1. Base on network: Network -> pathway
2. Extend existing pathway Pathway -> network -> network + new network data -> pathway

Base on network

• Load network
  • From table
  • From file
  • Query network database
    • cPath
    • InAct?
    • DIP
    • PathwayCommons?
    • MiM plugin
  • Generate network
    • Agilent Literature Search
    • MetaNetter?
    • MONET
• Annotate
  • Load GO annotations
  • Load node/edge attributes
• Layout
  • BubbleRouter?
  • Cerebral
• Export to pathway
  • Save as GPML
  • Create pathway on WikiPathways: will create a new pathway on WikiPathways? based on this network
  • Copy to clipboard: Copy the selected part of the network to the clipboard, to paste it in PathVisio or WikiPathways?

Extend existing pathway

• Import pathway
  • From file: Imports a GPML file
  • From clipboard: Paste GPML data (copied from PathVisio or WikiPathways?)
  • From WikiPathways: Specify a pathway title, and it will be downloaded from WikiPathways?

*Extend network

• Agilent Literature Search
• cPath/InAct: This should not create a new network based on cPath/InAct data, but merge it into the existing network. Is this possible?

• Layout
  • BubbleRouter?
  • Cerebral
• Export to pathway
  • Save as GPML
  • Create pathway on WikiPathways: will create a new pathway on WikiPathways? based on this network
  • Copy to clipboard: Copy the selected part of the network to the clipboard, to paste it in PathVisio or WikiPathways? *