Class/Object

org.clulab.processors.bionlp

BioNLPProcessor

Related Docs: object BioNLPProcessor | 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

Linear Supertypes
CoreNLPProcessor, ShallowNLPProcessor, Processor, AnyRef, Any
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Inherited
  1. BioNLPProcessor
  2. CoreNLPProcessor
  3. ShallowNLPProcessor
  4. Processor
  5. AnyRef
  6. Any
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Visibility
  1. Public
  2. All

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)

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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 addBioTokenizerOptions(props: Properties): Unit

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  5. def annotate(doc: Document): Document

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    Definition Classes
    Processor

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

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    Definition Classes
    Processor

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

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    Definition Classes
    Processor

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

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    Definition Classes
    Processor

  9. def arrayOrNone[T](b: ArrayBuffer[T])(implicit arg0: ClassTag[T]): Option[Array[T]]

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    Definition Classes
    ShallowNLPProcessor

  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. def beginsContext(label: String): Boolean

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  13. lazy val bioNer: BioNER

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  14. lazy val chunker: CRFChunker

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    Definition Classes
    ShallowNLPProcessor

  15. def chunking(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  16. def clone(): AnyRef

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

  17. lazy val coref: StanfordCoreNLP

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    Definition Classes
    CoreNLPProcessor

  18. def discourse(doc: Document): Unit

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    Definition Classes
    CoreNLPProcessor → ShallowNLPProcessor → Processor

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

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    Definition Classes
    AnyRef

  20. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  21. def finalize(): Unit

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

  22. def findEntityEnd(offset: Int, seq: Array[String]): Int

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  23. def findEntityStart(offset: Int, seq: Array[String]): Int

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

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    Definition Classes
    AnyRef → Any

  25. lazy val gsf: GrammaticalStructureFactory

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    Definition Classes
    CoreNLPProcessor

  26. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  27. lazy val headFinder: SemanticHeadFinder

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    Definition Classes
    CoreNLPProcessor

  28. def in(s: String): String

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    Definition Classes
    ShallowNLPProcessor

  29. val internStrings: Boolean

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    Definition Classes
    ShallowNLPProcessor

  30. def isCC(offset: MutableNumber[Int], tags: Array[String]): Boolean

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  31. def isEntity(offset: MutableNumber[Int], seq: Array[String]): Boolean

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  32. def isFigRef(lemmas: Array[String], offset: Int): Boolean

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  33. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  34. def isLowerCase(s: String): Boolean

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  35. def isUpperInitial(s: String): Boolean

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  36. def labelSemanticRoles(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  37. def lemmatize(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  38. lazy val lemmatizer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  39. val maxSentenceLength: Int

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    Definition Classes
    CoreNLPProcessor

  40. def mkChunker: CRFChunker

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    Definition Classes
    ShallowNLPProcessor

  41. def mkCoref: StanfordCoreNLP

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    Definition Classes
    CoreNLPProcessor

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

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    Definition Classes
    ShallowNLPProcessor → Processor

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

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    Definition Classes
    ShallowNLPProcessor → Processor

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

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    Definition Classes
    ShallowNLPProcessor → Processor

  45. def mkGSF: GrammaticalStructureFactory

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    Definition Classes
    CoreNLPProcessor

  46. def mkLemmatizer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  47. def mkLexicalizedParser: LexicalizedParser

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    Definition Classes
    CoreNLPProcessor

  48. def mkNer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  49. def mkPosTagger: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  50. def mkSent(sentence: Sentence): List[CoreLabel]

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  51. def mkSentence(annotation: CoreMap): Sentence

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    Definition Classes
    ShallowNLPProcessor

  52. def mkTokenizerWithSentenceSplitting: StanfordCoreNLP

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    Definition Classes
    BioNLPProcessor → ShallowNLPProcessor

  53. def mkTokenizerWithoutSentenceSplitting: StanfordCoreNLP

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    Definition Classes
    BioNLPProcessor → ShallowNLPProcessor

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

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    Definition Classes
    ShallowNLPProcessor

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

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    Definition Classes
    AnyRef

  56. lazy val ner: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  57. final def notify(): Unit

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    Definition Classes
    AnyRef

  58. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  59. def parse(doc: Document): Unit

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    Definition Classes
    CoreNLPProcessor → ShallowNLPProcessor → Processor

  60. lazy val posTagger: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  61. def postProcessNamedEntities(sent: Sentence): Unit

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    Fix common NER errors

  62. lazy val postProcessor: BioNLPTokenizerPostProcessor

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  63. 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

  64. def postprocessTokens(originalTokens: Array[CoreLabel]): Array[CoreLabel]

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    Implements the bio-specific post-processing steps from McClosky et al.

    Implements the bio-specific post-processing steps from McClosky et al. (2011)

    originalTokens

    Input CoreNLP sentence

    returns

    The modified tokens

    Definition Classes
    BioNLPProcessor → ShallowNLPProcessor

  65. def postprocessTokens(sentence: CoreMap): List[CoreLabel]

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    Attributes
    protected
    Definition Classes
    ShallowNLPProcessor

  66. lazy val preProcessor: BioNLPPreProcessor

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  67. def preprocessSentences(origSentences: Iterable[String]): Iterable[String]

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    Definition Classes
    Processor

  68. def preprocessText(origText: String): String

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    Definition Classes
    BioNLPProcessor → Processor

  69. def preprocessTokens(origSentences: Iterable[Iterable[String]]): Iterable[Iterable[String]]

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    Definition Classes
    Processor

  70. def recognizeNamedEntities(doc: Document): Unit

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    Definition Classes
    BioNLPProcessor → ShallowNLPProcessor → Processor

  71. def removeContextFromBeginningOfGenes(bc2Labels: Array[String], labelsWithContext: Array[String]): Unit

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  72. def resolveCoreference(doc: Document): Unit

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    Definition Classes
    BioNLPProcessor → CoreNLPProcessor → ShallowNLPProcessor → Processor

  73. lazy val rstConstituentParser: RSTParser

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    Definition Classes
    CoreNLPProcessor

  74. lazy val ruleNer: RuleNER

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  75. lazy val specialTokens: Set[String]

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  76. def stanfordParse(sentence: CoreMap): Tree

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    Definition Classes
    CoreNLPProcessor

  77. lazy val stanfordParser: LexicalizedParser

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    Definition Classes
    CoreNLPProcessor

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

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    Definition Classes
    AnyRef

  79. def tagPartsOfSpeech(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor

  80. def toString(): String

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    Definition Classes
    AnyRef → Any

  81. lazy val tokenizerWithSentenceSplitting: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  82. lazy val tokenizerWithoutSentenceSplitting: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor

  83. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  86. val withChunks: Boolean

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    Definition Classes
    ShallowNLPProcessor

  87. val withDiscourse: Int

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    Definition Classes
    CoreNLPProcessor

Inherited from CoreNLPProcessor

Inherited from ShallowNLPProcessor

Inherited from Processor

Inherited from AnyRef

Inherited from Any

Ungrouped