| Modifier and Type | Class and Description |
|---|---|
class |
GenericAttributeAnalysisEngine
This class provides a basic generic attribute extraction technique based on dependency parses. |
| Modifier and Type | Class and Description |
|---|---|
class |
JudgeAttributeInstances
A simple CAS consumer that generates XCAS (XML representation of the CAS) files in the
filesystem.
|
| Modifier and Type | Class and Description |
|---|---|
class |
GoldEntityAndAttributeReader
Read named entity annotations from knowtator xml files into the CAS
|
class |
I2B2Challenge2010CollectionReader |
class |
MiPACQKnowtatorXMLReader
assumes knowtator xml files are in "exported-xml" subdirectory w/ train/dev/test subsubdirs
and the original plaintext files are in "text" subdirectory w/ train/dev/test subsubdirs
|
class |
NegExCorpusReader
Reads lines from file named by AssertionConst.NEGEX_CORPUS
If use the main() method, uses this collection reader to
read the corpus and then uses the XMI writer to write
the XMI to directory given by AssertionConst.NEGEX_CORPUS_PREPROCESSED
|
class |
XmiCollectionReaderCtakes
A simple collection reader that reads CASes in XMI format from a directory in the filesystem.
|
| Modifier and Type | Class and Description |
|---|---|
class |
MergeGoldViewFromOneCasIntoInitialViewOfAnotherCas
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.
|
class |
XMIReader
UIMA CollectionReader that reads in CASes from XMI files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AssertionAnalysisEngine |
class |
AssertionAnalysisEngineFit |
class |
ConceptConverterAnalysisEngine |
| Modifier and Type | Class and Description |
|---|---|
class |
AlternateCuePhraseAnnotator |
class |
ConditionalCleartkAnalysisEngine |
class |
GenericCleartkAnalysisEngine |
class |
HistoryCleartkAnalysisEngine |
class |
PolarityCleartkAnalysisEngine |
class |
PolarityFedaCleartkAnalysisEngine |
| Modifier and Type | Class and Description |
|---|---|
class |
Chunker
This class provides a UIMA wrapper for the OpenNLP
opennlp.tools.chunker.Chunker class.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ChunkAdjuster
UIMA annotator that uses a pattern and a rule about that pattern to adjust
certain annotations.
|
| Modifier and Type | Class and Description |
|---|---|
static class |
ClinicalPipelineFactory.CopyNPChunksToLookupWindowAnnotations |
static class |
ClinicalPipelineFactory.RemoveEnclosedLookupWindows |
| Modifier and Type | Class and Description |
|---|---|
class |
ExtractionPrepAnnotator
UIMA annotator that prepares the CAS for output - performs
some (final) updates to the CAS
|
| Modifier and Type | Class and Description |
|---|---|
class |
ConstituencyParser |
class |
ParserEvaluationAnnotator |
| Modifier and Type | Class and Description |
|---|---|
class |
ParserTreeWriterConsumer |
| Modifier and Type | Class and Description |
|---|---|
class |
ContextDependentTokenizerAnnotator
Finds tokens based on context.
|
| Modifier and Type | Class and Description |
|---|---|
class |
BsvRegexSectionizer |
class |
CDASegmentAnnotator
Creates segment annotations based on the ccda_sections.txt file Which is
based on HL7/CCDA/LONIC standard headings Additional custom heading names can
be added to the file.
|
class |
CopyAnnotator
Utility annotator that copy's data from an existing JCas object into a new
JCas object.
|
class |
DocumentIdPrinterAnalysisEngine |
class |
FilterAnnotator |
class |
ListAnnotator |
class |
ListEntryNegator
Sets negation for disease/disorder and sign/symptom annotations in lists.
|
class |
ListSentenceFixer |
class |
NullAnnotator
This annotator does nothing.
|
class |
OverlapAnnotator |
class |
ParagraphAnnotator |
class |
ParagraphSentenceFixer |
class |
RegexSectionizer |
class |
SectionSegmentAnnotator
Creates a single segment annotation that spans the entire document.
|
class |
SentenceDetector
Wraps the OpenNLP sentence detector in a UIMA annotator
|
class |
SHARPKnowtatorXMLReader |
class |
SimpleSegmentAnnotator
Creates a single segment annotation that spans the entire document.
|
class |
SimpleSegmentWithTagsAnnotator
Creates a single segment annotation that spans the entire document.
|
class |
StartFinishLogger
All Annotation Engines should be logger their start and finish.
|
class |
TokenizerAnnotator
UIMA annotator that uses the Tokenizer module.
|
class |
TokenizerAnnotatorPTB
UIMA annotator that tokenizes based on Penn Treebank rules.
