Molecular_Interaction_Maps/SaveBioPax

<<TableOfContents: execution failed [Argument "maxdepth" must be an integer value, not "[2]"] (see also the log)>>

Summary

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

TBD

Importance

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

Comments

../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?