Table 1. PathVisio 3 feature table.

Feature	Description
File import	Default: GPML (http://www.pathvisio.org/gpml/) Plugins: MIMML ([24], MIM plugin), SBGNML ([23], SBGN plugin), SBML ([31], PathSBML), BioPAX ([22], BioPAX plugin), gene list (MAPPBuilder)
File export	Default: GPML, PNG, PDF, SVG, TIFF, Eu.Gene [32], datanode list Plugins: MIMML (MIM plugin), SBGNML (SBGN plugin), SBML (PathSBML), HTML (HTMLexporter), BioPAX (BioPAX plugin)
Pathway drawing standards	Default: Basic GPML style Plugins: SBGN, MIM
Identifier mapping	Integrated BridgeDb framework [20] for advanced identifier mapping for pathway elements and interactions in the pathways. All major database identifiers including probe ids for genes, proteins and metabolites are supported.
Pathway statistics	Default: Over-representation analysis (Z-Score) Plugins: Gene set enrichment analysis (GSEA plugin)
Data visualization	Pathway nodes: gradient-based visualization for numeric data, rule-based visualization for numeric and nonnumeric data Interactions: color and line thickness visualization (IntViz plugin)
Plugin extension system	Plugin manager allows one-click installation of plugins from central plugin repository to enable additional features.
Pathway database connection	WikiPathways: searching, browsing, updating, uploading biological pathways (WikiPathways plugin)
Workflow integration	The core module can be used as a library to read, write, store, convert and model pathway information. Calling PathVisio functionality from other programming languages through XML-RPC server (PathVisioRPC)
Online data access	Several plugins provide connections to other online resources to give more information about the individual elements in the pathway, like BiomartConnect about gene products, MetInfo about metabolites or PathwayLoom about known interaction partners.