Action description

current actions

EntityEngine

Actions:

• default
  • converts mentions to biomentions
• mkEntities
  • gets RelationMentions and decomposes the arguments into Seq[TextBoundMention]
  • converts results to BioMentions
  • deletes any other kind of mention
• mkNERMentions
  • filters out mentions that overlap any preexisting Mention
  • converts results to BioMentions

ModificationEngine

Actions:

• default
  • converts mentions to biomentions
• mkEntities
  • gets RelationMentions and decomposes the arguments into Seq[TextBoundMention]
  • converts results to BioMentions
  • deletes any other kind of mention
• mkModTrigger
  • takes a mention with args (relation or event) and replaces it with its first arg named "mod" as a TextBoundMention
  • converts results to BioMention
  • NOTE this can be simplified by using Rules with lookarounds (i.e. modification_trigger_1 can use nested lookaheads)
• mkModification
  • partial function; only gets RelationMentions with label PTM or Mutant
  • if PTM:
    • converts first relation("entity") into BioMention
    • retrieves optional first relation("site")
    • retrieves first relation("mod")
    • assigns label from mod
    • if label is not unknown then add PTM modification to entity
    • outputs entity
  • if Mutant:
    • converts first relation("mutated") into BioMention
    • retrieves first relation("evidence")
    • add Mutation modification to mutated
    • outputs mutated
• storeEventSite
  • gets mention with arguments
  • retrieves first entity from mention and converts to BioMention
  • retrieves first site from mention
  • finds token interval from (entity, site)
  • finds all sites withing interval that are already in the state
  • attaches found sites as EventSite modifications to entity
  • NOTE original site is included in found sites
• storeMutants
  • gets mention with arguments
  • retrieves first entity from mention and converts to BioMention
  • retrieves first mutant from mention
  • finds token interval from (entity, mutant)
  • finds all mutants withing interval that are already in the state
  • attaches found sites as Mutant modifications to entity
  • NOTE original mutant is included in found mutants

EventEngine

Actions:

• default
  • converts mentions to biomentions
• mkUbiquitination
  • filters mentions with argument that contains text "ubiq"
  • converts mentions to BioMentions
• mkRegulation
  • sort mentions so that mentions with a controller event appear first
    • this is done so that when overlapping mentions are found, the ones with event controllers are preferred
  • flip mention label if needed
  • remove dummy arg if needed
  • get controller if available (controlled is required but controller is optional)
  • if controller is BioChemicalEntity return regulation event unmodified
  • if controller is SimpleEvent and regulation is BioEventMention:
    • convert controller event to entity using convertEventToEntity
    • if converted controller is undefined return regulation event unmodified
    • else return new regulation event by replacing controller event with controller entity
  • if controller is not SimpleEvent or regulation is not BioEventMention return regulation event unmodified
• mkActivation
  • Prefer Activations with SimpleEvents as the controller by using preferSimpleEventControllers
  • flip mention label if needed
  • remove dummy arg if needed
  • retrieve ComplexEvents that overlap this activation (NOTE: safer to retrieve "Regulations")
  • if this activation overlaps any Regulation, filter it out
  • if not hasDistinctControllerControlled filter activation out
  • if activation has no controller, return activation unmodified
  • if activation has entity controller, return activation unmodified
  • if activation has event controller:
    • convert controller event to entity using convertEventToEntity
    • if converted controller is undefined return activation event unmodified
    • else return new activation event by replacing controller event with controller entity
• mkBinding
  • if mention is EventMention:
    • retrieve all theme1 and theme2 args from mention
    • if we only have one theme and it is not Unresolved, filter out binding mention
    • if a theme is Unresolved, return exact copy of binding mention
    • if theme1 is empty or theme2 is empty:
      • concatenate themes into mergedThemes (Note: should call distinct)
      • if only two themes and they have different ids (according to sameEntityID) and one theme contains text "ubiquitin":
        • discard ubiquitin theme
        • return new Ubiquitination event with theme=remaining theme
      • else:
        • get all combinations of 2 themes from mergedThemes
        • filter out pairs where sameEntityID returns true
        • if either member of the pair contains text "ubiquitin":
          • return new Ubiquitination event with theme=remaining theme
        • else:
          • return binarized Binding event
    • else: (if we have both theme1 and theme2)
      • for each (theme1, theme2) pair
      • filter pair if sameEntityID returns true
      • if either member of the pair contains text "ubiquitin":
        • return new Ubiquitination event with theme=remaining theme
        • else:
          • return binarized Binding event

Functions:

• preferSimpleEventControllers
  • gets mentions with arguments or it breaks
  • if any mention has a SimpleEvent controller:
    • return only mentions with SimpleEvent Controllers
  • else return all mentions
• switchLabel
  • if not BioEventMention return mention
  • make excluded token set with all tokens in trigger and arguments
  • use countSemanticNegatives to collect negative tokens for all trigger-argument pairs
  • if negative.size is odd:
    • use flipLabel to flip the main event label
    • return new BioEventMention with flipped label
• removeDummy
  • get a BioMention
  • if it is a BioEventMention:
    • if it has argument(dummy) return event copy without dummy
    • else return event
  • else return mention
• hasDistinctControllerControlled
  • gets a Mention
  • if mention does not have a controller, a controlled or both, return true
  • distinctArgs = check if controller and controlled are different mention
  • distinctGrounding = if they are both grounded check that they are different, else true
  • if distinctArgs and distinctGrounding return true, else false
• convertEventToEntity
  • gets a BioEventMention
  • returns an Option[BioMention]
  • if event is not SimpleEvent return None
  • if event is Binding:
    • return BioRelationMention by dropping trigger and changing label to Complex
  • else:
    • retrieve event(theme)
    • retrieve event(site) if it exists
    • copy theme to new BioTextBoundMention (copy not convert)
    • get modification label from event.trigger
    • attach PTM modification to BioTextBoundMention
• countSemanticNegatives
  • gathers tokens that are considered negative
  • gets set of token ids that should be excluded from consideration
  • gets a trigger and an arg as Mentions
  • finds shortest path between some token in trigger and some token in arg
  • collects token ids from shortest path that match semantic negative pattern
• flipLabel
  • gets a string that starts with "Positive" or "Negative"
  • returns label with flipped polarity
• sameEntityID
  • gets a list of mentions
  • if there are grounded mentions:
    • ignore ungrounded mentions
    • if all grounded mentions have same id return true
    • else return false
  • else return false

globalAction (applied in this order):

• siteSniffer (these seems to hurt us, we forget to which entity each site belongs)
  • Propagate any Sites in the Modifications of any argument of a SimpleEvent to the event "Site" argument, and remove them from each argument
  • if mention is not SimpleEvent return it unmodified
  • collect into additionalSites all EventSite.site modification from each arguments and remove them from each argument
  • allSites = additionalSites + mention("site")
  • if no sites return return mention unmodified
  • else:
    • remove "site" from mention arguments
    • create a copy of mention for each site in allSites
• detectNegations
• detectHypotheses
• splitSimpleEvents