Journal article

Extracting reaction networks from databases-opening Pandora's box

Liam G Feamley, Melissa J Davis, Mark A Ragan, Lars K Nielsen

BRIEFINGS IN BIOINFORMATICS | OXFORD UNIV PRESS | Published : 2014

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 re..

View full abstract

Grants

Awarded by Australian Research Council


Funding Acknowledgements

L. G. F. is funded by an Australian Postgraduate Award funded by the Australian Government's Department of Industry, Innovation, Climate Change, Science, Research and Tertiary Education. M.J.D. and M. A. R. are funded by the Australian Research Council [grant number DP110103384].