Arabidopsis reactome: a foundation knowledgebase for plant systems biology.

摘要

This paper describes Arabidopsis Reactome, a knowledgebase of biological processes from the model plant Arabidopsis thaliana. A key feature of Reactome is its elegant data model that extends the notion of biochemical reaction where substrates go in, products come out, and a catalyst is frequently required to lower the free energy of the transformation. The data model expresses molecular processes in the same way that scientists understand them and allows connected reactions to represent biological processes (e.g. transcription and cell cycle) in terms of their underlying molecular transformations, associations and translocations. Using examples based on the mitotic cell cycle, the knowledgebase is shown to have wide applicability for exchanging structured data with other databases, for comparative network analysis, data integration and for visualization and protein interaction analysis. The straightforward authoring tool and realistic detailed descriptions of biological processes inherent in Reactome's data model provide an excellent foundation for representing, exchanging, and integrating biological information, suggesting that it will find wide application in the Arabidopsis community as a gold standard for pathway knowledge and key foundation for systems biology research.