Syntactic Rule Variants

For any rule you construct, consider the following syntactic variations. Note that most of these examples are made up, so don't take the specific wording too seriously.

Don't forget to include all synonyms for a reaction that have the same syntax! E.g. make sure to match 'transport' as well as 'translocation' and 'trafficking' if these have functionally identical meanings.

Don't forget to exclude similar words you don't want to match, e.g. a trigger of word=/phosphor/ will match 'dephosphorylate'.

Declarative

The theme (the thing acted on by the verb) is the direct object of a verb.

Example: "Smurf1 and Smurf2 degrade and ubiquitinate RhoA"

- name: degradation_decl
  priority: 4
  action: mkDegradation
  example: "Smurf1 and Smurf2 degrade and ubiquitinate RhoA"
  type: dependency
  label: Degradation
  pattern: |
    trigger: [word=/(?i)^degrad/ & tag=/^VB[^N]?/]
    theme: dobj [mention=/Gene_or_gene_product|Complex/]
    cause: nsubj [mention=/Simple_chemical|Gene_or_gene_product/]

Passive

The theme is the syntactic subject of a verb phrase.

Example: "RhoA is ubiquitinated and degraded by Smurf1 and Smurf2"

- name: degradation_pass
  priority: 4
  action: mkDegradation
  example: "RhoA is ubiquitinated and degraded by Smurf1 and Smurf2"
  type: dependency
  label: Degradation
  pattern: |
    trigger: [word=/(?i)^degrad/ & tag=/^VBN/]
    theme: nsubjpass [mention=/Gene_or_gene_product|Complex/]
    cause: agent [mention=/Simple_chemical|Gene_or_gene_product/]

Prepositional Nominalization

The trigger is in noun form and entities are in prepositional phrases. Note that because of the difficulty of prepositional attachment, the parse will usually be wrong, so be sure to run examples through the visualizer and/or use a surface rule.

Example: "The ubiquitination and degradation of RhoA by Smurf1 and Smurf2 increased."

- name: degradation_prepnom
  priority: 4
  action: mkDegradation
  example: "The ubiquitination and degradation of RhoA by Smurf1 and Smurf2 increased."
  type: dependency
  label: Degradation
  pattern: |
    trigger: [word=/(?i)^degrad/ & tag=/^N/]
    theme: <conj_and* prep_of [mention=/Gene_or_gene_product|Complex/]
    cause: <conj_and* prep_by [mention=/Simple_chemical|Gene_or_gene_product/]

Object Nominalization

The trigger is in noun form and with the theme in NN attachment.

Example: "RhoA ubiquitination and degradation by Smurf1 and Smurf2 increased."

Example: "We compared the rate of GTP hydrolysis for Ras and mUbRas..."

- name: degradation_objnom
  priority: 4
  action: mkDegradation
  example: "RhoA ubiquitination and degradation by Smurf1 and Smurf2 increased."
  type: dependency
  label: Degradation
  pattern: |
    trigger: [word=/(?i)^degrad/ & tag=/^N/]
    theme: <conj_and* nn [mention=/Gene_or_gene_product|Complex/]
    cause: <conj_and* (prep_by | prep_for) [mention=/Simple_chemical|Gene_or_gene_product/]

Subject Nominalization

The trigger is in noun form and with the cause in NN attachment.

Example: "Smurf1 ubiquitination and degradation of RhoA increased."

- name: degradation_subjnom
  priority: 4
  action: mkDegradation
  example: "Smurf1 ubiquitination and degradation of RhoA increased."
  type: dependency
  label: Degradation
  pattern: |
    trigger: [word=/(?i)^degrad/ & tag=/^N/]
    theme: <conj_and* prep_of [mention=/Gene_or_gene_product|Complex/]
    cause: <conj_and* nn [mention=/Simple_chemical|Gene_or_gene_product/]

Subject Relative Clause (with optional Apposition)

Example: "Its many abnormal phenotypes can be rescued via Pde2, which specifically hydrolyzes cAMP."

Example: "its many abnormal phenotypes can be rescued via overexpressing Pde2, a phosphodiesterase that specifically hydrolyzes cAMP."

- name: hydrolysis_subjrel
  priority: 4
  action: mkHydrolysis
  example: "Its many abnormal phenotypes can be rescued via Pde2, which specifically hydrolyzes cAMP."
  type: dependency
  label: Hydrolysis
  pattern: |
    trigger: [word=/(?i)^hydrolyz/ & tag=/^VB[^N]?/]
    theme: dobj [mention=/Gene_or_gene_product|Complex/]
    cause: <rcmod (<appos)? [mention=/Simple_chemical|Gene_or_gene_product/]

Object Relative Clause (with optional Apposition)

Example: "We measured transcription activation in the presence of cAMP, which is hydrolyzed by CRP."

Example: "We measured transcription activation in the presence of cAMP, a regulatory protein that is hydrolyzed by CRP."

- name: hydrolysis_objrel
  priority: 4
  action: mkHydrolysis
  example: "We measured transcription activation in the presence of cAMP, which is hydrolyzed by CRP."
  type: dependency
  label: Hydrolysis
  pattern: |
    trigger: [word=/(?i)^hydrolyz/ & tag=VBN]
    theme: <rcmod (<appos)? [mention=/Gene_or_gene_product|Complex/]
    cause: agent [mention=/Simple_chemical|Gene_or_gene_product/]

Subject Apposition

Example: "Via yeast two-hybrid screening, we found that a novel protein, A20, binds to ABIN."

Object Apposition

Example: "Via yeast two-hybrid screening, we found that A20 binds to a novel protein, ABIN"

Paraphrastic Causative

The trigger is separated from an entity by a verb.

Example: "Smurf1 causes the degradation of RhoA."

Example: "The degradation of RhoA is catalyzed by Smurf1."

Combinations of the Above

Appositive subject relative plus passivization: "Pde2, which has been found to hydrolyze Ras, activates MEK."