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Table 1 The BioNLP'13 GE task annotation scheme, automatically learned from the corresponding corpus.

From: TEES 2.2: Biomedical Event Extraction for Diverse Corpora

Type

Name

Arguments

ENTITY

Anaphora

 

ENTITY

Entity

 

ENTITY

Protein

 

EVENT

Acetylation [2,2]

Site {Theme} [1,1] Entity / Theme [1,1] Protein

EVENT

Binding [1,4]

Site {Theme} [0,2] Entity / Theme [1,2] Protein

EVENT

Deacetylation [2,2]

Cause [0,1] Protein / Site {Theme} [0,1] Entity / Theme [1,1] Protein

EVENT

Gene expression [1,1]

Theme [1,1] Protein

EVENT

Localization [1,2]

Theme [1,1] Protein / ToLoc [0,1] Entity

EVENT

Negative regulation [1,3]

Cause [0,1] Acetylation, Binding, Gene expression, Negative regulation, Phosphorylation, Positive regulation, Protein, Protein catabolism, Regulation, Ubiquitination / Site {Cause,Theme} [0,1] Entity / Theme [1,1] Binding, Gene expression, Localization, Negative regulation, Phosphorylation, Positive regulation, Protein, Protein catabolism, Regulation, Transcription, Ubiquitination

EVENT

Phosphorylation [1,3]

Cause [0,1] Protein / Site {Theme} [0,1] Entity / Theme [1,1] Protein

EVENT

Positive regulation [1,3]

Cause [0,1] Acetylation, Binding, Gene expression, Negative regulation, Phosphorylation, Positive regulation, Protein, Protein catabolism, Regulation, Ubiquitination / Site {Cause,Theme} [0,1] Entity / Theme [1,1] Binding, Deacetylation, Gene expression, Localization, Negative regulation, Phosphorylation, Positive regulation, Protein, Protein catabolism, Protein modification, Regulation, Transcription, Ubiquitination

EVENT

Protein catabolism [1,1]

Theme [1,1] Protein

EVENT

Protein modification [1,1]

Theme [1,1] Protein

EVENT

Regulation [1,3]

Cause [0,1] Binding, Gene expression, Localization, Negative regulation, Phosphorylation, Positive regulation, Protein, Protein modification, Regulation / Site {Cause,Theme} [0,1] Entity / Theme [1,1] Binding, Gene expression, Localization, Negative regulation, Phosphorylation, Positive regulation, Protein, Protein catabolism, Protein modification, Regulation, Transcription

EVENT

Transcription [1,1]

Theme [1,1] Protein

EVENT

Ubiquitination [1,2]

Cause [0,1] Protein / Site {Theme} [0,1] Entity / Theme [1,1] Protein

RELATION

Coreference, directed

Subject(Anaphora) / Object(Anaphora, Entity, Protein)

RELATION

SiteParent, directed

Arg1(Entity) / Arg2(Protein)

MODIFIER

negation

Binding, Gene expression, Localization, Negative regulation, Phosphorylation, Positive regulation, Protein catabolism, Regulation, Transcription

MODIFIER

speculation

Binding, Gene expression, Localization, Negative regulation, Phosphorylation, Positive regulation, Protein catabolism, Regulation,

Transcription, Ubiquitination

TARGET

ENTITY

Acetylation, Anaphora, Binding, Deacetylation, Entity, Gene expression, Localization, Negative regulation, Phosphorylation, Positive regulation, Protein catabolism, Protein modification, Regulation, Transcription, Ubiquitination

TARGET

INTERACTION

Cause, Coreference, Site, SiteParent, Theme, ToLoc

  1. The entities form the nodes of the graph. The events and relations connect the nodes together and are defined by a type and a specific, limited set of arguments. Both event and relation arguments have specified valid target node types. Site-argument primary argument types are shown in wavy brackets. Event arguments have also a minimum and maximum amount of each argument allowed per event, and the event itself has a minimum and maximum number of arguments. The relations must always have two arguments and can optionally be directed. Modifiers are binary attributes that can be applied to a limited set of node types. The targets define the types of nodes and edges to be automatically extracted.