Reactome: A Curated Reactome: A Curated Database of Human Database of Human Biological PathwaysBiological Pathways

Lincoln SteinInfectious Disease Ontologies

CSHL 2007

My Screen Found Lots of My Screen Found Lots of Genes: Now What?Genes: Now What?

Fuzzy Hairball?Fuzzy Hairball?

Long List of GO Terms?Long List of GO Terms?

Boehringer-Mannheim, ca 1970

Fauré et al Bioinformatics 22 (14): e124 (2002)

Reactome A computable representation of human

pathways and reactions. Uses a “chemical” reaction model to represent

causality. Molecules identified explicitly – including small

molecules, proteins, complexes, post-translational modifications, compartments.

Exportable as SBML, BioPax, PDF and MySQL dumps.

Open Source Authored & curated by experts in the

field.

Home Page

A Pathway Page

A Reaction Page

Reaction Details

Where the Data Comes From

1) Recruit bench scientists to write modules.2) Authors use a software tool to describe

their pathway.1) All molecules must be identified explicitly.

2) All assertions backed up by literature references.

3) Curators work with authors to ensure consistency and completeness.

4) Module checked by peer review & software before publication.

Author Tool

SkyPainter – Overrepresentation Analysis

Increasing Coverage Add non-Reactome data sets to create a

“corona” of less reliable data around each pathway.

Corona connected to pathway components by probable functional interaction links.

Enhanced Skypainter

Reactome & Infectious Disease

Via collaboration with Richard Scheuermann, have created an influenza lifecycle module. 64 reactions, 338 molecules Modeling issues:

Is the virion a molecular complex? A compartment? A cell?

When is it OK for the proteins of two species to interact?

We’d encourage other groups to do this for more pathogens.

Physiology vs Pathophysiology

Reactome databases Normal physiological pathways Pathophysiological pathways

Non-Reactome databases specialized for infecious disease Ontology dbs WIKIs Pathogen metagenome databases etc

Pathophysiology<->PhysiologyPathogen-specific database

Reactome Database

Credits

Cold Spring Harbor Laboratory

European Bioinformatics Institute

Gene Ontology Consortium

Lincoln SteinPeter D'EustachioGopal GopinathraoLisa MatthewsMarc GillespieGuanming Wu

Ewan BirneyImre VastrikBernardo de BonoEsther SchmidtBijay JassalDavid Croft

Suzanna Lewis

NHGRI Grant # R01 HG002639and a subcontract from the NIGMS-funded Cell Migration Consortium

Richard Scheuermann & Co.