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

Tópicos

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Resumo

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.

Resumo Limpo

larg quantiti inform describ mechan biolog pathway continu collect public avail databas time experi increas scale biologist increas use pathway defin onlin databas interpret result experi generat hypothes emerg comput techniqu exploit rich biolog inform captur reaction system requir formal standard descript pathway extract reaction network avoid altern timeconsum larg manual literaturebas network reconstruct systemat evalu effect common use knowledg represent seem simpl task extract reaction network describ signal transduct pathway databas show process fact surpris difficult pathway represent adopt various knowledg base dramat consequ reaction network extract connect captur pathway crosstalk model cellcel interact research construct comput model built automat extract reaction network must therefor consid issu outlin review maxim valu exist pathway knowledg

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