Use Case Name : Black box pathways

For Feature : Groups

Editors: Gary Bader

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Sometimes it is useful to represent an entire pathway as a simple node or 'black box'. This is done either to simplify the pathway diagram, indicate connections to other pathways that are not the focus of the current map or represent generic or relatiively unknown processes. BioPAX allows a pathway to be defined using only a name, not any subcomponents.

Step-by-Step User Action

  1. User can create a black box pathway, by creating a new node of type 'black box pathway'. This would be a group and user may add other nodes to it. A black box pathway node can be connected to any other node, including a group node.
  2. Or user can load an existing black box pathway from a BioPAX file

Visual Aides

Requirements for Cytoscape


Other Examples


groupAPI/UseCase8 (last edited 2009-02-12 01:03:15 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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