Negation of protein-protein interactions: analysis and extraction.
BACKGROUND
Negative information about protein-protein interactions--from uncertainty about the occurrence of an interaction to knowledge that it did not occur--is often of great use to biologists and could lead to important discoveries. Yet, to our knowledge, no proposals focusing on extracting such information have been proposed in the text mining literature.


RESULTS
In this work, we present an analysis of the types of negative information that is reported, and a heuristic-based system using a full dependency parser to extract such information. We performed a preliminary evaluation study that shows encouraging results of our system. Finally, we have obtained an initial corpus of negative protein-protein interactions as basis for the construction of larger ones.


BACKGROUND
The corpus is available by request from the authors.
Sanchez-Graillet
Olivia
O
Department of Computer Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK. osanch@essex.ac.uk
Poesio
Massimo
M
D000465:Algorithms; D016247:Information Storage and Retrieval / Q000379:methods*; D008954:Models, Biological; D009323:Natural Language Processing; D010506:Periodicals as Topic; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
D020543:Proteome