Cytoscape WikiUse Case Name : Black box pathways |
For Feature : Groups |
Editors: Gary Bader |
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Summary
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
- 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.
- Or user can load an existing black box pathway from a BioPAX file
Visual Aides
Requirements for Cytoscape
- Similar to the requirements for other group use cases. Some special requirements may exists for editing pathways that contain black box pathways, like having a special type of group node and being able to add nodes to the black box pathway.
Importance
- The PANTHER, PATIKA and INOH databases all allow black box pathways. BioPAX supports this construct, however, it is not used that much. It will become increasingly important as more signaling pathways are represented in BioPAX.
Other Examples