org.clulab.assembly.grammars.precedence.yml Maven / Gradle / Ivy

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# assembly sub-tree moved to main taxonomy
# these rules make use of labels that exist in that taxonomy
# rather than duplicate it here, the assembly branch was grafted there
taxonomy: org/clulab/reach/biogrammar/taxonomy.yml

# vars for assembly sieve
vars:
  mylabel: "Precedence"
  deprulepriority: "1"
  surfacerulepriority: "2"
  # < operator should be outside of regex
  after_type: "Event"
  # "after" should be some kind of Event that transforms "before"
  before_type: "Event"
  beforesurface: "[lemma=/^(before|prior|precede)$/]"
  aftersurface: "[lemma=/^follow|after$/]"

# rules for assembly sieve
rules:
  # Event rules
  - name: assembly-prep-syntax-1
    label: ${mylabel}
    priority: ${deprulepriority}
    example: "BEF is ubiquitinated before the phosphorylation of AFT."
    pattern: |
      before:${before_type}
      # before the AFT
      # TODO: Write surface rule for prior_to relations
      after:${after_type} = prep_before

  - name: assembly-prep-surface-1
    label: ${mylabel}
    priority: ${deprulepriority}
    example: "BEF is ubiquitinated before the phosphorylation of AFT."
    type: token
    pattern: |
      (? ${before_type}) (before | prior to) [tag=/^(DT|CD|JJ)$/]* (? ${after_type})

  - name: assembly-prep-syntax-2
    label: ${mylabel}
    priority: ${deprulepriority}
    example: "AFT is ubiquitinated following the phosphorylation of BEF."
    pattern: |
      after:${after_type}
      # after BEF
      before:${before_type} = /^prep_(after|following)$/

  - name: assembly-prep-surface-2
    label: ${mylabel}
    priority: ${surfacerulepriority}
    example: "AFT is ubiquitinated following the phosphorylation of BEF."
    type: token
    pattern: |
      (? ${after_type}) (after | [lemma=follow]) [tag=/^(DT|CD|JJ)$/]* (? ${before_type})

  - name: assembly-prep-syntax-3
    label: DirectConnection
    priority: ${deprulepriority}
    example: "AFT is ubiquitinated due to the phosphorylation of BEF."
    pattern: |
      after:${after_type}
      # due to BEF
      before:${before_type} = prep_due_to | prep_because_of

  - name: assembly-prep-surface-3
    label: ${mylabel}
    priority: ${surfacerulepriority}
    example: "AFT is ubiquitinated due to the phosphorylation of BEF."
    type: token
    pattern: |
      (? ${after_type}) (due to | because of) [tag=/^(DT|CD|JJ)$/]* (? ${before_type})

#  - name: assembly-verb-syntax-1
#    label: DirectConnection
#    priority: ${deprulepriority}
#    example: "the ubiquitination of BEF leads to the phosphorylation of AFT."
#    pattern: |
#      before:${before_type}
#      # ... leads to AFT
#      after:${after_type} =  ${before_type}) [lemma=/^(precede|precipitat)/] [tag=/^(DT|CD|JJ)$/]* (? ${after_type})

  - name: assembly-verb-syntax-3
    example: "AFT ubiquitination is a result of BEF phosphorylation.  AFT ubiquitination results from BEF phosphorylation."
    label: ${mylabel}
    priority: ${deprulepriority}
    pattern: |
     before:${after_type}
     # AFT results from BEF
     after:${before_type} =  ${after_type}) [lemma=be] [tag=/^(DT|CD|JJ)$/] [lemma=result] of [tag=/^(DT|CD|JJ)$/]* (? ${before_type})

  - name: assembly-verb-surface-3b
    label: ${mylabel}
    priority: ${surfacerulepriority}
    example: "AFT ubiquitination results from BEF phosphorylation."
    type: token
    pattern: |
      (? ${after_type}) ","? [tag=RB]? [lemma=result & tag=/^VB/] from [tag=/^(DT|CD|JJ)$/]* (? ${before_type})

  - name: assembly-verb-syntax-4
    example: "BEF is ubiquitinated, resulting in the phosphorylation of AFT."
    label: ${mylabel}
    priority: ${deprulepriority}
    pattern: |
     after:${after_type}
     # BEF ..., resulting from ...
     before:${before_type} = xcomp nsubjpass

  - name: assembly-verb-surface-4and6
    label: ${mylabel}
    priority: ${surfacerulepriority}
    example: "BEF is ubiquitinated, resulting in the phosphorylation of AFT."
    type: token
    pattern: |
      (? ${before_type}) ","? [tag=RB]? [lemma=result & tag=/^VB/] in [tag=/^(DT|CD|JJ)$/]* (? ${after_type})

  - name: assembly-verb-syntax-5
    example: "As a result of BEF phosphorylation, AFT is ubiquitinated. AFT is phosphorylated as a result of BEF ubiqutination."
    label: ${mylabel}
    priority: ${deprulepriority}
    pattern: |
     after:${after_type}
     before:${before_type} = prep_as [lemma=result] /prepc?_of/

  - name: assembly-verb-syntax-6
    example: "AFT phosphorylation results in BEF ubiqutination."
    label: ${mylabel}
    priority: ${deprulepriority}
    pattern: |
     before:${before_type}
     after:${after_type} =  ${before_type}) ","? when (? ${after_type})

  # Passives
  - name: assembly-syntax-pass-1
    label: DirectConnection
    priority: ${deprulepriority}
    example: "the ubiquitination of BEF is followed by the phosphorylation of AFT."
    pattern: |
      before:${before_type}
      after:${after_type} =