Class

org.clulab.processors.bionlp

BioNLPProcessor

Related Doc: package bionlp

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class BioNLPProcessor extends CoreNLPProcessor

A processor for biomedical texts, based on CoreNLP, but with different tokenization and NER User: mihais Date: 10/27/14 Last Modified: Update for Scala 2.12: java converters.

Linear Supertypes
CoreNLPProcessor, ShallowNLPProcessor, Processor, ProcessorAnnotator, ProcessorCSController, AnyRef, Any
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Inherited
  1. BioNLPProcessor
  2. CoreNLPProcessor
  3. ShallowNLPProcessor
  4. Processor
  5. ProcessorAnnotator
  6. ProcessorCSController
  7. AnyRef
  8. Any
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Visibility
  1. Public
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Instance Constructors

  1. new BioNLPProcessor(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. def annotate(doc: Document): Document

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    Definition Classes
    Processor

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

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    Definition Classes
    Processor → ProcessorAnnotator

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

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    Definition Classes
    Processor → ProcessorAnnotator

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

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    Definition Classes
    Processor → ProcessorAnnotator

  8. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

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

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    Definition Classes
    ShallowNLPProcessor

  10. lazy val chunker: CRFChunker

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    Definition Classes
    ShallowNLPProcessor

  11. def chunking(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  12. def clone(): AnyRef

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

  13. lazy val coref: StanfordCoreNLP

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    Definition Classes
    CoreNLPProcessor

  14. def discourse(doc: Document): Unit

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    Definition Classes
    CoreNLPProcessor → ShallowNLPProcessor → Processor

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

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    Definition Classes
    AnyRef

  16. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  17. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  19. lazy val gsf: GrammaticalStructureFactory

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    Definition Classes
    CoreNLPProcessor

  20. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  21. lazy val headFinder: SemanticHeadFinder

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    Definition Classes
    CoreNLPProcessor

  22. def in(s: String): String

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    Definition Classes
    ShallowNLPProcessor

  23. val internStrings: Boolean

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    Definition Classes
    ShallowNLPProcessor

  24. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  25. def lemmatize(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  26. lazy val lemmatizer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  27. val maxSentenceLength: Int

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    Definition Classes
    CoreNLPProcessor

  28. def mkChunker: CRFChunker

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    Definition Classes
    ShallowNLPProcessor

  29. def mkCoref: StanfordCoreNLP

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    Definition Classes
    CoreNLPProcessor

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

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    Definition Classes
    ShallowNLPProcessor → Processor

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

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    Definition Classes
    ShallowNLPProcessor → Processor

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

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    Definition Classes
    ShallowNLPProcessor → Processor

  33. def mkGSF: GrammaticalStructureFactory

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    Definition Classes
    CoreNLPProcessor

  34. def mkLemmatizer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  35. def mkLexicalizedParser: LexicalizedParser

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    Definition Classes
    CoreNLPProcessor

  36. def mkNer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  37. def mkPosTagger: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

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

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    Definition Classes
    ShallowNLPProcessor

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

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    Definition Classes
    AnyRef

  40. lazy val ner: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

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

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    Attributes
    protected
    Definition Classes
    ShallowNLPProcessor

  42. final def notify(): Unit

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    Definition Classes
    AnyRef

  43. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  44. def parse(doc: Document): Unit

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    Definition Classes
    CoreNLPProcessor → ShallowNLPProcessor → Processor

  45. lazy val posTagger: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  46. 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
    BioNLPProcessor → ShallowNLPProcessor

  47. def recognizeNamedEntities(doc: Document): Unit

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    Definition Classes
    BioNLPProcessor → ShallowNLPProcessor → Processor

  48. def resolveCoreference(doc: Document): Unit

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    Definition Classes
    BioNLPProcessor → CoreNLPProcessor → ShallowNLPProcessor → Processor

  49. lazy val rstConstituentParser: RSTParser

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    Definition Classes
    CoreNLPProcessor

  50. def shutdownClient: Unit

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    Definition Classes
    ProcessorCSController

  51. def shutdownClientServer: Unit

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    Definition Classes
    ProcessorCSController

  52. def shutdownServer: Unit

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    Definition Classes
    ProcessorCSController

  53. def stanfordParse(sentence: CoreMap): Tree

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    Definition Classes
    CoreNLPProcessor

  54. lazy val stanfordParser: LexicalizedParser

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    Definition Classes
    CoreNLPProcessor

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

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    Definition Classes
    AnyRef

  56. def tagPartsOfSpeech(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  57. def toString(): String

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    Definition Classes
    AnyRef → Any

  58. lazy val tokenizer: Tokenizer

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    Definition Classes
    ShallowNLPProcessor

  59. val tokenizerPostProcessor: Option[TokenizerStep]

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    Definition Classes
    ShallowNLPProcessor

  60. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  63. val withChunks: Boolean

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    Definition Classes
    ShallowNLPProcessor

  64. val withDiscourse: Int

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    Definition Classes
    CoreNLPProcessor

Inherited from CoreNLPProcessor

Inherited from ShallowNLPProcessor

Inherited from Processor

Inherited from ProcessorAnnotator

Inherited from ProcessorCSController

Inherited from AnyRef

Inherited from Any

Ungrouped