Class

org.clulab.processors.bionlp

FastBioNLPProcessor

Related Doc: package bionlp

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class FastBioNLPProcessor extends FastNLPProcessor

A processor for biomedical texts, based on FastNLP with the NN parser, but with different tokenization and NER User: mihais Date: 2/9/17 Last Modified: Update for Scala 2.12: java converters.

Linear Supertypes
FastNLPProcessor, OpenIEAnnotator, ShallowNLPProcessor, Processor, ProcessorAnnotator, ProcessorCSController, AnyRef, Any
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Inherited
  1. FastBioNLPProcessor
  2. FastNLPProcessor
  3. OpenIEAnnotator
  4. ShallowNLPProcessor
  5. Processor
  6. ProcessorAnnotator
  7. ProcessorCSController
  8. AnyRef
  9. Any
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Visibility
  1. Public
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Instance Constructors

  1. new FastBioNLPProcessor(internStrings: Boolean = false, withChunks: Boolean = true, withCRFNER: Boolean = true, withRuleNER: Boolean = true, withContext: Boolean = true, withDiscourse: Int = ShallowNLPProcessor.NO_DISCOURSE, maxSentenceLength: Int = 100, removeFigTabReferences: Boolean = true, removeBibReferences: Boolean = true)

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. val LEFT_PARENS: Regex

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    Definition Classes
    ShallowNLPProcessor

  5. val RIGHT_PARENS: Regex

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    Definition Classes
    ShallowNLPProcessor

  6. def annotate(doc: Document): Document

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    Definition Classes
    Processor

  7. def annotate(text: String, keepText: Boolean): Document

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    Definition Classes
    Processor → ProcessorAnnotator

  8. def annotateFromSentences(sentences: Iterable[String], keepText: Boolean): Document

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    Definition Classes
    Processor → ProcessorAnnotator

  9. def annotateFromTokens(sentences: Iterable[Iterable[String]], keepText: Boolean): Document

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    Definition Classes
    Processor → ProcessorAnnotator

  10. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  11. def basicSanityCheck(doc: Document, checkAnnotation: Boolean = true): Option[Annotation]

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    Definition Classes
    ShallowNLPProcessor

  12. lazy val chunker: CRFChunker

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    Definition Classes
    ShallowNLPProcessor

  13. def chunking(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  14. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  15. def discourse(doc: Document): Unit

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    Definition Classes
    FastNLPProcessor → ShallowNLPProcessor → Processor

  16. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  17. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  18. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  19. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  20. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  21. def in(s: String): String

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    Definition Classes
    ShallowNLPProcessor

  22. val internStrings: Boolean

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    Definition Classes
    ShallowNLPProcessor

  23. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  24. def lemmatize(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  25. lazy val lemmatizer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  26. def mkChunker: CRFChunker

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    Definition Classes
    ShallowNLPProcessor

  27. def mkDocument(text: String, keepText: Boolean): Document

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    Definition Classes
    ShallowNLPProcessor → Processor

  28. def mkDocumentFromSentences(sentences: Iterable[String], keepText: Boolean, charactersBetweenSentences: Int = 1): Document

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    Definition Classes
    ShallowNLPProcessor → Processor

  29. def mkDocumentFromTokens(sentences: Iterable[Iterable[String]], keepText: Boolean, charactersBetweenSentences: Int = 1, charactersBetweenTokens: Int = 1): Document

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    Definition Classes
    ShallowNLPProcessor → Processor

  30. def mkLemmatizer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  31. def mkNer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  32. def mkOpenIE: StanfordCoreNLP

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    Definition Classes
    OpenIEAnnotator

  33. def mkPosTagger: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  34. def namedEntitySanityCheck(doc: Document): Option[Annotation]

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    Definition Classes
    ShallowNLPProcessor

  35. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  36. lazy val ner: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  37. def newStanfordCoreNLP(props: Properties, enforceRequirements: Boolean = true): StanfordCoreNLP

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    Attributes
    protected
    Definition Classes
    ShallowNLPProcessor

  38. final def notify(): Unit

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    Definition Classes
    AnyRef

  39. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  40. lazy val openIE: StanfordCoreNLP

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    Definition Classes
    OpenIEAnnotator

  41. def parse(doc: Document): Unit

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    Definition Classes
    FastNLPProcessor → ShallowNLPProcessor → Processor

  42. lazy val posTagger: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  43. def postprocessTags(annotation: Annotation): Unit

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    Improve POS tagging in the Bio domain

    Improve POS tagging in the Bio domain

    annotation

    The CoreNLP annotation

    Definition Classes
    FastBioNLPProcessor → ShallowNLPProcessor

  44. def recognizeNamedEntities(doc: Document): Unit

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    Definition Classes
    FastBioNLPProcessor → ShallowNLPProcessor → Processor

  45. def relationExtraction(doc: Document): Unit

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    Definition Classes
    OpenIEAnnotator

  46. def relationExtractionSanityCheck(doc: Document): Option[Annotation]

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    Definition Classes
    OpenIEAnnotator

  47. def resolveCoreference(doc: Document): Unit

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    Definition Classes
    FastBioNLPProcessor → ShallowNLPProcessor → Processor

  48. lazy val rstDependencyParser: RSTParser

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    RST discourse parser using only dependency based syntax

    RST discourse parser using only dependency based syntax

    Definition Classes
    FastNLPProcessor

  49. def shutdownClient: Unit

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    Definition Classes
    ProcessorCSController

  50. def shutdownClientServer: Unit

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    Definition Classes
    ProcessorCSController

  51. def shutdownServer: Unit

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    Definition Classes
    ProcessorCSController

  52. lazy val stanfordDepParser: DependencyParser

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    Stanford's NN dependency parser

    Stanford's NN dependency parser

    Definition Classes
    FastNLPProcessor

  53. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  54. def tagPartsOfSpeech(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  55. def toString(): String

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    Definition Classes
    AnyRef → Any

  56. lazy val tokenizer: Tokenizer

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    Definition Classes
    ShallowNLPProcessor

  57. val tokenizerPostProcessor: Option[TokenizerStep]

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    Definition Classes
    ShallowNLPProcessor

  58. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  59. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  60. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  61. val withChunks: Boolean

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    Definition Classes
    ShallowNLPProcessor

  62. val withRelationExtraction: Boolean

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    Definition Classes
    ShallowNLPProcessor

Inherited from FastNLPProcessor

Inherited from OpenIEAnnotator

Inherited from ShallowNLPProcessor

Inherited from Processor

Inherited from ProcessorAnnotator

Inherited from ProcessorCSController

Inherited from AnyRef

Inherited from Any

Ungrouped