Skip to main content

Table 3 Cancer Genetics task event types and their arguments.

From: Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013

Type

Core arguments

Additional arguments

Anatomical

  

  DEVELOPMENT

Theme (Anatomy)

 

  BLOOD VESSEL DEVELOPMENT

Theme?(Anatomy)

AtLoc?

  GROWTH

Theme (Anatomy)

 

  DEATH

Theme (Anatomy)

 

  CELL DEATH

Theme?(Cell)

 

  BREAKDOWN

Theme (Anatomy)

 

  CELL PROLIFERATION

Theme (Cell)

 

  CELL DIVISION

Theme (Cell)

 

  CELL DIFFERENTIATION

Theme (Cell)

AtLoc?

  REMODELING

Theme (Tissue)

 

  REPRODUCTION

Theme (Organism)

 

Pathological

  

  MUTATION

Theme (GGP)

AtLoc?, Site?

  CARCINOGENESIS

Theme?(Anatomy)

AtLoc?

  CELL TRANSFORMATION

Theme (Cell)

AtLoc?

  METASTASIS

Theme?(Anatomy)

ToLoc

  INFECTION

Theme?(Anatomy), Participant?(Organism)

 

Molecular

  

  METABOLISM

Theme (Molecule)

 

    SYNTHESIS

Theme (Simple chemical)

 

    CATABOLISM

Theme (Molecule)

 

      AMINO ACID CATABOLISM

Theme?(Molecule)

 

      GLYCOLYSIS

Theme?(Molecule)

 

    GENE EXPRESSION

Theme+(GGP)

 

      TRANSCRIPTION

Theme (GGP)

 

      TRANSLATION

Theme (GGP)

 

      PROTEIN PROCESSING

Theme (GGP)

 

  PHOSPHORYLATION

Theme (Molecule)

Site?

(other chemical modifications defined similarly to Phosphorylation)

  PATHWAY

Participant (Molecule)

 

General

  

  BINDING

Theme+(Molecule)

Site?

  DISSOCIATION

Theme (Molecule)

Site?

  LOCALIZATION

Theme+(Molecule)

At/From/ToLoc?

Regulation

Theme (Any), Cause?(Any)

 

  POSITIVE REGULATION

Theme (Any), Cause?(Any)

 

  NEGATIVE REGULATION

Theme (Any), Cause?(Any)

 

PLANNED PROCESS

Theme*(Any), Instrument*(Entity)

 
  1. The indentation corresponds to ontological structure (is-a/part-of relations). The suffixes ?, *, and + denote zero or one, zero or more, and one or more arguments of the shown type (respectively). GGP stands for Gene or gene product. For brevity, additional argument types are not shown in table: the AtLoc, FromLoc and ToLoc arguments take an anatomical entity type, and Site arguments take a Protein domain or region or DNA domain or region entity type.