Pathway visualizers

= About visualization issues =

Tools that visualize BioPAX files

 * ) VisAnt http://visant.bu.edu/
 * ) Cytoscape http://cytoscape.org

Tools under development to visualize BioPAX files

 * ) PathPort - ProNet plugin http://pathport.vbi.vt.edu/main/home.php

Languages and extensions to specifiy biological networks' graphics

 * ) VisML
 * ) http://projects.villa-bosch.de/bcb/sbml/

Other possible approaches

 * ) Semantic lenses http://www.w3.org/2005/04/swls/BioDash/Demo/Lenses.html

Papers on pathway visualisation

 * ) A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems
 * ) Kitano's proposed graphical notations for various entities, reactions, etc. implemented in the Cell Designer software. There are references to some publications at the end of this page
 * ) Semantic Visualization of Biochemical Databases
 * ) The Standard Graphical Notation for Biological Networks
 * ) Representations of Metabolic Knowledge: Pathways
 * ) The visual display of regulatory information and networks
 * ) Molecular interaction map of the mammalian cell cycle control and DNA repair systems
 * ) KEGG pathway annotation

Papers on visualizing RDF

 * ) Visualizing RDF(S)-based Information