Table 2

Event types

Event type

Corpora

Core arguments

Optional arguments


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)

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)


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.

Bj√∂rne et al. BMC Bioinformatics 2012 13(Suppl 11):S4   doi:10.1186/1471-2105-13-S11-S4

Open Data