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Reactome: A Curated Database of Human Biological Pathways

Reactome: A Curated Database of Human Biological Pathways. Lincoln Stein Infectious Disease Ontologies CSHL 2007. My Screen Found Lots of Genes: Now What?. Fuzzy Hairball?. Long List of GO Terms?. Boehringer-Mannheim, ca 1970. Fauré et al Bioinformatics 22 (14): e124 (2002). Reactome.

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Reactome: A Curated Database of Human Biological Pathways

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  1. Reactome: A Curated Database of Human Biological Pathways Lincoln Stein Infectious Disease Ontologies CSHL 2007

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

  3. Fuzzy Hairball?

  4. Long List of GO Terms?

  5. Boehringer-Mannheim, ca 1970

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

  7. 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.

  8. Home Page

  9. A Pathway Page

  10. A Reaction Page

  11. Reaction Details

  12. Where the Data Comes From • Recruit bench scientists to write modules. • Authors use a software tool to describe their pathway. • All molecules must be identified explicitly. • All assertions backed up by literature references. • Curators work with authors to ensure consistency and completeness. • Module checked by peer review & software before publication.

  13. Author Tool

  14. SkyPainter – Overrepresentation Analysis

  15. 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.

  16. Enhanced Skypainter

  17. 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.

  18. Physiology vs Pathophysiology Reactome databases • Normal physiological pathways • Pathophysiological pathways Non-Reactome databases specialized for infecious disease • Ontology dbs • WIKIs • Pathogen metagenome databases • etc

  19. Pathophysiology<->Physiology Pathogen-specific database Reactome Database

  20. Credits Richard Scheuermann & Co. NHGRI Grant # R01 HG002639 and a subcontract from the NIGMS-funded Cell Migration Consortium

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