BioPAX The Birth of A Data Exchange Language for Biological Pathways Joanne Luciano BioPAX Core Group 7 th International Annual Bio-Ontologies Meeting 30 July 2004 Glasgow, Scotland United Kingdom

30 July 20047th BioOntologies Workshop2 Introduction BioPAX = Biopathway Exchange Language Emerged at ISMB conceived at ISMB 01 born at ISMB 02 crawling at ISMB 03 (Level 0.5) walking at ISMB 04 (Level 1.0) now approaching the terrible twos

30 July 20047th BioOntologies Workshop3 What is a pathway? Depends on who you ask

30 July 20047th BioOntologies Workshop4 WIT BioCyc Reactome aMAZE KEGG BIND DIP HPRD MINT IntAct PSI format CSNDB TRANSPATH TRANSFAC PubGene GeneWays Integrated Pathway Database Research Community Need Pathway Databases Metabolic Protein Interaction Signal Transduction Gene Regulatory

30 July 20047th BioOntologies Workshop5 Design Goals Encapsulation: An entire pathway in one record Compatible: Use existing standards wherever possible Computable: From file reading to logical inference Successful: Buy-in from the research community

30 July 20047th BioOntologies Workshop6 Technical Logistics & Goals Interoperability –Integration and exchange of pathway data –Interchange through a common (standard) representation –accommodate existing database representations –provide a basis for future databases –enables development of tools for searching and reasoning over the data base

30 July 20047th BioOntologies Workshop7 Technical Logistics (contd) Why OWL? Why OWL DL? Expressivity (biology = complex relationships) W3C Standard (use existing standards) Semantic Web enabled XML based (the exchange language in computing) Machine Computable –Facilitate integration of knowledge, data, tool development –Uncover inconsistencies and new knowledge –OWL DL Enable full reasoning capability for users from file reading to logical inference Complete: all conclusions are guaranteed to be computed Decidable: all computations will finish in finite time (with OWL Lite, short amount of time)

30 July 20047th BioOntologies Workshop8 Social Logistics Get organized Make the decision & commitment 2 or 3 dedicated individuals Small core group –Bi-weekly conference calls, bi-monthly F2F –Commitment & resources Participants willing and able cover their costs Outside funding (DOE) Special interests and needs form subgroup task forces Core group member(s) Outside experts International representation & participation (Outreach & Community Building) conferences and mailing lists follow-up and individual Collaborate with complementary/competing representations

30 July 20047th BioOntologies Workshop9 Social Logistics How we engendered buy in from the field which made life much easier Take things in steps: Pathway Database vision -> Data Exchange Format as 1 st step Data Exchange Format -> Release in Levels of increasing complexity Level 1 supports Metabolic pathways, Level 2 Early success leads to early adoption, leads to increased probability of overall project success. Get buy in and get involvement -leads to acceptance later Support the existing databases (BioCYC, WIT, BIND, etc.) –Got database sources to agree to participate in the development to assure that their DBs will be properly represented Got database sources to agree to export in the new format once it is defined

30 July 20047th BioOntologies Workshop10 Social Logistics (contd) Get buy in (continued) Community Involvement and Support Core group (represents voice of community, small, committed) Mailing List User community Subgroups International Meetings and Presentations Tool developers Modelers Users (researchers) Ontology developers Database providers Complementary representations (SBML, CellML) Like minds General Community

30 July 20047th BioOntologies Workshop11 Implementation of BioPAX Designed using GKB Editor and Protégé BioPAX uses OWL to define the Schema BioPAX Instances to store the data

30 July 20047th BioOntologies Workshop12 BioPAX – Ontology

30 July 20047th BioOntologies Workshop13 OWL (schema) Instances (Individuals) data

30 July 20047th BioOntologies Workshop14 Complex Relationships Captured

30 July 20047th BioOntologies Workshop15 Ontology Slot Definitions

30 July 20047th BioOntologies Workshop16 Integration -> Knowledge Knowledge is Power Data in the same format: MetabolicProtein Protein Interaction Signal Transduction Gene Regulation Facilitates –Centralized public pathway DB –Share data between existing DBs –Distribute public and proprietary data –Knowledge Assembly –Reasoning

30 July 20047th BioOntologies Workshop17 A Common Exchange Language Without BioPAX >100 DBs and tools BioPAX Promotes collaboration (big science), accessibility Database Application User

30 July 20047th BioOntologies Workshop18 Biomass Consistency Checking: Nutrient-related analysis of a BioPAX knowledge base Fired Reaction Missing essential compound Known Nutrient set Essential compounds Unfired Reaction

30 July 20047th BioOntologies Workshop19 What Next? BioPAX future Development –Level 2, 3, future levels –BOF (check schedule) –Talk later today by Gary Bader at BioPathways SIG –Poster in Main Conference (check program) Development of tools and API –libBioPAX Semantic Web Life Science Initiatives –BOF Sunday

30 July 20047th BioOntologies Workshop20 BioPAX Supporting Groups Groups Memorial Sloan-Kettering Cancer Center: G. Bader, M. Cary, J. Luciano, 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, J. Luciano, 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 ( BIND ( WIT (wit.mcs.anl.gov/WIT2) PharmGKB ( Grants Department of Energy (Workshop) The BioPAX Community

30 July 20047th BioOntologies Workshop21 PSI Biochemical Reactions SBML, CellML Regulatory Pathways Low Detail High Detail Protein Interaction Networks Metabolic Pathways Low Detail High Detail Database Exchange Formats Simulation Model Exchange Formats Rate Formulas Exchange Formats in the Pathway Data Space

30 July 20047th BioOntologies Workshop22 Level 1 BioPAX Released July 2004 BioPAX Level 1 PSI SBML, CellML Genetic Interactions Molecular Interactions Pro:Pro All:All Interaction Networks Molecular Non-molecular Pro:Pro TF:Gene Genetic Regulatory Pathways Low Detail High Detail Database Exchange Formats Simulation Model Exchange Formats Rate Formulas Metabolic Pathways Low Detail High Detail Biochemical Reactions Small Molecules Low Detail High Detail

30 July 20047th BioOntologies Workshop23 Exchange Formats in the Pathway Data Space BioPAX PSI SBML, CellML Genetic Interactions Molecular Interactions Pro:Pro All:All Interaction Networks Molecular Non-molecular Pro:Pro TF:Gene Genetic Regulatory Pathways Low Detail High Detail Database Exchange Formats Simulation Model Exchange Formats Rate Formulas Metabolic Pathways Low Detail High Detail Biochemical Reactions Small Molecules Low Detail High Detail