edu.arizona.sista.reach.grounding

GendProteinFamilyKBML

Related Doc: package grounding

class GendProteinFamilyKBML extends IMKBFamilyMentionLookup

KB accessor to resolve protein family names via KBs generated from the BioPax model.

Linear Supertypes
IMKBFamilyMentionLookup, IMKBMentionLookup, KBAltMentionLookup, KBMentionLookup, IMKBLookup, ReachKBKeyTransforms, KBAltLookup, KBKeyTransforms, KBLookup, Speciated, AnyRef, Any
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Inherited
  1. GendProteinFamilyKBML
  2. IMKBFamilyMentionLookup
  3. IMKBMentionLookup
  4. KBAltMentionLookup
  5. KBMentionLookup
  6. IMKBLookup
  7. ReachKBKeyTransforms
  8. KBAltLookup
  9. KBKeyTransforms
  10. KBLookup
  11. Speciated
  12. AnyRef
  13. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new GendProteinFamilyKBML()

Type Members

  1. type KeyTransforms = Seq[(String) ⇒ String]

    Type alias for functions which take a text string and return a potential key string.

    Type alias for functions which take a text string and return a potential key string.

    Definition Classes
    KBKeyTransforms

  2. type SpeciesNameSet = Set[String]

    Species name sets.

    Species name sets.

    Definition Classes
    Speciated

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 HumanLabels: SpeciesNameSet

    A set of label strings for humans, found in KBs.

    A set of label strings for humans, found in KBs.

    Definition Classes
    Speciated

  5. def SpeciesNameSet(xs: String*): Set[String]

    Definition Classes
    Speciated

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  9. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  10. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  12. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  13. def isHumanSpecies(species: String): Boolean

    Tell whether the given species string is label for humans or not.

    Tell whether the given species string is label for humans or not.

    Definition Classes
    Speciated

  14. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  15. def isMemberOf(species: String, speciesSet: SpeciesNameSet): Boolean

    Tell whether the given species string is a member of the given set of species.

    Tell whether the given species string is a member of the given set of species.

    Definition Classes
    Speciated

  16. def makeAlternateKeys(text: String, transformFns: KeyTransforms): Seq[String]

    Return a sequence of alternate keys, one for each of the given key transforms.

    Return a sequence of alternate keys, one for each of the given key transforms.

    Definition Classes
    KBKeyTransforms

  17. def makeCanonicalKey(text: String): String

    Canonicalize the given text string into a key for both storage and lookup.

    Canonicalize the given text string into a key for both storage and lookup.

    Definition Classes
    ReachKBKeyTransforms

  18. val memoryKB: InMemoryKB

    The in-memory knowledge base that all lookups will work against.

    The in-memory knowledge base that all lookups will work against.

    Definition Classes
    GendProteinFamilyKBML → IMKBLookup

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

    Definition Classes
    AnyRef

  20. final def notify(): Unit

    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  22. def reachAlternateKeys(text: String, transformFns: KeyTransforms): Seq[String]

    Return alternate lookup keys created from the given text string and transform functions.

    Return alternate lookup keys created from the given text string and transform functions.

    Definition Classes
    ReachKBKeyTransforms

  23. def resolve(mention: Mention): Option[KBResolution]

    Resolve the given Mention to an optional entry in a knowledge base.

    Resolve the given Mention to an optional entry in a knowledge base. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBFamilyMentionLookup → IMKBMentionLookup → KBMentionLookup

  24. def resolve(text: String): Option[KBResolution]

    Resolve the given text string to an optional entry in a knowledge base.

    Resolve the given text string to an optional entry in a knowledge base. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBLookup → KBLookup

  25. def resolveAlt(mention: Mention, transforms: KeyTransforms): Option[KBResolution]

    Resolve the given Mention to an optional entry in a knowledge base.

    Resolve the given Mention to an optional entry in a knowledge base. If the mention is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBMentionLookup → KBAltMentionLookup

  26. def resolveAlt(text: String, transforms: KeyTransforms): Option[KBResolution]

    Resolve the given text string to an optional entry in a knowledge base.

    Resolve the given text string to an optional entry in a knowledge base. If the text is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBLookup → KBAltLookup

  27. def resolveByASpecies(mention: Mention, species: String): Option[KBResolution]

    Resolve the given Mention to an optional entry in a knowledge base, for the single named species.

    Resolve the given Mention to an optional entry in a knowledge base, for the single named species. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBFamilyMentionLookup → IMKBMentionLookup → KBMentionLookup

  28. def resolveByASpecies(text: String, species: String): Option[KBResolution]

    Resolve the given text string to an optional entry in a knowledge base, for the single named species.

    Resolve the given text string to an optional entry in a knowledge base, for the single named species. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBLookup → KBLookup

  29. def resolveByASpeciesAlt(mention: Mention, species: String, transforms: KeyTransforms): Option[KBResolution]

    Resolve the given Mention to an optional entry in a knowledge base, for the single named species.

    Resolve the given Mention to an optional entry in a knowledge base, for the single named species. If the mention is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBMentionLookup → KBAltMentionLookup

  30. def resolveByASpeciesAlt(text: String, species: String, transforms: KeyTransforms): Option[KBResolution]

    Resolve the given text string to an optional entry in a knowledge base, for the single named species.

    Resolve the given text string to an optional entry in a knowledge base, for the single named species. If the text is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBLookup → KBAltLookup

  31. def resolveBySpecies(mention: Mention, speciesSet: SpeciesNameSet): Option[Iterable[KBResolution]]

    Resolve the given Mention to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.

    Resolve the given Mention to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.

    Definition Classes
    IMKBFamilyMentionLookup → IMKBMentionLookup → KBMentionLookup

  32. def resolveBySpecies(text: String, speciesSet: SpeciesNameSet): Option[Iterable[KBResolution]]

    Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.

    Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.

    Definition Classes
    IMKBLookup → KBLookup

  33. def resolveBySpeciesAlt(mention: Mention, speciesSet: SpeciesNameSet, transforms: KeyTransforms): Option[Iterable[KBResolution]]

    Resolve the given Mention to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.

    Resolve the given Mention to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB. If the mention is not found, use the given text transforming functions to create and lookup alternate keys.

    Definition Classes
    IMKBMentionLookup → KBAltMentionLookup

  34. def resolveBySpeciesAlt(text: String, speciesSet: SpeciesNameSet, transforms: KeyTransforms): Option[Iterable[KBResolution]]

    Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.

    Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB. If the text is not found, use the given text transforming functions to create and lookup alternate keys.

    Definition Classes
    IMKBLookup → KBAltLookup

  35. def resolveHuman(mention: Mention): Option[KBResolution]

    Resolve the given Mention to an optional entry in a knowledge base, failing if the entry is not for humans.

    Resolve the given Mention to an optional entry in a knowledge base, failing if the entry is not for humans. Return a resolution for a human entry, if any found.

    Definition Classes
    IMKBFamilyMentionLookup → IMKBMentionLookup → KBMentionLookup

  36. def resolveHuman(text: String): Option[KBResolution]

    Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans.

    Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans. Return a resolution for a human entry, if any found.

    Definition Classes
    IMKBLookup → KBLookup

  37. def resolveHumanAlt(mention: Mention, transforms: KeyTransforms): Option[KBResolution]

    Resolve the given Mention to an optional entry in a knowledge base, failing if the entry is not for humans.

    Resolve the given Mention to an optional entry in a knowledge base, failing if the entry is not for humans. If the mention is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for a human entry, if any found.

    Definition Classes
    IMKBMentionLookup → KBAltMentionLookup

  38. def resolveHumanAlt(text: String, transforms: KeyTransforms): Option[KBResolution]

    Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans.

    Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans. If the text is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for a human entry, if any found.

    Definition Classes
    IMKBLookup → KBAltLookup

  39. def resolveNoSpecies(mention: Mention): Option[KBResolution]

    Resolve the given Mention to an optional entry in a knowledge base which explicitly does not have an associated species.

    Resolve the given Mention to an optional entry in a knowledge base which explicitly does not have an associated species. Fail if all entries have species. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBFamilyMentionLookup → IMKBMentionLookup → KBMentionLookup

  40. def resolveNoSpecies(text: String): Option[KBResolution]

    Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species.

    Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species. Fail if all entries have species. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBLookup → KBLookup

  41. def resolveNoSpeciesAlt(mention: Mention, transforms: KeyTransforms): Option[KBResolution]

    Resolve the given Mention to an optional entry in a knowledge base which explicitly does not have an associated species.

    Resolve the given Mention to an optional entry in a knowledge base which explicitly does not have an associated species. Fail if all entries have species. If the mention is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBMentionLookup → KBAltMentionLookup

  42. def resolveNoSpeciesAlt(text: String, transforms: KeyTransforms): Option[KBResolution]

    Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species.

    Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species. Fail if all entries have species. If the text is not found, use the given text transforming functions to create and lookup alternate keys. Return a resolution for the entry, if any found.

    Definition Classes
    IMKBLookup → KBAltLookup

  43. def stripFamilySuffixes(key: String): String

    Return the portion of the key string minus one of the protein family suffixes, if found in the given key string, else return the key unchanged.

    Return the portion of the key string minus one of the protein family suffixes, if found in the given key string, else return the key unchanged.

    Definition Classes
    ReachKBKeyTransforms

  44. def stripMutantProtein(key: String): String

    Return the portion of the key string before a trailing mutation phrase, if found in the given key string, else return the key unchanged.

    Return the portion of the key string before a trailing mutation phrase, if found in the given key string, else return the key unchanged.

    Definition Classes
    ReachKBKeyTransforms

  45. def stripOrganCellTypeSuffixes(key: String): String

    Return the portion of the key string minus one of the organ-cell-type suffixes, if found in the given key string, else return the key unchanged.

    Return the portion of the key string minus one of the organ-cell-type suffixes, if found in the given key string, else return the key unchanged.

    Definition Classes
    ReachKBKeyTransforms

  46. def stripProteinSuffixes(key: String): String

    Return the portion of the key string minus one of the protein suffixes, if found in the given key string, else return the key unchanged.

    Return the portion of the key string minus one of the protein suffixes, if found in the given key string, else return the key unchanged.

    Definition Classes
    ReachKBKeyTransforms

  47. def stripSuffixes(suffixes: Seq[String], text: String): String

    Try to remove all of the suffixes in the given set from the given text.

    Try to remove all of the suffixes in the given set from the given text.

    Definition Classes
    KBKeyTransforms

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

    Definition Classes
    AnyRef

  49. def toString(): String

    Definition Classes
    AnyRef → Any

  50. def unmutateProteinKey(key: String): String

    Return the protein portion of a mutatation-protein string, if found in the given key string, else return the key unchanged.

    Return the protein portion of a mutatation-protein string, if found in the given key string, else return the key unchanged.

    Definition Classes
    ReachKBKeyTransforms

  51. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from IMKBFamilyMentionLookup

Inherited from IMKBMentionLookup

Inherited from KBAltMentionLookup

Inherited from KBMentionLookup

Inherited from IMKBLookup

Inherited from ReachKBKeyTransforms

Inherited from KBAltLookup

Inherited from KBKeyTransforms

Inherited from KBLookup

Inherited from Speciated

Inherited from AnyRef

Inherited from Any

Ungrouped