DarpaActions

Value Members

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

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

   Definition Classes

   AnyRef → Any

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

   

   Definition Classes

   AnyRef → Any

4. val MODIFIER_LABELS: Regex

   

5. val NOUN_LABELS: Regex

   

6. val OF_LABELS: Regex

   

7. val REG_LABELS: List[String]

   

8. val SEMANTIC_NEGATIVE_PATTERN: Regex

   

9. def addAdjectivalModifiers(tokens: Seq[Int], deps: DirectedGraph[String]): Seq[Int]

   

   Adds adjectival modifiers to all elements in the given path This is necessary so we can properly inspect the semantic negatives, which are often not in the path, but modify tokens in it, "*decreased* PTPN13 expression increases phosphorylation of EphrinB1"

10. final def asInstanceOf[T0]: T0

    

    Definition Classes

    Any

11. def bioprocessValid(m: Mention): Boolean

    

    Test whether the mention has a bioprocess controller and, if so, if its use is legitimate

12. def clone(): AnyRef

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

13. def consecutivePreps(path: Seq[Int], deps: DirectedGraph[String]): Boolean

    

14. final def convertEventToEntity(m: Mention, asOutput: Boolean = true, negated: Boolean = false): BioMention

    

    Recursively converts an Event to an Entity with the appropriate modifications representing its state.

    Recursively converts an Event to an Entity with the appropriate modifications representing its state. SimpleEvent -> theme + PTM
    Binding -> Complex (treated as an Entity)
    ComplexEvent -> recursive call on controlled (the event's "output")
    

    asOutput

    value of true to generate a Mention's output (ex. theme or controlled)

    Annotations

    @tailrec()

15. def countSemanticNegatives(trigger: Mention, arg: Mention, excluded: Set[Int]): Seq[Int]

    

    Gets a trigger, an argument and a set of tokens to be ignored.

    Gets a trigger, an argument and a set of tokens to be ignored. Returns the number of semantic negatives found in the shortest possible path between the trigger and the argument.

16. val deAcetylatPat: Regex

    

17. val deFarnesylatPat: Regex

    

18. val deGlycosylatPat: Regex

    

19. val deHydrolyPat: Regex

    

20. val deHydroxylatPat: Regex

    

21. val deMethylatPat: Regex

    

22. val dePhosphorylatPat: Regex

    

23. val deRibosylatPat: Regex

    

24. val deSumoylatPat: Regex

    

25. val deUbiquitinatPat: Regex

    

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

    

    Definition Classes

    AnyRef

27. def equals(arg0: Any): Boolean

    

    Definition Classes

    AnyRef → Any

28. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

29. def flipLabel(label: String): String

    

    gets a polarized label and returns it flipped

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

    

    Definition Classes

    AnyRef → Any

31. def getModificationLabel(text: String): String

    

    retrieves the appropriate modification label

32. def getModifiers(token: Int, deps: DirectedGraph[String]): Seq[Int]

    

33. def getNounModifiers(token: Int, deps: DirectedGraph[String]): Seq[Int]

    

34. def getOfModifiers(token: Int, deps: DirectedGraph[String]): Seq[Int]

    

35. def hasController(mention: Mention): Boolean

    

    Test whether the given mention has a controller argument.

36. def hasDistinctControllerControlled(m: Mention): Boolean

    

    Gets a mention and checks that the controller and controlled are different.

    Gets a mention and checks that the controller and controlled are different. Returns true if either the controller or the controlled is missing, or if they are both present and are distinct.

37. def hasNegativePolarity(m: Mention): Boolean

    

38. def hasSynPathOverlap(m: Mention): Boolean

    

    checks if a mention has a controller/controlled arguments with syntactic paths from the trigger that overlap

39. def hashCode(): Int

    

    Definition Classes

    AnyRef → Any

40. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

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

    

    Definition Classes

    AnyRef

42. final def notify(): Unit

    

    Definition Classes

    AnyRef

43. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

44. def nounModifiers(tokens: Seq[Int], deps: DirectedGraph[String]): Seq[Int]

    

45. def ofModifiers(tokens: Seq[Int], deps: DirectedGraph[String]): Seq[Int]

    

46. def overlappingSpansControllerControlled(m: Mention): Boolean

    

    Checks if the token spans of the controlled and controller overlap.

    Checks if the token spans of the controlled and controller overlap. Returns true if they do

47. def preferEventControllers(mentions: Seq[Mention]): Seq[Mention]

    

    Gets a sequence of mentions and returns only the ones that have Event controllers.

    Gets a sequence of mentions and returns only the ones that have Event controllers. If none is found, returns all mentions.

48. def proteinBetween(trigger: Mention, arg: Mention, state: State): Boolean

    

49. def removeDummy(m: BioMention): BioMention

    

50. def sameEntityID(m1: BioMention, m2: BioMention): Boolean

    

    Returns true if both mentions are grounded to the same entity

51. def switchLabel(mention: Mention): BioMention

    

    Gets a mention.

    Gets a mention. If it is an EventMention with a polarized label and it is negated an odd number of times, returns a new mention with the label flipped. Or else it returns the mention unmodified

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

    

    Definition Classes

    AnyRef

53. def toString(): String

    

    Definition Classes

    AnyRef → Any

54. def validArguments(mention: Mention, state: State): Boolean

    

55. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )