edu.arizona.sista.reach.grounding

IMKBOrganCellTypeLookup

Related Doc: package grounding

class IMKBOrganCellTypeLookup extends IMKBLookup

Class implementing alternate key lookups for cell types which can be inferred from the organ name and specific contextual suffixes. Written by Tom Hicks. 12/20/2015. Last Modified: Change to class, add IMKB ctor argument.

Linear Supertypes
IMKBLookup, ReachKBKeyTransforms, KBAltLookup, KBKeyTransforms, KBLookup, Speciated, AnyRef, Any
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Inherited
  1. IMKBOrganCellTypeLookup
  2. IMKBLookup
  3. ReachKBKeyTransforms
  4. KBAltLookup
  5. KBKeyTransforms
  6. KBLookup
  7. Speciated
  8. AnyRef
  9. Any
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Visibility
  1. Public
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Instance Constructors

  1. new IMKBOrganCellTypeLookup(memoryKB: InMemoryKB = new InMemoryKB())

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

    Definition Classes
    Speciated

  5. def applyTransforms(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

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

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

  8. def containsHumanNsId(nsIdSeq: Seq[String]): Boolean

    Tell whether the given sequence of namespace/ID strings contains a human nsId.

    Tell whether the given sequence of namespace/ID strings contains a human nsId.

    Definition Classes
    Speciated

  9. def containsHumanSpecies(speciesSeq: Seq[String]): Boolean

    Tell whether the given sequence of species strings contain a human species label.

    Tell whether the given sequence of species strings contain a human species label.

    Definition Classes
    Speciated

  10. def entries: Seq[KBEntry]

    Return a sequence over the entries in this KB.

    Return a sequence over the entries in this KB.

    Definition Classes
    IMKBLookup

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

    Definition Classes
    AnyRef

  12. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  13. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  15. def hasHumanNsId(nsId: String): Boolean

    Tell whether the given namespace/ID string is an ID for humans or not.

    Tell whether the given namespace/ID string is an ID for humans or not.

    Definition Classes
    Speciated

  16. def hasSpeciesInfo: Boolean

    Tell whether this KB contains species information or not.

    Tell whether this KB contains species information or not.

    Definition Classes
    IMKBLookup

  17. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  18. def hyphenatedProteinKey(text: String): String

    Check for one of several types of hyphen-separated strings and, if found, extract and return the candidate text portion, else return the text unchanged.

    Check for one of several types of hyphen-separated strings and, if found, extract and return the candidate text portion, else return the text unchanged.

    Definition Classes
    ReachKBKeyTransforms

  19. 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

  20. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  21. 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

  22. 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

  23. var memoryKB: InMemoryKB

    Definition Classes
    IMKBLookup

  24. def metaInfo: IMKBMetaInfo

    Return meta information about the external KB from which this KB was created.

    Return meta information about the external KB from which this KB was created.

    Definition Classes
    IMKBLookup

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

    Definition Classes
    AnyRef

  26. final def notify(): Unit

    Definition Classes
    AnyRef

  27. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  28. 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

  29. def resolve(text: String): Resolutions

    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
    IMKBOrganCellTypeLookup → IMKBLookup → KBLookup

  30. def resolveAlt(text: String, transforms: KeyTransforms): Resolutions

    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

  31. def resolveByASpecies(text: String, species: String): Resolutions

    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
    IMKBOrganCellTypeLookup → IMKBLookup → KBLookup

  32. def resolveByASpeciesAlt(text: String, species: String, transforms: KeyTransforms): Resolutions

    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

  33. def resolveBySpecies(text: String, speciesSet: SpeciesNameSet): Resolutions

    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
    IMKBOrganCellTypeLookup → IMKBLookup → KBLookup

  34. def resolveBySpeciesAlt(text: String, speciesSet: SpeciesNameSet, transforms: KeyTransforms): Resolutions

    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(text: String): Resolutions

    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
    IMKBOrganCellTypeLookup → IMKBLookup → KBLookup

  36. def resolveHumanAlt(text: String, transforms: KeyTransforms): Resolutions

    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

  37. def resolveNoSpecies(text: String): Resolutions

    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
    IMKBOrganCellTypeLookup → IMKBLookup → KBLookup

  38. def resolveNoSpeciesAlt(text: String, transforms: KeyTransforms): Resolutions

    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

  39. def stripFamilySuffixes(text: String): String

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

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

    Definition Classes
    ReachKBKeyTransforms

  40. def stripMutantProtein(text: String): String

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

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

    Definition Classes
    ReachKBKeyTransforms

  41. def stripOrganCellTypeSuffixes(text: String): String

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

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

    Definition Classes
    ReachKBKeyTransforms

  42. def stripPTMPrefixes(text: String): String

    Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return the text unchanged.

    Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return the text unchanged.

    Definition Classes
    ReachKBKeyTransforms

  43. def stripProteinSuffixes(text: String): String

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

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

    Definition Classes
    ReachKBKeyTransforms

  44. 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

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

    Definition Classes
    AnyRef

  46. def toString(): String

    Definition Classes
    AnyRef → Any

  47. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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