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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.

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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