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] |