|
| Modifier and Type | Class and Description |
|---|---|
class |
CasConsumer
CasConsumer that writes a JCas (the current view) to an xml file
|
class |
CuiCountFileWriter
Writes a file with two bar-separated columns, the first is the cui, the second the number of cuis in the document.
|
class |
FilesInDirectoryCasConsumer
For each CAS a local file with the document text is written to a directory specifed by a parameter.
|
class |
FileTreeXmiWriter
Write xmi files in a directory tree mimicking that of the input files
|
class |
HtmlTableCasConsumer
Outputs an HTML table that visualizes the specified Annotation objects over
the document text.
|
class |
JdbcWriterTemplate
Template Cas Consumer to write a table to a sql database using jdbc
|
class |
NormalizedFilesInDirectoryCasConsumer
For each CAS a local file with the document text is written to a directory specifed by a parameter.
|
class |
SentenceTokensPrinter
Saves the (base) tokens of each sentence on a separate line, separated by spaces
|
class |
TextSpanWriter |
class |
TokenFreqCasConsumer
This class creates a file that contains the frequencies of the word tokens found in a set
in a text collection.
|
class |
TokenOffsetsCasConsumer
For each CAS a local file with the offsets of the BaseToken annotations is written to a directory specifed by a parameter.
|
class |
XmiWriterCasConsumerCtakes
A simple CAS consumer that writes the CAS to XMI format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
HtmlTextWriter |
| Modifier and Type | Class and Description |
|---|---|
class |
PrettyTextWriterFit
Writes Document text, pos, semantic types and cuis.
|
class |
PrettyTextWriterUima
Writes Document text, pos, semantic types and cuis.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PropertyTextWriterFit
Writes Document event and anatomic information to file.
|
class |
PropertyTextWriterUima
Writes Document event and anatomic information to file.
|
| Modifier and Type | Class and Description |
|---|---|
class |
FilesInDirectoryCollectionCyclicalReads |
class |
FilesInDirectoryCollectionReader |
class |
FileTreeReader
Recursively reads a directory tree of files, sorted by level (root first),
creating the DocumentID from the file name and the DocumentIdPrefix by the subdirectory path between
the root and the leaf file
|
class |
JdbcCollectionReader
Collection Reader that pulls documents to be processed from a database.
|
class |
LinesFromFileCollectionReader
The original code was copied from org.apache.uima.examples.cpe.FileSystemCollectionReader
and modified for Mayo use.
|
class |
LuceneCollectionReader |
class |
TextReader
UIMA CollectionReader that reads in Text from text files.
|
class |
XmiCollectionReaderCtakes
A simple collection reader that reads CASes in XMI format from a directory in the filesystem.
|
class |
XMIReader
UIMA CollectionReader that reads in CASes from XMI files.
|
| Modifier and Type | Class and Description |
|---|---|
static class |
CuiCollector.CuiCollectorEngine
Analysis Engine that stores collections of cuis by document id in the CuiCollector
|
static class |
EntityCollector.EntityCollectorEngine
Analysis Engine that stores collections of cuis by document id in the CuiCollector
|
| Modifier and Type | Method and Description |
|---|---|
static PipeBitInfo |
PipeBitInfoUtil.getInfo(Class<?> pipeBitClass) |
| Modifier and Type | Method and Description |
|---|---|
static Collection<PipeBitInfo> |
PipeBitInfoUtil.getAllInfos(Class<?> pipeBitClass) |
| Modifier and Type | Method and Description |
|---|---|
static boolean |
PipeBitInfoUtil.isUnknown(PipeBitInfo info) |
| Modifier and Type | Class and Description |
|---|---|
class |
CoreferenceChainScoringOutput |
class |
DeterministicMarkableAnnotator |
class |
EventCoreferenceAnnotator |
class |
MarkableHeadTreeCreator |
class |
MarkableSalienceAnnotator |
class |
MentionClusterCoreferenceAnnotator |
class |
MentionClusterRankingCoreferenceAnnotator |
class |
MipacqMarkableCreator |
class |
MipacqMarkableExpander |
class |
MipacqMarkablePairGenerator |
class |
MipacqSvmChainCreator |
class |
PersonChainAnnotator |
| Modifier and Type | Class and Description |
|---|---|
class |
ODIEVectorFileWriter |
| Modifier and Type | Class and Description |
|---|---|
static class |
EvaluationOfEventCoreference.CopyCoreferenceRelations |
static class |
EvaluationOfEventCoreference.CopyGoldMarkablesInChains |
| Modifier and Type | Class and Description |
|---|---|
class |
DependencyNodeWriter
CasConsumer that writes a JCas (the current view) to an xml file
|
| Modifier and Type | Class and Description |
|---|---|
class |
ClearNLPDependencyParserAE
This class provides a UIMA wrapper for the CLEAR dependency parser. |
class |
ClearNLPSemanticRoleLabelerAE
This class provides a UIMA wrapper for the ClearNLP Semantic Role Labeler, which is
available here.
