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events_master.yml
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events_master.yml
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taxonomy: org/clulab/reach/biogrammar/taxonomy.yml
vars:
# triggers and lookaheads/behinds for regulations and activations
auxtriggers: "activ|regul"
posTriggers: "acceler|accept|activat|aid|allow|augment|cataly|caus|contribut|direct|driv|elev|elicit|enabl|enhanc|increas|induc|initi|interconvert|lead|led|mediat|modul|necess|overexpress|potenti|produc|prolong|promot|rais|reactivat|re-express|rescu|restor|retent|signal|stimul|support|synerg|synthes|target|trigger|underli|up-regul|upregul"
negTriggers: "attenu|abolish|abrog|antagon|arrest|attenu|block|deactiv|decreas|degrad|deplet|deregul|diminish|disrupt|down-reg|downreg|dysregul|elimin|impair|imped|inactiv|inhibit|knockdown|limit|loss|lower|negat|nullifi|perturb|prevent|reduc|reliev|repress|resist|restrict|revers|sequester|shutdown|slow|starv|suppress|supress"
# For the record: OLD triggers, no longer used
#posnouns: "acceler|activ|augment|cataly|caus|driv|elev|elicit|enhanc|increas|induc|induct|initi|produc|promot|promot|rais|reactiv|re-express|releas|stimul|trigger|up-regul|upregul"
#negnouns: "decreas|inhibit|loss|repress|suppress|supress"
#posRegTriggers: "acceler|accept|accumul|action|activat|aid|allow|associ|augment|cataly|caus|cleav|confer|contribut|convert|direct|driv|elev|elicit|enabl|enhanc|escort|export|gener|high|increas|induc|induct|initi|interact|interconvert|involv|lead|led|major|mediat|modul|necess|overexpress|potent|proce|produc|prolong|promot|rais|reactivat|re-express|releas|render|requir|rescu|respons|restor|result|retent|signal|stimul|support|synerg|synthes|target|trigger|underli|up-regul|upregul"
#posActTriggers: "acceler|activat|aid|allow|augment|direct|elev|elicit|enabl|enhanc|increas|induc|initi|modul|necess|overexpress|potenti|produc|prolong|promot|rais|reactivat|rescu|respons|restor|re-express|retent|sequest|signal|stimul|support|synerg|synthes|trigger|up-regul|upregul"
#negRegTriggers: "abolish|abrog|absenc|antagon|arrest|attenu|block|blunt|deactiv|decreas|defect|defici|degrad|delay|deplet|deregul|diminish|disengag|disrupt|down|down-reg|downreg|drop|dysregul|elimin|impair|imped|inactiv|inhibit|interf|knockdown|lack|limit|loss|lost|lower|negat|neutral|nullifi|oppos|overc|perturb|prevent|reduc|reliev|remov|repress|resist|restrict|revers|sequester|shutdown|slow|starv|suppress|supress|uncoupl"
#negActTriggers: "inhibit|knockdown|limit|lower|negat|reduc|reliev|repress|restrict|revers|sequester|slow|starv|suppress|supress"
rules:
- import: org/clulab/reach/biogrammar/events/bind_events.yml
vars:
priority: "7"
- import: org/clulab/reach/biogrammar/events/transcription_events.yml
vars:
priority: "7"
- import: org/clulab/reach/biogrammar/events/decrease_events.yml
vars:
triggerLemma: "loss"
priority: "7"
- import: org/clulab/reach/biogrammar/events/amount_events.yml
vars:
triggerLemma: "amount|level|quantity"
priority: "7"
- import: org/clulab/reach/biogrammar/events/hydrolysis_events.yml
vars:
priority: "7"
- import: org/clulab/reach/biogrammar/events/dehydrolysis_events.yml
vars:
priority: "7"
- import: org/clulab/reach/biogrammar/events/translocation_events.yml
vars:
priority: "7"
###############################################################################
#
# Simple events
#
###############################################################################
# Phosphorylations
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Phosphorylation"
actionFlow: "mkBioMention"
label: "Phosphorylation"
verbalTriggerLemma: "phosphorylate"
nominalTriggerLemma: "phosphorylation"
triggerPrefix: "!word=/(?i)^(de|auto)/"
priority: "7"
# AutoPhosphorylations
- import: org/clulab/reach/biogrammar/events/simple-event-auto_template.yml
vars:
eventName: "AutoPhosphorylation"
actionFlow: "handleAutoEvent"
label: "AutoPhosphorylation"
verbalTriggerLemma: "auto-?phosphorylate"
