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BioNLP-ST-ID
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annotation.conf

annotation.conf 2.0 KB
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  1. # -*- Mode: Text; tab-width: 8; indent-tabs-mode: nil; coding: utf-8; -*-
    2. 

  2. # vim:set ft=conf ts=2 sw=2 sts=2 autoindent:
    3. 

  3. 

  4. # Simple text-based definitions of entity, relation and event types
    5. 

  5. # and event attributes for the BioNLP Shared Task 2011 ID task.
    6. 

  6. 

  7. [entities]
    8. 

  8. 

  9. Protein
    10. 

  10. Entity
    11. 

  11. Chemical
    12. 

  12. Organism
    13. 

  13. Two-component-system
    14. 

  14. Regulon-operon
    15. 

  15. 

  16. 

  17. [relations]
    18. 

  18. 

  19. Equiv	Arg1:Protein, Arg2:Protein, <REL-TYPE>:symmetric-transitive
    20. 

  20. Equiv	Arg1:Chemical, Arg2:Chemical, <REL-TYPE>:symmetric-transitive
    21. 

  21. Equiv	Arg1:Organism, Arg2:Organism, <REL-TYPE>:symmetric-transitive
    22. 

  22. Equiv	Arg1:Two-component-system, Arg2:Two-component-system, <REL-TYPE>:symmetric-transitive
    23. 

  23. Equiv	Arg1:Regulon-operon, Arg2:Regulon-operon, <REL-TYPE>:symmetric-transitive
    24. 

  24. Equiv	Arg1:Entity, Arg2:Entity, <REL-TYPE>:symmetric-transitive
    25. 

  25. 

  26. # "ENTITY-NESTING" is a special relation type used to define
    27. 

  27. # which entity annotations can nest.
    28. 

  28. 

  29. ENTITY-NESTING	Arg1:Protein, Arg2:Two-component-system
    30. 

  30. ENTITY-NESTING	Arg1:Protein, Arg2:Organism
    31. 

  31. ENTITY-NESTING	Arg1:Protein, Arg2:Regulon-operon
    32. 

  32. ENTITY-NESTING	Arg1:Two-component-system, Arg2:Organism
    33. 

  33. ENTITY-NESTING	Arg1:Chemical, Arg2:Organism
    34. 

  34. 

  35. 

  36. [events]
    37. 

  37. 

  38. <CORE-ENTITY>=Protein|Chemical|Organism|Two-component-system|Regulon-operon
    39. 

  39. 

  40. Gene_expression	Theme:Protein|Regulon-operon
    41. 

  41. Transcription	Theme:Protein|Regulon-operon
    42. 

  42. Protein_catabolism	Theme:Protein
    43. 

  43. Localization	Theme:<CORE-ENTITY>, ToLoc?:Entity, AtLoc?:Entity
    44. 

  44. Binding	Theme+:<CORE-ENTITY>, Site*:Entity
    45. 

  45. ----------------------------------------
    46. 

  46. Phosphorylation	Theme:Protein, Site?:Entity
    47. 

  47. ----------------------------------------
    48. 

  48. Process	Participant?:Organism
    49. 

  49. ----------------------------------------
    50. 

  50. Regulation	Theme:<CORE-ENTITY>|<EVENT>, Cause?:<CORE-ENTITY>|<EVENT>, Site?:Entity, CSite?:Entity
    51. 

  51. Positive_regulation	Theme:<CORE-ENTITY>|<EVENT>, Cause?:<CORE-ENTITY>|<EVENT>, Site?:Entity, CSite?:Entity
    52. 

  52. Negative_regulation	Theme:<CORE-ENTITY>|<EVENT>, Cause?:<CORE-ENTITY>|<EVENT>, Site?:Entity, CSite?:Entity
    53. 

  53. 

  54. 

  55. [attributes]
    56. 

  56. 

  57. Negation	Arg:<EVENT>
    58. 

  58. Speculation	Arg:<EVENT>
    59.