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Table 3 Overview of standards and tools for encoding and working with pathway knowledge

From: New perspectives: systems medicine in cardiovascular disease

Name Description Reference Software Tools
BioPax A standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. [69] Biopax [115]
Paxtools [116]
SBML - The Systems Biology Markup Language An XML-based format for representing biochemical reaction networks. Software-independent language for describing common models, including cell signaling pathways, metabolic pathways, gene regulation, andothers. [70] libSBML [117]
SBGN - The Systems Biology Graphical Notation A visual language to encode pathways in three different granularities: process diagram, entity relationship diagram and activity flow diagram. [118] LibSBGN [119]
HUPO-PSI Molecular Interaction format A community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO). [71] PSICQUIC [120]
Cytoscape Cyberinfrastructure Network Interchange Format (CX) A light weight REST-based aspect-oriented interchange protocol for generic network data exchange. [121] [122]