Extracting reaction networks from databases-opening Pandora's box.

ABSTRACT: Large quantities of information describing the mechanisms of biological pathways continue to be collected in publicly available databases. At the same time, experiments have increased in scale, and biologists increasingly use pathways defined in online databases to interpret the results of experiments and generate hypotheses. Emerging computational techniques that exploit the rich biological information captured in reaction systems require formal standardized descriptions of pathways to extract these reaction networks and avoid the alternative: time-consuming and largely manual literature-based network reconstruction. Here, we systematically evaluate the effects of commonly used knowledge representations on the seemingly simple task of extracting a reaction network describing signal transd

SUBMITTER: Fearnley LG 

PROVIDER: S-EPMC4239801 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature