Computational Systems Toxicology

Part of the series Methods in Pharmacology and Toxicology pp 181-208

Weaving Knowledge into Biological Pathways in a Collaborative Manner

  • Yukiko MatsuokaAffiliated withThe Systems Biology Institute
  • , Kazuhiro FujitaAffiliated withThe Systems Biology Institute
  • , Samik GhoshAffiliated withThe Systems Biology Institute
  • , Hiroaki KitanoAffiliated withThe Systems Biology Institute Email author 

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Toxicity pathway modeling is an effective approach to understanding how biological systems function under chemical perturbations. Many efforts have been made to construct pathways by data-driven or literature-based approaches to elucidate the mechanisms of action of toxicity. In this chapter, we explain how to build a literature-based pathway map in a collaborative manner using in silico platforms such as CellDesigner to draw pathways and networks, Payao as the curation platform, iPathways+ as the publishing platform, and Garuda to integrate curated pathways while adopting model-descriptive standards such as Systems Biology Markup Language as a file format and Systems Biology Graphical Notation as the graphical representation.

Key words

CellDesigner Collaboration Garuda platform Pathway curation SBGN (systems biology graphical notation) SBML (systems biology markup language)