Day 1

MIM discussion

• Allan began by presenting his mapping from MIM shapes to Cytoscape graphical elements, presented on ["Molecular Interaction Maps"].
• Need to map MIM to both model and view
  • How to represent 'non covalent binding'?
    • Model: Best mapped to a group. A and B are connected and are part of the group.
    • View: this is a use case for the group view
  • Asymmetric binding
    • Model: Regular edge between A and B, just needs a specific edge type
    • View: New type of custom edge graphic (will take some care with Nerius' edge drawing code)
  • Representation of multimolecular complexes
    • Model: A group of groups
    • View: part of the use case for group view
  • Covalent modification of protein A (post-translational modification = PTM)
    • Model: A is a node (representing unmodified protein); central node is a node (represented modified A) - every state is represented as a node. The PTM e.g. P is not a node, it is an annotation on the 'central' state node. The edge between A and its state is of type 'state of'. The set of all states is grouped to represent the set of all states of A.
    • View: Constraint: the states always move together (would be like a template)
  • Cleavage of of a covalent modification of protein A
    • Model: Hyperedge containing node1: Phtase (hyperedge attribute: enzyme), node2: phosphorylated A, node3: unphosphorylated A
    • View: Use case for hyperedge view
• General constraints for automatic layout and the editor
  • Snap to grid
  • All lines need to be routed with only right or acute angles
  • Central node is only there if it is used (connected to something else in the diagram)
• Next step: a special interest group should get together to hash the above out further. Current interested people are: Allan, Mirit, David, Gary, Aditya, Scooter, Alex; also general interest from Nathan, Kristina (GenMAPP editing), Ethan, Ben (BioPAX editing)
• Implementation: Cytoscape core would ensure that the model and view requirements are met. Users: like GenMAPP, MIM, BioPAX editing would use the core functionality to create their own plugins that implemented their own pathway editing features.