Data model in a nutshell
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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)
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Divide reaction space into ~160 “canonical pathways”, each represented by
an SBGN-like diagram
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Components of “amyloid fibrils”
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Interactors – small molecules; links to external data sources
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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.
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A somatic mutation changes the function of a protein: IDH1
usually
in many glioblastomas
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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