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

BMC Bioinformatics

Table 5 Pathway Curation task event types and arguments.

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
			GO:0048518,
POSITIVE REGULATION	Theme(Any), Cause(Any)
ACTIVATION	Theme(Molecule), Cause(Any)		SBO:0000412
			GO:0048519,
NEGATIVE REGULATION	Theme(Any), Cause(Any)
INACTIVATION	Theme(Molecule), Cause(Any)		SBO:0000412
PATHWAY	Participant(Molecule)		SBO:0000375

"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

ISSN: 1471-2105