|
| Modifier and Type | Class and Description |
|---|---|
class |
XMIReader
UIMA CollectionReader that reads in CASes from XMI files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
DependencyFileCollectionReader
This collection reader reads in dependency tree training/test data in a tab-
delimited format.
|
| Modifier and Type | Class and Description |
|---|---|
class |
DictionaryLookupAnnotator
UIMA annotator that identified entities based on lookup.
|
class |
UmlsDictionaryLookupAnnotator
UIMA annotator that identified entities based on lookup.
|
| Modifier and Type | Class and Description |
|---|---|
class |
DefaultJCasTermAnnotator
A direct string match using phrase permutations
Author: SPF
Affiliation: CHIP-NLP
Date: 11/19/13
|
class |
OverlapJCasTermAnnotator
Checks for terms that overlap a window.
|
| Modifier and Type | Class and Description |
|---|---|
class |
CopyDrugAnnotator
Utility annotator that copy's data from an existing JCas object into a new
JCas object.
|
class |
DrugMentionAnnotator
Finds tokens based on context.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ConsumeNamedEntityRecordModel
UIMA annotator that preps the CAS for extraction into DB2.
|
| Modifier and Type | Field and Description |
|---|---|
protected PipeBitInfo |
BitInfoPanel._pipeBitInfo |
| Modifier and Type | Method and Description |
|---|---|
PipeBitInfo |
BitInfoPanel.getPipeBitInfo() |
| Modifier and Type | Method and Description |
|---|---|
void |
PipeBitPainter.paintPipeBitInfo(Component renderer,
PipeBitInfo info,
boolean isSelected) |
| Modifier and Type | Method and Description |
|---|---|
PipeBitInfo |
AvailablesListModel.getElementAt(int index) |
| Modifier and Type | Method and Description |
|---|---|
Class<?> |
AvailablesListModel.getPipeBit(PipeBitInfo pipeBitInfo) |
| Modifier and Type | Method and Description |
|---|---|
int |
PipeBitInfoComparator.compare(PipeBitInfo info1,
PipeBitInfo info2) |
| Modifier and Type | Method and Description |
|---|---|
void |
PipeBitInfoPanel.setPipeBitInfoList(JList<PipeBitInfo> pipeBitList) |
| Modifier and Type | Method and Description |
|---|---|
PipeBitInfo |
DefaultUserBit.getPipeBitInfo() |
PipeBitInfo |
UserBit.getPipeBitInfo() |
| Constructor and Description |
|---|
DefaultUserBit(PipeBitInfo pipeBitInfo,
Class<?> pipeBitClass) |
| Modifier and Type | Class and Description |
|---|---|
class |
LvgAnnotator
UIMA annotator that uses the UMLS LVG package to find the canonical form of
WordTokens.
|
class |
LvgBaseTokenAnnotator
UIMA annotator that uses the UMLS LVG package to find the canonical form of
BaseTokens.
|
class |
ThreadSafeLvg
Utilizes a singleton to access a single instance of the LvgAnnotator.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ContextAnnotator
The context annotator iterates through focus annotations and analyzes the
surrounding context of each.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ClearNLPPOSTaggerAE
This class provides a UIMA wrapper for the CLEAR POSTagger. |
class |
OpenNLPPOSCollectionReader
This collection reader reads in part-of-speech training/test data in the
OpenNLP format.
|
class |
POSTagger |
| Modifier and Type | Class and Description |
|---|---|
class |
CdaCasInitializer
Bootstraps the CAS by:
Transforms document's original CDA text into plain text,
inserting section (segment) markers into text .
Transformation also inserts hyphens into words that should be hyphenated
Stores the resulting text in a new View (which has its own Sofa)
Detects sections and adds Segment (aka section) annotations
Extracts document level data and stores in CAS as Property annotations.
|
| Modifier and Type | Class and Description |
|---|---|
class |
CausesBringsAboutRelationExtractorAnnotator
Identifies causes/brings_about relation.
|
class |
DegreeOfRelationExtractorAnnotator
Identifies Degree_Of relations between
EventMentions and
Modifiers. |
class |
IdentifiedAnnotationExpander |
class |
LocationOfRelationExtractorAnnotator
Identifies Location_Of relations between
EventMentions and
AnatomicalSiteMentions. |
class |
ManagesTreatsRelationExtractorAnnotator
Identifies manages/treats relation.
|
class |
ManifestationOfRelationExtractorAnnotator
Identifies manifestation_of relation.
