SBGN Activity Flow
Huaiyu Mi For the SBGN Team
Oct. 6, 2010, COMBINE, Edinburgh, UK
Motivations • Most signaling pathways are drawn in this way in
published papers by biologists.
• Example: STKE.
• Details of the pathway are not known or irrelevant.
• It provides a simple, abstractive view of the pathway.
• It allows ambiguity.
SBGN-AF level 1 Specification
• Released in Sept. 2009.
• No update since the release
• Flawless?
• Useless?
• Laziness
Activity Flow Diagram Symbols
• Activity nodes
- Auxiliary information
• Compartment node
• Submap
• Modulation arcs
• Logic operators
AF Refcard
Unit of Information���-Examples
Activity Flow Diagram Example ���- EGF Receptor
8
Pan et. al., (2009) Cell, 137:73-86
Example of AF Map ���-PPARδ regulation in brown fat metabolism
EGFR pathway
• AF diagrams are ambiguous.
• An AF diagram should be associated with either a PD or ER diagram, if possible.
• Automatic conversion between PD and/or ER to AF.
11
Activity Flow map is ambiguous MEK
ERK
IGF
IGFR
IGF
IGFR
IGF
IGFR
IGF
IGFR
Autoconversion from AF to PD in PANTHER
Issue with the unit of information
• Too small, and can be useless when the diagram is large.
• Proposals have been received.
Biological Activity Node Current Proposal 1 Proposal 2 Proposal 3 Proposal 4
Entity Decoration Current Proposal 1 Proposal 2 Proposal 3
none
Proposal 4
The following are examples of three pathways drawn in different proposals.
EGFR Signaling���-Current AF spec.
EGFR Signaling���-Proposal 1
EGFR Signaling���-Proposal 2
EGFR Signaling���-Proposal 3
EGFR Signaling���-Proposal 4
PPAR Signaling���-Current AF spec.
PPAR Signaling���-Proposal 1
PPAR Signaling���-Proposal 2
PPAR Signaling���-Proposal 3
PPAR Signaling���-Proposal 4
TGF beta pathway���-Current AF spec
TGF beta pathway���-Proposal 1
TGF beta pathway���-Proposal 2
TGF beta pathway���-Proposal 3
TGF beta pathway���-Proposal 4
Acknowledgement • The entire SBGN community