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Data model in a nutshell

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

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Data model in a nutshell

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

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

  3. Components of “amyloid fibrils”

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

  5. 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.

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

  7. Credits Ontario Institutefor 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 NYU Langone Medical Center Peter D'Eustachio Lisa Matthews Marc Gillespie Veronica Shamovsky Ralf Stephan EU 6th Framework Programme grant LSHG-CT-2005-518254 NHGRI Grant # P41 HG003751

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