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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 transduction from a pathway database. We show that this process is in fact surprisingly difficult, and the pathway representations adopted by various knowledge bases have dramatic consequences for reaction network extraction, connectivity, capture of pathway crosstalk and in the modelling of cell-cell interactions. Researchers constructing computational models built from automatically extracted reaction networks must therefore consider the issues we outline in this review to maximize the value of existing pathway knowledge.

SUBMITTER: Fearnley LG

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

REPOSITORIES: biostudies-literature

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

Fearnley Liam G LG Davis Melissa J MJ Ragan Mark A MA Nielsen Lars K LK

Briefings in bioinformatics 20130814 6

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 ...[more]

PMID: 23946492

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

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

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