExitForcer Forcibly Exits cTAKES. Use only at the end of a pipeline.
Finished Logger Writes a banner message COMPLETE to the log when all processing is finished.
Gold Annotation Copier Copies an annotation type from the Gold view to the System view.
Gold Stats Calculator Count various stats such as token and relation counts based on the gold standard data.
Gold View Merger Read in gold annotations from XMI and create a view within the current CAS, and copy the gold annotations into the new view within the current CAS.
I2B2 Challenge Reader Reads entities and their properties from file.
I2B2 XML Reader (THYME) Reads annotations from THYME schema I2B2 XML files in a directory.
Identified Annotation Expander Enlarges the text span of an identified annotation based upon part of speech.
JCas Copy Annotator Copies document text and all annotations into a new JCas.
Knowtator XML Reader (Generic) Read named entity annotations from knowtator xml files into the CAS.
Knowtator XML Reader (MiPACQ) Reads annotations from MiPACQ schema Knowtator XML files in a directory.
Knowtator XML Reader (SHARP) Reads annotations from SHARP schema Knowtator XML files in a directory.
Knowtator XML Reader (THYME) Reads annotations from THYME schema Knowtator XML files in a directory.
Markable Expander (MiPACQ) Expands Markable text spans to cover a noun phrase.
Markable Pair Creator (MiPACQ) Pairs Markables using a stop word list.
Metamap Annotation xlater Create MedicationEventMention/EntityMention annotations for each set of CandidateConcept annotations that span the same text.
MrsDrSentenceJoiner Joins Sentences with person titles Mr. Mrs. Dr. that have been split by SentenceDetectorBIO.
Null Annotator Does absolutely nothing.
Overlap Annotator Removes or modifies annotations that overlap.
PatientNoteCollector Caches each Document JCas in a Patient JCas as a View.
PbjJmsSender Sends jcas to Artemis Queue using JMS
PbjPipper Will pip PBJ based upon user request.
PbjReceiver Populates JCas based upon XMI content read from an Artemis Queue.
PbjStompSender Sends jcas to Artemis Queue using Stomp
PiperFileRunEngine Analysis Engine that executes the PiperFileRunner. Kludge for desc files (CPE).
PythonPipper Will pip a specified python package.
PythonRunner Starts a Python process with the given parameters.
Start or Finish Logger Simple Annotator to place before and after other annotators that do not Log their Start and Finish.
Timex Annotator Annotates absolute time / date Temporal expressions into a View.

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