2. Data model in a nutshell Pathway (GO biol process) PathwayReaction CatalystActivity (GO mol function) Output 1 Reaction Input 1 Input 2 Output 2 Regulation (GO biol process) location (GO cell component) protein (UniProt) or  molecule (ChEBI) or complex (GO/PRO)

5. Divide reaction space into ~160 “canonical pathways”, each represented by an SBGN-like diagram

7. Components of “amyloid fibrils”

9. Interactors – small molecules; links to external data sources

10. Representing disease processes -The amount of a normal protein is changed (expression overlays). - An infection introduces new proteins into the body (HIV, flu, TB, and “Microme”). - A mutation (somatic or germline) changes the function of a protein.

11. A somatic mutation changes the function of a protein: IDH1 usually in many glioblastomas

12. NYU Langone Medical Center Peter D'Eustachio Lisa Matthews Marc Gillespie Veronica Shamovsky Ralf Stephan Credits NHGRI Grant # P41 HG003751 EU 6th Framework Programme grant LSHG-CT-2005-518254 Ontario Institute for Cancer Research Lincoln Stein Robin Haw Marija Orlicic Karen Rothfels Joel Weiser Guanming Wu Michael Caudy Bruce May European Bioinformatics Institute Henning Hermjakob Bijay Jassal Steve Jupe Phani Garapati Mark Williams David Croft Antonio Fabregat-Mundo Ewan Birney