Associating biological context with protein-protein interactions through text mining at PubMed scale

Daniel N. Sosa, Rogier Hintzen, Betty Xiong, Alex de Giorgio, Julien Fauqueur, Mark Davies, Jake Lever, Russ B. Altman

Abstract: Highlights•We present a new feature-based classifier for text-mined context-PPI association.•Context relevancy to main findings leads to interpretable classification.•We develop precise datasets based on linguistic cues for the task.•Models trained with cell type contexts can be transferred to tissue contexts.•We demonstrate our approach to augment a knowledge base of dengue PPI.