BioPAX The Birth of A Data Exchange Language for Biological Pathways Joanne Luciano BioPAX Group 7...

BioPAXThe Birth of A Data Exchange

Language for Biological PathwaysJoanne LucianoBioPAX Group

www.biopax.org

7th International Annual Bio-Ontologies Meeting

30 July 2004Glasgow, ScotlandUnited Kingdom

http://www.biopax.org/

30 July 2004 7th BioOntologies Workshop 2

IntroductionBioPAX = Biopathway Exchange Language

Emerged at ISMB

•conceived at ISMB ’01•born just before ISMB ’02 (Protégé

workshop)•crawling at ISMB ’03 (Level 0.5)•walking at ISMB ’04 (Level 1.0)•approaching the “terrible twos”


What is a pathway?

Depends on who you ask


WITBioCycReactomeaMAZEKEGGBINDDIPHPRDMINTIntActPSI formatCSNDBTRANSPATHTRANSFACPubGeneGeneWays

IntegratedPathwayDatabase

Research Community Need

PathwayDatabases

MetabolicProtein InteractionSignal Transduction

Gene Regulatory


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


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


Technical Logistics (cont’d)Why OWL DL?

• Expressivity (biology = “complex relationships” • W3C Standard (use existing standards)

“Semantic Web enabled.”• XML based (the exchange language in computing)• Machine Computable

Enable full reasoning capability from file reading to logical inference– facilitate integration of knowledge, data, tool development– uncover inconsistencies and new knowledge

– OWL DL• Complete: all conclusions are guaranteed to be

computed• Decidable: all computations will finish in finite time

(with OWL Lite, short amount of time


Social LogisticsHow we engendered buy in from the field.

Made it much easier

Take things in steps:• Pathway Database -> Data Exchange Format• Data Exchange Format -> Release in Levels of increasing

complexity (early success leads to early adoption leads to the possibility 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


Social Logistics(cont’d)Get “buy in” (continued) • Community Involvement and Support

Core group (from community, small, meet regularly)Mailing ListUser communitySubgroupsInternational Meetings and Presentations Tool developers

ModelersUsers (researchers)Ontology developersDatabase providersComplementary representations (SBML, CellML)Like mindsGeneral Community


Social Logistics(cont’d)

Get organized• Small core group advancing standard• International representation via mailing lists• Collaborate complementary representations• Bi-weekly conference calls, bi-monthly F2F• Cost paid by participants and DOE• Special interests have subgroups

– Core group member + outside experts– Tackle specific challenges


Implementation of BioPAX

Designed using GKB Editor and Protégé

BioPAX uses OWL to define the Schema

BioPAX Instances to store the data


BioPAX – Ontology


OWL(schema)

Instances (Individuals)

data


Complex Relationships Captured


Ontology Slot Definitions


Integration -> KnowledgeKnowledge is Power

Data in the same format: Metabolic Protein Protein

InteractionSignal Transduction Gene Regulation

Facilitates– Centralized public pathway DB– Share data between existing DBs– Distribute public and proprietary data– Knowledge Assembly– Reasoning


A Common Exchange Language

Without BioPAX>100 DBs and tools

BioPAX

Promotes collaboration (big science), accessibility

Database

Application

User


Biomass

Consistency Checking: Nutrient-related analysis of a BioPAX knowledge base

Fired Reaction

Missing essentialcompound

Known Nutrient set

Essentialcompounds

Unfired Reaction


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

• Development of tools and API– libBioPAX

• Semantic Web Life Science Initiatives– BOF Sunday


BioPAX Supporting GroupsGroups • 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 (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

http://www.pharmgkb.org/


PSI

Biochemical Reactions

SBML,CellML

Regulatory PathwaysLow Detail High Detail

ProteinInteractionNetworks

Metabolic PathwaysLow Detail High Detail

Database ExchangeFormats

Simulation ModelExchange Formats

RateFormulas

Exchange Formats in the Pathway Data Space


Level 1 BioPAXReleased July 2004

BioPAX Level 1

PSISBML,CellML

GeneticInteractions

Molecular InteractionsPro:Pro All:All

Interaction NetworksMolecular Non-molecularPro:Pro TF:Gene Genetic




RateFormulas



Small MoleculesLow Detail High Detail


Exchange Formats in the Pathway Data Space

BioPAX

PSISBML,CellML

GeneticInteractions

Molecular InteractionsPro:Pro All:All

Interaction NetworksMolecular Non-molecularPro:Pro TF:Gene Genetic




RateFormulas



Small MoleculesLow Detail High Detail

BioPAX The Birth of A Data Exchange Language for Biological Pathways Joanne Luciano BioPAX Group 7...

Documents

Transcript of BioPAX The Birth of A Data Exchange Language for Biological Pathways Joanne Luciano BioPAX Group 7...