Table 2 |
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Event types |
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|
Event type |
Corpora |
Core arguments |
Optional arguments |
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|
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Gene expression |
GE, ID |
Theme(Protein, Regulon/OperonID) |
|
|
Transcription |
GE, ID |
Theme(Protein, Regulon/OperonID) |
|
|
Protein catabolism |
GE, ID |
Theme(Protein) |
|
|
Phosphorylation* |
GE, EPI, ID |
Theme(Protein) |
Site(Entity) |
|
Localization |
GE, ID, BB |
ThemeGE, ID(Protein, Core entityID), BacteriumBB(Bacterium), LocalizationBB(Host, HostPart, Geographical, Environmental, Food, Medical, Soil, Water) |
AtLocGE, ID(Entity), ToLocGE, ID(Entity) |
|
Binding |
GE, ID |
Theme(Protein, Core entityID)+ |
Site(Entity)+ |
|
Regulation |
GE, ID |
Theme(Protein, Core entityID, Event), Cause(Core entityID, Event) |
Site(Entity), CSite(Entity) |
|
Positive regulation |
GE, ID |
Theme(Protein, Core entityID, Event), Cause(Protein, Core entityID, Event) |
Site(Entity), CSite(Entity) |
|
Negative regulation |
GE, ID |
Theme(Protein, Core entityID, Event), Cause(Core entityID, Event) |
Site(Entity), CSite(Entity) |
|
Process |
ID |
Participant(Core entity) |
|
|
Hydroxylation* |
EPI |
Theme(Protein) |
Site(Entity) |
|
Ubiquitination* |
EPI |
Theme(Protein) |
Site(Entity) |
|
DNA methylation* |
EPI |
Theme(Protein) |
Site(Entity) |
|
Glycosylation* |
EPI |
Theme(Protein) |
Site(Entity) |
|
Acetylation* |
EPI |
Theme(Protein) |
Site(Entity) |
|
Methylation* |
EPI |
Theme(Protein) |
Site(Entity) |
|
Catalysis |
EPI |
Theme(Event), Cause(Protein) |
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|
PartOf |
BB |
HostPart(HostPart), Host(Host) |
|
|
RegulonDependence |
BI |
Regulon(Regulon), Target(GeneEntity, ProteinEntity) |
|
|
BindTo |
BI |
Agent(ProteinEntity), Target(Site, Promoter, Gene, GeneComplex) |
|
|
TranscriptionFrom |
BI |
Transcription(Transcription, Expression), Site(Site, Promoter) |
|
|
RegulonMember |
BI |
Regulon(Regulon), Member(GeneEntity, ProteinEntity) |
|
|
SiteOf |
BI |
Site(Site), Entity(Site, Promoter, GeneEntity) |
|
|
TranscriptionBy |
BI |
Transcription(Transcription), Agent(ProteinEntity) |
|
|
PromoterOf |
BI |
Promoter(Promoter), Gene(GeneEntity, ProteinEntity) |
|
|
PromoterDependence |
BI |
Promoter(Promoter), Protein(GeneEntity, ProteinEntity) |
|
|
ActionTarget |
BI |
Action(Action, Expression, Transcription), Target(Any type) |
|
|
Interaction |
BI |
Agent(GeneEntity, ProteinEntity), Target(GeneEntity, ProteinEntity) |
|
|
Coref |
CO |
Anaphora(Exp), Antecedent(Exp), Reference(Protein)+ |
|
|
Protein-Component |
REL |
Arg1(Protein), Arg2(Entity) |
|
|
Subunit-Complex |
REL |
Arg1(Protein), Arg2(Entity) |
|
|
Renaming |
REN |
Former(Gene), New(Gene) |
|
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The event types for all tasks, their core arguments used for the primary evaluation and optional arguments for secondary evaluation. Superscripts show the arguments and targets limited to a specific task for events present in multiple tasks. Starred events have in the EPI task a corresponding reverse event (e.g. Dephosphorylation) with identical argument types. The plus-sign indicates where multiple arguments of the same type are allowed for one event. |
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Björne et al. BMC Bioinformatics 2012 13(Suppl 11):S4 doi:10.1186/1471-2105-13-S11-S4 |
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