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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




Software Tools


A standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data.


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.


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.


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).



Cytoscape Cyberinfrastructure Network Interchange Format (CX)

A light weight REST-based aspect-oriented interchange protocol for generic network data exchange.