Skip to main content

Table 5 Pathway Curation task event types and arguments.

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

Event type Core arguments Additional arguments Ontology ID
CONVERSION Theme(Molecule), Product(Molecule)   SBO:0000182
  PHOSPHORYLATION Theme(Molecule), Cause(Molecule) Site(Simple chemical) SBO:0000216
  DEPHOSPHORYLATION Theme(Molecule), Cause(Molecule) Site(Simple chemical) SBO:0000330
(Other modifications, such as Acetylation, defined similarly.)
LOCALIZATION Theme(Molecule) At/From/ToLoc(Cell. comp.) GO:0051179
  TRANSPORT Theme(Molecule) From/ToLoc(Cell. comp.) SBO:0000185
GENE EXPRESSION Theme(Gene or gene product)   GO:0010467
  TRANSCRIPTION Theme(Gene or gene product)   SBO:0000183
Translation Theme(Gene or gene product)   SBO:0000184
DEGRADATION Theme(Molecule)   SBO:0000179
BINDING Theme(Molecule), Product(Complex)   SBO:0000177
DISSOCIATION Theme(Complex), Product(Molecule)   SBO:0000180
REGULATION Theme(Any), Cause(Any)   GO:0065007
  POSITIVE REGULATION Theme(Any), Cause(Any)   
    ACTIVATION Theme(Molecule), Cause(Any)   SBO:0000412
  NEGATIVE REGULATION Theme(Any), Cause(Any)   
    INACTIVATION Theme(Molecule), Cause(Any)   SBO:0000412
PATHWAY Participant(Molecule)   SBO:0000375
  1. "Molecule" represents any of Simple chemical, Gene or gene product, or Complex. "Any" refers to an annotation of any type. The indentation of the types corresponds to ontological relations (is-a and part-of ) between the event types