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

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FastNLPProcessor, ShallowNLPProcessor, Processor, AnyRef, Any
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Inherited
  1. FastBioNLPProcessor
  2. FastNLPProcessor
  3. ShallowNLPProcessor
  4. Processor
  5. AnyRef
  6. 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)

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

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

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    Definition Classes
    Processor
  8. def arrayOrNone[T](b: ArrayBuffer[T])(implicit arg0: ClassTag[T]): Option[Array[T]]

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    Definition Classes
    ShallowNLPProcessor
  9. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  10. def basicSanityCheck(doc: Document, checkAnnotation: Boolean = true): Option[Annotation]

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    Definition Classes
    ShallowNLPProcessor
  11. lazy val chunker: CRFChunker

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    Definition Classes
    ShallowNLPProcessor
  12. def chunking(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor
  13. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  14. def discourse(doc: Document): Unit

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    Definition Classes
    FastNLPProcessorShallowNLPProcessor → 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. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  20. def in(s: String): String

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    Definition Classes
    ShallowNLPProcessor
  21. val internStrings: Boolean

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    Definition Classes
    ShallowNLPProcessor
  22. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  23. def labelSemanticRoles(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor
  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. lazy val maltService: ThreadLocal[MaltParserService]

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    One maltparser instance for each thread MUST have one separate malt instance per thread! malt uses a working directory which is written at runtime using ThreadLocal variables guarantees that each thread gets its own working directory

    One maltparser instance for each thread MUST have one separate malt instance per thread! malt uses a working directory which is written at runtime using ThreadLocal variables guarantees that each thread gets its own working directory

    Definition Classes
    FastNLPProcessor
  27. def mkChunker: CRFChunker

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    Definition Classes
    ShallowNLPProcessor
  28. def mkDocument(text: String, keepText: Boolean): Document

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    Definition Classes
    ShallowNLPProcessor → Processor
  29. def mkDocumentFromSentences(sentences: Iterable[String], keepText: Boolean, charactersBetweenSentences: Int = 1): Document

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    Definition Classes
    ShallowNLPProcessor → Processor
  30. def mkDocumentFromTokens(sentences: Iterable[Iterable[String]], keepText: Boolean, charactersBetweenSentences: Int = 1, charactersBetweenTokens: Int = 1): Document

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    Definition Classes
    ShallowNLPProcessor → Processor
  31. def mkLemmatizer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor
  32. def mkNer: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor
  33. def mkPosTagger: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor
  34. def mkSentence(annotation: CoreMap): Sentence

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    Definition Classes
    ShallowNLPProcessor
  35. def mkTokenizerWithSentenceSplitting: StanfordCoreNLP

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  36. def mkTokenizerWithoutSentenceSplitting: StanfordCoreNLP

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

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    Definition Classes
    ShallowNLPProcessor
  38. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  39. lazy val ner: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor
  40. final def notify(): Unit

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    Definition Classes
    AnyRef
  41. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  42. def parse(doc: Document): Unit

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    Definition Classes
    FastNLPProcessorShallowNLPProcessor → Processor
  43. lazy val posTagger: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor
  44. 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
    FastBioNLPProcessorShallowNLPProcessor
  45. def postprocessTokens(originalTokens: Array[CoreLabel]): Array[CoreLabel]

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    Hook to allow postprocessing of CoreNLP tokenization This is useful for domain-specific corrections, such as the ones in BioNLPProcessor If you change the tokens, make sure to store them back in the sentence!

    Hook to allow postprocessing of CoreNLP tokenization This is useful for domain-specific corrections, such as the ones in BioNLPProcessor If you change the tokens, make sure to store them back in the sentence!

    originalTokens

    Input CoreNLP sentence

    returns

    The modified tokens

    Definition Classes
    FastBioNLPProcessorShallowNLPProcessor
  46. def postprocessTokens(sentence: CoreMap): List[CoreLabel]

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    Attributes
    protected
    Definition Classes
    ShallowNLPProcessor
  47. def preprocessSentences(origSentences: Iterable[String]): Iterable[String]

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    Definition Classes
    Processor
  48. def preprocessText(origText: String): String

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    Definition Classes
    FastBioNLPProcessor → Processor
  49. def preprocessTokens(origSentences: Iterable[Iterable[String]]): Iterable[Iterable[String]]

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    Definition Classes
    Processor
  50. def recognizeNamedEntities(doc: Document): Unit

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    Definition Classes
    FastBioNLPProcessorShallowNLPProcessor → Processor
  51. def resolveCoreference(doc: Document): Unit

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    Definition Classes
    FastBioNLPProcessorShallowNLPProcessor → Processor
  52. 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
  53. lazy val stanfordDepParser: DependencyParser

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    Stanford's NN dependency parser

    Stanford's NN dependency parser

    Definition Classes
    FastNLPProcessor
  54. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef
  55. def tagPartsOfSpeech(doc: Document): Unit

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    Definition Classes
    ShallowNLPProcessor → Processor
  56. def toString(): String

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    Definition Classes
    AnyRef → Any
  57. lazy val tokenizerWithSentenceSplitting: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor
  58. lazy val tokenizerWithoutSentenceSplitting: StanfordCoreNLP

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    Definition Classes
    ShallowNLPProcessor
  59. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  60. final def wait(arg0: Long, arg1: Int): Unit

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    AnyRef
    Annotations
    @throws( ... )
  61. final def wait(arg0: Long): Unit

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    AnyRef
    Annotations
    @throws( ... )
  62. val withChunks: Boolean

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    Definition Classes
    ShallowNLPProcessor

Inherited from FastNLPProcessor

Inherited from ShallowNLPProcessor

Inherited from Processor

Inherited from AnyRef

Inherited from Any

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