BioPAX Biological Pathway Data Exchange Format

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BioPAX - Biological Pathway Data Exchange Format

• Intro
• Mon.Oct.15.2007
• SRI

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Logistics

• Wireless internet access password
• Name tags
• Restrooms
• Presentations - any demos Tues pm?
• Expenses

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Pathway Databases
220 Pathway Databases!

• Arguably the most accessible data source, but...
• Varied formats, representation, coverage
• Pathway data extremely difficult to combine and
  use

Pathguide Pathway Resource List
(http//www.pathguide.org)
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http//pathguide.org
Vuk Pavlovic
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Biological Pathway Exchange (BioPAX)
Before BioPAX
After BioPAX Unifying language
gt100 DBs and tools Tower of Babel
Reduces work, promotes collaboration, increases
accessibility
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History

• July.2001 - ISMB Copenhagen BOF
• Aug.2002 - ISMB Edmonton BOF
• Nov.2002 - First workshop, NYC
• July 2004 - BioPAX Level 1 release
• Dec.2005 - BioPAX Level 2 release
• Oct.2007 - 14th workshop

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BioPAX users

• Data providers
• BioCyc, BioModels, Cancer Cell Map, INOH, KEGG,
  NCI/Nature, NetPath, PUMA2, Reactome
• Software
• BCDE, BioPAX validator (OHSU), Biowarehouse,
  cPath, Cytoscape, Pathway Commons, Pathway
  Knowledge Base, Pathway Tools, PATIKA, PaxTools,
  PSI-MI to BioPAX converter, QPACA, The gateway to
  biological pathways, VisANT
• Publications
• 297 Google Scholar
• 8 PubMed
• 37 Highwire press full search
• 121,000 Google results

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Meeting Goals

• Gain consensus on Level 3
• Make decisions where we can, modules
• Define process for gaining consensus before end
  of 2007
• Plan BioPAX future
• BioPAX Paper - communication effort
• Covering new data types
• Increased data sharing
• Community best practices (normalization)
• Evolve community - include new data providers in
  a scalable way
• Where will we be in 5 years?

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Agenda - Day 1

• 9am - Intro
• 920am - BioPAX Level release candidate 3
  overview
• 1030am - Coffee break
• 11am - Gene regulation session
• 1pm - Box lunch catered
• 2pm - Gene regulation discussion
• 330pm - Coffee break
• 4pm - Future BioPAX roadmap
• 430pm - Semantic integration discussion
• 530pm - Data exchange discussion
• 6pm - End of Day 1
• 7pm - Dinner at Trellis Italian restaurant

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Agenda - Day 2

• Start 830am - light breakfast coffee
• 830am - Pathway databases, data types and data
  sets - new developments
• 915am - Visualization
• 1000am - Progress on PaxTools
• 1100am - Curation/collection/author entry tools
• 1230am - lunch/discussion - end of main workshop
  
• Tuesday afternoon technical workshop

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Funding

• NIH NIGMS
• 1 R13 GM076939-01

Thanks! Hosts Paul Thomas, Peter Karp _at_ SRI Pre
meeting discussions
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