Data model in a nutshell

Pathway (GO biol process)

Pathway Reaction Reaction

CatalystActivity(GO mol function)

Output 1

Reaction

Input 1

Input 2 Output 2

Regulation(GO biol process)

location(GO cell component)

protein (UniProt) ormmolecule (ChEBI)

orcomplex (GO/PRO)

Divide reaction space into ~160 “canonical pathways”, each represented by

an SBGN-like diagram

Components of “amyloid fibrils”

Interactors – small molecules; links to external data sources

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.

A somatic mutation changes the function of a protein: IDH1

usually

in many glioblastomas

NYU Langone Medical CenterPeter D'EustachioLisa MatthewsMarc GillespieVeronica Shamovsky

Ralf Stephan

Credits

NHGRI Grant # P41 HG003751EU 6th Framework Programme grant LSHG-CT-2005-518254

Ontario Institutefor Cancer ResearchLincoln SteinRobin HawMarija OrlicicKaren RothfelsJoel WeiserGuanming WuMichael CaudyBruce May

European BioinformaticsInstituteHenning HermjakobBijay JassalSteve JupePhani GarapatiMark WilliamsDavid CroftAntonio Fabregat-MundoEwan Birney