|
class |
ModifierExtractorAnnotator |
| Modifier and Type | Class and Description |
|---|---|
class |
Baseline1DegreeOfRelationExtractorAnnotator
Annotated degree_of relation in sentences containing a single entity mention
of a valid degree_of type and a single modifier.
|
class |
Baseline1EntityMentionPairRelationExtractorAnnotator
Annotate location_of relation between two entities in sentences containing
exactly two entities (where the entities are of the correct types).
|
class |
Baseline2DegreeOfRelationExtractorAnnotator
Annotated degree_of relation between two entities in sentences with multiple modifiers (arg2)
and a single legitimate degree_of arg1 (i.e.
|
class |
Baseline2EntityMentionPairRelationExtractorAnnotator
Annotate location_of relation between two entities in sentences with multiple anatomical sites
and a single legitimate location_of arg2.
|
class |
Baseline3DegreeOfRelationExtractorAnnotator
This baseline links each modifier with the closest entity of a type
that's suitable for degree_of, as long as there is no intervening modifier.
|
class |
Baseline3EntityMentionPairRelationExtractorAnnotator
This baseline 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.
|
class |
Baseline4DegreeOfRelationExtractorAnnotator
Annotate degree_of relation between two entities whenever
they are enclosed within the same noun phrse.
|
class |
Baseline4EntityMentionPairRelationExtractorAnnotator
Annotate location_of relation between two entities whenever
they are enclosed within the same noun phrse.
|
| Modifier and Type | Class and Description |
|---|---|
class |
GoldAnnotationStatsCalculator
Count various stats such as token and relation counts
based on the gold standard data.
|
| Modifier and Type | Class and Description |
|---|---|
static class |
RelationExtractorEvaluation.AddPotentialRelations |
static class |
SHARPXMI.CopyDocumentTextToGoldView |
class |
XMIReader
UIMA CollectionReader that reads in CASes from XMI files.
|
| Modifier and Type | Class and Description |
|---|---|
class |
MetastasisAnaforaXMLReader |
| Modifier and Type | Class and Description |
|---|---|
class |
F1BaselineEventTimeRelationAnnotator |
class |
PrecisionBaselineEventTimeRelationAnnotator |
| Modifier and Type | Class and Description |
|---|---|
static class |
EventEventDurationStatistics.AnalyseRelationArgumentDuration
Look at event-event relations whose event arguments have duration data.
|
static class |
EventTimeDurationStatistics.AnalyseRelationArgumentDuration
Look at those event-time relations whose event argument has duration data
and whose time argument can be normalized using Bethard timex normalizer.
|
| Modifier and Type | Class and Description |
|---|---|
class |
EventEventPosBasedAnnotator |
class |
EventEventPositionBasedAnnotator |
class |
EventEventTokenAndBIOBasedAnnotator |
class |
EventEventTokenAndPosBasedAnnotator |
class |
EventEventTokenBasedAnnotator |
class |
EventTimePosBasedAnnotator |
class |
EventTimePositionBasedAnnotator |
class |
EventTimeTokenAndBIOBasedAnnotator |
class |
EventTimeTokenAndPosBasedAnnotator |
class |
EventTimeTokenBasedAnnotator |
| Modifier and Type | Class and Description |
|---|---|
static class |
EvaluationOfNeuralEEAndETRelations.AddClosure |
static class |
EvaluationOfNeuralEEAndETRelations.AddContain2Overlap |
static class |
EvaluationOfNeuralEEAndETRelations.AddFlippedOverlap |
static class |
EvaluationOfNeuralEEAndETRelations.AddTransitiveContainsRelations |
static class |
EventEventNeuralEvaluation.AddClosure |
static class |
EventEventNeuralEvaluation.AddEEPotentialRelations |
static class |
EventEventNeuralEvaluation.CountCloseRelation |
static class |
EventTimeNeuralEvaluation.AddClosure |
static class |
EventTimeNeuralEvaluation.AddContain2Overlap |
static class |
EventTimeNeuralEvaluation.AddFlippedOverlap |
static class |
EventTimeNeuralEvaluation.AddPotentialRelations |
static class |
EventTimeNeuralEvaluation.AddTransitiveContainsRelations |
static class |
EventTimeNeuralEvaluation.CountCloseRelation |
| Modifier and Type | Class and Description |
|---|---|
class |
DBCollectionReader
Read documents from db.
|
| Modifier and Type | Class and Description |
|---|---|
class |
DateAnnotator
The cTAKES date doesn't actually parse the date.
|
class |
DBConsumer
Store the document text, cas, and annotations in the database.
|
class |
MetaMapToCTakesAnnotator
Convert metamap concepts to ctakes named entities.
|
class |
NamedEntityRegexAnnotator
Create NamedEntity annotations.
|
class |
NegexAnnotator
Negex adapted to cTAKES.
|
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