• Login 

Instructions

• HowToInstall
• How to work with analysis contexts
• How to load ontologies
• Selecting namespaces
• How to make queries
• How to browse ontologies*
• How to define visual queries*
• How to work with visual queries
• How to tune visualization options
• Linking graphs in Cytoscape and ontologies
• How to use inference

see also a step by step examples:

 how to represent pathway information as interaction networks
 how to represent pathway information as a cause-effect graph

* Pattern and Visual query are synonyms in this context

How to browse and query ontologies