baseVerbalTriggerLemma: "phosphorylate"
nominalTriggerLemma: "auto-?phosphorylation"
triggerPrefix: "!word=/(?i)^de/"
priority: "7"
# Ubiquitination
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Ubiquitination"
actionFlow: "mkUbiquitination"
label: "Ubiquitination"
verbalTriggerLemma: "ubiquit(in|yl)ate"
nominalTriggerLemma: "ubiquit(in|yl)ation"
triggerPrefix: "!word=/(?i)^de/"
priority: "7"
# Hydroxylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Hydroxylation"
actionFlow: "mkBioMention"
label: "Hydroxylation"
verbalTriggerLemma: "hydroxylate"
nominalTriggerLemma: "hydroxylation"
triggerPrefix: "!word=/(?i)^de/"
priority: "7"
# Sumoylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Sumoylation"
actionFlow: "mkBioMention"
label: "Sumoylation"
verbalTriggerLemma: "sumoylate"
nominalTriggerLemma: "sumoylation"
triggerPrefix: "!word=/(?i)^de/"
priority: "7"
# Glycosylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Glycosylation"
actionFlow: "mkBioMention"
label: "Glycosylation"
verbalTriggerLemma: "glycosylate"
nominalTriggerLemma: "glycosylation"
triggerPrefix: "!word=/(?i)^de/"
priority: "7"
# Acetylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Acetylation"
actionFlow: "mkBioMention"
label: "Acetylation"
verbalTriggerLemma: "acetylate"
nominalTriggerLemma: "acetylation"
triggerPrefix: "!word=/(?i)^de/"
priority: "7"
# Farnesylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Farnesylation"
actionFlow: "mkBioMention"
label: "Farnesylation"
verbalTriggerLemma: "farnesylate"
nominalTriggerLemma: "farnesylation"
triggerPrefix: "!word=/(?i)^de/"
priority: "7"
# Ribosylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Ribosylation"
actionFlow: "mkBioMention"
label: "Ribosylation"
verbalTriggerLemma: "ribosylate"
nominalTriggerLemma: "ribosylation"
triggerPrefix: "!word=/(?i)^de/"
priority: "7"
# Methylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Methylation"
actionFlow: "mkBioMention"
label: "Methylation"
verbalTriggerLemma: "methylate"
nominalTriggerLemma: "methylation"
triggerPrefix: "!word=/(?i)^de/"
priority: "7"
#
# "Reverse" Simple Events:
#
# Dephosphorylations
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Dephosphorylation"
actionFlow: "mkBioMention"
label: "Dephosphorylation"
verbalTriggerLemma: "de-?phosphorylate"
nominalTriggerLemma: "de-?phosphorylation"
triggerPrefix: "word=/(?i)^de/"
priority: "7"
# Deubiquitination
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Deubiquitination"
actionFlow: "mkUbiquitination"
label: "Deubiquitination"
verbalTriggerLemma: "de-?ubiquit(in|yl)ate"
nominalTriggerLemma: "de-?ubiquit(in|yl)ation"
triggerPrefix: "word=/(?i)^de/"
priority: "7"
# Dehydroxylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Dehydroxylation"
actionFlow: "mkBioMention"
label: "Dehydroxylation"
verbalTriggerLemma: "de-?hydroxylate"
nominalTriggerLemma: "de-?hydroxylation"
triggerPrefix: "word=/(?i)^de/"
priority: "7"
# Desumoylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Desumoylation"
actionFlow: "mkBioMention"
label: "Desumoylation"
verbalTriggerLemma: "de-?sumoylate"
nominalTriggerLemma: "de-?sumoylation"
triggerPrefix: "word=/(?i)^de/"
priority: "7"
# Deglycosylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Deglycosylation"
actionFlow: "mkBioMention"
label: "Deglycosylation"
verbalTriggerLemma: "de-?glycosylate"
nominalTriggerLemma: "de-?glycosylation"
triggerPrefix: "word=/(?i)^de/"
priority: "7"
# Deacetylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Deacetylation"
actionFlow: "mkBioMention"
label: "Deacetylation"
verbalTriggerLemma: "de-?acetylate"
nominalTriggerLemma: "de-?acetylation"
triggerPrefix: "word=/(?i)^de/"
priority: "7"
# Defarnesylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Defarnesylation"
actionFlow: "mkBioMention"
label: "Defarnesylation"
verbalTriggerLemma: "de-?farnesylate"
nominalTriggerLemma: "de-?farnesylation"
triggerPrefix: "word=/(?i)^de/"
priority: "7"
# Deribosylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Deribosylation"
actionFlow: "mkBioMention"
label: "Deribosylation"
verbalTriggerLemma: "de-?ribosylate"
nominalTriggerLemma: "de-?ribosylation"
triggerPrefix: "word=/(?i)^de/"
priority: "7"
# Demethylation
- import: org/clulab/reach/biogrammar/events/simple-event_template.yml
vars:
eventName: "Demethylation"
actionFlow: "mkBioMention"
label: "Demethylation"
verbalTriggerLemma: "de-?methylate"
nominalTriggerLemma: "de-?methylation"
triggerPrefix: "word=/(?i)^de/"
priority: "7"
# Generic (incomplete) events
- import: org/clulab/reach/biogrammar/coref/generic_events.yml
vars:
actionFlow: "mkBioMention"
priority: "8"
###############################################################################
#
# Nested events
#
###############################################################################
# A very specific class of "early" regulations: "Y-induced Z" (where Z is an event)
# These must be recognized first, so the nested event in "X activates Y-induced Z" works
- import: org/clulab/reach/biogrammar/events/early-pos-reg_template.yml
vars:
label: "Positive_regulation"
ruleType: "regulation"
triggers: "induced|mediated"
actionFlow: "mkRegulation"
priority: "9" # must be priority of regulations - 1!
controlledType: "SimpleEvent"
controllerType: "BioEntity"
# A very specific class of "early" activations: "Y-induced Z" (where Z is an entity)
# These must be recognized first, so the nested event in "X activates Y-induced Z" works
- import: org/clulab/reach/biogrammar/events/early-pos-reg_template.yml
vars:
label: "Positive_activation"
ruleType: "activation"
triggers: "induced|mediated"
actionFlow: "mkActivation"
priority: "10" # must be priority of regulations - 1!
controlledType: "BioEntity"
controllerType: "BioEntity"
# Positive Regulation
- import: org/clulab/reach/biogrammar/events/pos-reg_template.yml
vars:
label: "Positive_regulation"
ruleType: "regulation"
triggers: ${posTriggers}
actionFlow: "mkRegulation"
priority: "12-13"
controlledType: "Event"
controllerType: "PossibleController"
# Positive regulation, from patterns that apply ONLY to regulations
- import: org/clulab/reach/biogrammar/events/pos-reg-only_template.yml
vars:
label: "Positive_regulation"
ruleType: "regulation"
triggers: ${posTriggers}
actionFlow: "mkRegulation"
priority: "12-13"
controlledType: "Event"
controllerType: "PossibleController"
# Negative Regulation
- import: org/clulab/reach/biogrammar/events/neg-reg_template.yml
vars:
label: "Negative_regulation"
ruleType: "regulation"
triggers: ${negTriggers}
actionFlow: "mkRegulation"
priority: "12-13"
controlledType: "Event"
controllerType: "PossibleController"
# Negative Regulation, from patterns that apply ONLY to regulations
- import: org/clulab/reach/biogrammar/events/neg-reg-only_template.yml
vars:
label: "Negative_regulation"
ruleType: "regulation"
triggers: ${negTriggers}
actionFlow: "mkRegulation"
priority: "12-13"
controlledType: "Event"
controllerType: "PossibleController"
# Positive Activation
- import: org/clulab/reach/biogrammar/events/pos-reg_template.yml
vars:
label: "Positive_activation"
ruleType: "activation"
triggers: ${posTriggers}
actionFlow: "mkActivation"
priority: "14" # must be 1 + priority of regulations!
controlledType: "BioEntity"
controllerType: "PossibleController"
# Positive Activation, from patterns that apply ONLY to activations
- import: org/clulab/reach/biogrammar/events/pos-act-only_template.yml
vars:
label: "Positive_activation"
ruleType: "activation"
triggers: ${posTriggers}
actionFlow: "mkActivation"
priority: "14" # must be 1 + priority of regulations!
controlledType: "BioEntity"
controllerType: "PossibleController"
# Negative Activation
- import: org/clulab/reach/biogrammar/events/neg-reg_template.yml
vars:
label: "Negative_activation"
ruleType: "activation"
triggers: ${negTriggers}
actionFlow: "mkActivation"
priority: "14" # must be 1 + priority of regulations!
controlledType: "BioEntity"
controllerType: "PossibleController"