Use Case Name : ../SaveBioPax

For Feature : self:MIMEditor

Editors: DavidKane

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A user wants to save a BioPax representation of a map.

Step-by-Step User Action

  1. User has edited a map
  2. The user specifies that the map is to be saved
  3. The systems writes out an appropriate BioPax repressentation

Visual Aides

Requirements for Cytoscape



Many pathway repositories are moving towards adopting BioPax as a standard of exchange. If the Kohn maps are exchangeable as BioPax, they could be exchanged and used more widely.

Other Examples


../Shared MimEditorUseCaseComments

It is not clear if saving as BioPax should be part of how the maps are normally saved, or if BioPax should be a “Save As” option. It is also not clear how to pair the visualization layout information with the BioPax representation.

AllanKuchinsky - 2007-01-23 05:18:23

This would be subsumed by general BioPAX export functionality in Cytoscape.  What are current plans for this?

Would XGMML be a good vehicle for storing the visual layout information?  If that is the case, then would we want to build on top of the 'session' abstraction to store/retrieve associated BioPAX and XGMML representations of networks?

Molecular_Interaction_Maps/SaveBioPax (last edited 2009-02-12 01:03:41 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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