BioPAX A Data Exchange Format for Biological Pathways

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BioPAXA Data Exchange Format for Biological
Pathways

• Michael Cary, Joanne Luciano
• BioPAX Workgroup
• www.biopax.org
• SOFG October 2004

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Introduction

• BioPAX Biological pathway exchange
• An open source community effort to build a data
  exchange format for biological pathways
• Began at ISMB 02
• First draft (Level 0.5) released Sept 2003
• Level 1 released July 2004
• Focuses on representing metabolic pathways
• Later levels will expand this scope

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The domain Biological pathways
Main categories
Metabolic Pathways
Molecular Interaction Networks
Signalling Pathways
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The Problem

• So many pathway databases, all with their own
  data models, formats, and data access methods.

Source Pathway Resource List (http//cbio.mskcc.o
rg/prl/)
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BioPAX Motivation
gt150 DBs and tools
Application
Database
User
Before BioPAX
With BioPAX
Common format will make data more accessible,
promoting data sharing and distributed curation
efforts
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Exchange Formats in the Pathway Data Space
Database Exchange Formats
Simulation Model Exchange Formats
SBML, CellML
PSI-MI
Biochemical Reactions
Protein Interaction Networks
Rate Formulas
Metabolic Pathways Low Detail High
Detail
Regulatory Pathways Low Detail High
Detail
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Exchange Formats in the Pathway Data Space
Database Exchange Formats
Simulation Model Exchange Formats
BioPAX
SBML, CellML
Genetic Interactions
PSI-MI 2
Rate Formulas
Biochemical Reactions
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Exchange Formats in the Pathway Data Space
Database Exchange Formats
Simulation Model Exchange Formats
SBML, CellML
Genetic Interactions
PSI-MI 2
Rate Formulas
BioPAX Level 1
Biochemical Reactions
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BioPAX Ontology

• Conceptual framework based upon existing DB
  schemas
• aMAZE, BIND, EcoCyc, WIT, KEGG, Reactome, etc.
• Allows wide range of detail, multiple levels of
  abstraction
• BioPAX ontology in OWL (XML)
• Ontology built using GKB Editor and Protégé
• Semantic mapping still a manual process
• Level 1 represents metabolic pathway data
• Large body of well understood data
• Stable representations (old data)

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BioPAX Ontology Overview
Level 1 v1.0 (Released July 7th, 2004)
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BioPAX Ontology Top Level

• Pathway
• A set of interactions
• E.g. Glycolysis, MAPK, Apoptosis
• Interaction
• A set of entities and some relationship between
  them
• E.g. Reaction, Molecular Association, Catalysis
• Physical Entity
• A building block of simple interactions
• E.g. Small molecule, Protein, DNA, RNA

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BioPAX Ontology Interactions
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BioPAX Ontology Physical Entities
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How it works
A typical pathway would be decomposed into A
single pathway instance, which would contain
several pathway steps, which would each contain
one or more interactions occurring between
physical entity participants, which each point to
one physical entity.
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Using other ontologies

• Use pointers to existing ontologies to provide
  supplemental annotation where appropriate
• Cellular location ? GO Component
• Cell type ? Cell.obo
• Organism ? NCBI taxon DB
• Incorporate other standards where appropriate
• Chemical structure ? SMILES, CML, INCHI

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BioPAX Workgroup Organizational Structure

• Small core group advancing the standard
• Increased representation from mailing lists and
  subgroups
• Cost paid by participants/DOE workshop grant
• Special topics have subgroups
• Core group member outside experts
• Tackle specific challenges
• E.g. States, small molecules, examples

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Current status

• Converting data into Level 1
• EcoCyc and other BioCyc DBs done
• KEGG, Reactome, WIT, aMAZE in progress
• Finishing Level 2
• Adding support for binding interactions
• Draft release coming soon
• Organizing Level 3
• Focusing on signaling pathways

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BioPAX Supporting Groups

• Groups
• Memorial Sloan-Kettering Cancer Center G. Bader,
  M. Cary, C. Sander
• SRI Bioinformatics Research Group P. Karp, S.
  Paley, J. Pick
• University of Colorado Health Sciences Center I.
  Shah
• BioPathways Consortium J. Luciano, E. Neumann,
  A. Regev, V. Schachter
• Argonne National Laboratory N. Maltsev, E.
  Marland
• Samuel Lunenfeld Research Institute C. Hogue
• Harvard Medical School E. Brauner, D. Marks, A.
  Regev
• NIST R. Goldberg
• Stanford T. Klein
• Columbia A. Rzhetsky
• Dana Farber Cancer Institute J. Zucker
• Collaborating Organizations
• Proteomics Standards Initiative (PSI)
• Systems Biology Markup Language (SBML)
• CellML
• Chemical Markup Language (CML)

• Databases
• BioCyc (www.biocyc.org)
• BIND (www.bind.ca)
• WIT (wit.mcs.anl.gov/WIT2)
• PharmGKB (www.pharmgkb.org)
• Grants
• Department of Energy (Workshop)

The BioPAX Community