edu.arizona.sista.reach.grounding

KnowledgeBaseConstants

Related Doc: package grounding

trait KnowledgeBaseConstants extends AnyRef

Trait for defining constants used by grounding and entity checking code. Written by Tom Hicks. 5/26/2015. Last Modified: Add auxiliary KB filenames.

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AuxBioProcessKBAccessor, AuxMetaboliteKBAccessor, AuxProteinKBAccessor, EntityChecker, GendCellLocationKBAccessor, GendChemicalKBAccessor, GendProteinFamilyKBAccessor, GendProteinKBAccessor, LocalKBAccessor, LocalKBLookup, LocalKBUtils, LocalKeyTransforms, LocalProteinFamilyKBAccessor, LocalProteinKBAccessor, ManualCellLocationKBAccessor, ManualChemicalKBAccessor, ManualProteinFamilyKBAccessor, ManualProteinKBAccessor, StaticCellLocationKBAccessor, StaticCellLocationKBLookup, StaticChemicalKBAccessor, StaticChemicalKBLookup, StaticMetaboliteKBAccessor, StaticMetaboliteKBLookup, StaticProteinFamilyKBAccessor, StaticProteinFamilyKBLookup, StaticProteinKBAccessor, StaticProteinKBLookup, StaticTissueTypeKBAccessor, StaticTissueTypeKBLookup
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  4. val AllKeysStopSuffixes: Set[String]

    The set of words to remove from all keys to create a lookup key.

  5. val AuxBioProcessFilename: String

    Filename of the auxiliary biological processes file.

  6. val AuxCellLocationFilename: String

    Filename of the auxiliary cellular location file.

  7. val AuxChemicalFilename: String

    Filename of the auxiliary small molecule (chemical) file.

  8. val AuxMetaboliteFilename: String

    Filename of the auxiliary small molecule (metabolite) file.

  9. val AuxProteinFamilyFilename: String

    Filename of the auxiliary protein family file.

  10. val AuxProteinFilename: String

    Filename of the auxiliary protein file.

  11. val AuxTissueTypeFilename: String

    Filename of the auxiliary protein file.

  12. val FamilyStopSuffixes: Set[String]

    The set of words to remove from a key to create a protein family lookup key.

  13. val GendCellLocationFilename: String

    Filename of the cellular location file generated by the entity checker.

  14. val GendCellLocationPrefix: String

    Prefix string for cellular location IDs generated by the entity checker.

  15. val GendChemicalFilename: String

    Filename of the small molecule file generated by the entity checker.

  16. val GendChemicalPrefix: String

    Prefix string for small molecule IDs generated by the entity checker.

  17. val GendProteinFilename: String

    Filename of the protein/family file generated by the entity checker.

  18. val GendProteinPrefix: String

    Prefix string for protein/family IDs generated by the entity checker.

  19. val HumanLabels: Set[String]

    The set of words to remove from the text to create a lookup key.

  20. val KBDirFilePath: String

    File Path to the directory which holds the entity knowledge bases.

  21. val KBDirResourcePath: String

    Resource Path to the directory which holds the entity knowledge bases.

  22. val KeyCharactersToRemove: Set[Char]

    The set of characters to remove from the text to create a lookup key.

  23. val ManualCellLocationFilename: String

    Filename of the manually maintained cellular location file.

  24. val ManualChemicalFilename: String

    Filename of the manually maintained small molecule file.

  25. val ManualProteinFamilyFilename: String

    Filename of the manually maintained protein family file.

  26. val ManualProteinFilename: String

    Filename of the manually maintained protein file.

  27. val ProteinStopSuffixes: Set[String]

    The set of words to remove from a key to create a protein lookup key.

  28. val StaticCellLocationFilename: String

    Filename of the static cellular location file.

  29. val StaticChemicalFilename: String

    Filename of the static small molecule (chemical) file.

  30. val StaticMetaboliteFilename: String

    Filename of the static small molecule (chemical) file.

  31. val StaticProteinFamilyFilename: String

    Filename of the static protein family file.

  32. val StaticProteinFilename: String

    Filename of the static protein file.

  33. val StaticTissueTypeFilename: String

    Filename of the static tissue type file.

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