sbgn activity flow - sbml.orgsbml.org/images/2/2c/mi_combine_sbgn_af_2010-10-06.pdf · sbgn...
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SBGN Activity Flow
Huaiyu Mi For the SBGN Team
Oct. 6, 2010, COMBINE, Edinburgh, UK
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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.
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SBGN-AF level 1 Specification
• Released in Sept. 2009.
• No update since the release
• Flawless?
• Useless?
• Laziness
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Activity Flow Diagram Symbols
• Activity nodes
- Auxiliary information
• Compartment node
• Submap
• Modulation arcs
• Logic operators
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AF Refcard
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Unit of Information���-Examples
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Activity Flow Diagram Example ���- EGF Receptor
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8
Pan et. al., (2009) Cell, 137:73-86
Example of AF Map ���-PPARδ regulation in brown fat metabolism
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EGFR pathway
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• 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.
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Activity Flow map is ambiguous MEK
ERK
IGF
IGFR
IGF
IGFR
IGF
IGFR
IGF
IGFR
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Autoconversion from AF to PD in PANTHER
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Issue with the unit of information
• Too small, and can be useless when the diagram is large.
• Proposals have been received.
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Biological Activity Node Current Proposal 1 Proposal 2 Proposal 3 Proposal 4
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Entity Decoration Current Proposal 1 Proposal 2 Proposal 3
none
Proposal 4
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The following are examples of three pathways drawn in different proposals.
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EGFR Signaling���-Current AF spec.
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EGFR Signaling���-Proposal 1
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EGFR Signaling���-Proposal 2
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EGFR Signaling���-Proposal 3
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EGFR Signaling���-Proposal 4
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PPAR Signaling���-Current AF spec.
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PPAR Signaling���-Proposal 1
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PPAR Signaling���-Proposal 2
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PPAR Signaling���-Proposal 3
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PPAR Signaling���-Proposal 4
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TGF beta pathway���-Current AF spec
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TGF beta pathway���-Proposal 1
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TGF beta pathway���-Proposal 2
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TGF beta pathway���-Proposal 3
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TGF beta pathway���-Proposal 4
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Acknowledgement • The entire SBGN community