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The Barcode Initiative and the Consortium for the Barcode of Life

The Barcode Initiative and the Consortium for the Barcode of Life. David E. Schindel, Executive Secretary Consortium for the Barcode of Life National Museum of Natural History Smithsonian Institution SchindelD@si.edu ; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938.

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The Barcode Initiative and the Consortium for the Barcode of Life

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  1. The Barcode Initiative and the Consortium for the Barcode of Life David E. Schindel, Executive Secretary Consortium for the Barcode of Life National Museum of Natural History Smithsonian Institution SchindelD@si.edu; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938 Data Analysis Working Group, Paris, 6 July 2006

  2. Consortium for the Barcode of Life (CBOL) • First barcoding publications in 2002 • Cold Spring Harbor planning workshops in 2003 • Sloan Foundation grant, launch in May 2004 • Secretariat opens at Smithsonian, September 2004 • First international conference February 2005 • Now an international affiliation of: • 120+ Members Org’s, 40 countries, 6 continents • Natural history museums, biodiversity organizations • Users: e.g., government agencies • Private sector biotech companies, database providers Data Analysis Working Group, Paris, 6 July 2006

  3. Consortium for the Barcode of Life (CBOL)Smithsonian Institution/Sloan Foundation125 Member Organizations, 40 Countries as of June 2006 Data Analysis Working Group, Paris, 6 July 2006

  4. CBOL-Initiated Projects • Fish Barcode of Life (FISH-BOL) • 30,000 marine/freshwater species by 2010 • All Birds Barcoding Initiative (ABBI) • 10,000 species by 2010 • Tephritid fruit flies • 2,000 pest/beneficial species and relatives by 2008 • Mosquitoes • 3,300 species by 2008 • Endangered vertebrates (bushmeat) • Successive phases of African mammals Data Analysis Working Group, Paris, 6 July 2006

  5. Projects initiated by others • CMarZ: Marine habitat, multiple taxa • All-Leps: Multiple regions/habitats, single taxon • BioCode, Moorea: Single location, multiple habitats, multiple taxa Data Analysis Working Group, Paris, 6 July 2006

  6. Using DNA Barcodes • Establish reference library of barcodes from identified voucher specimens • If necessary, revise species limits • Identify unknowns by searching against reference sequences • Create barcode arrays for identifying species in mixtures (e.g., ballast water) • Before long: Analyze relative abundance in multi-species samples (ecosamples) Data Analysis Working Group, Paris, 6 July 2006

  7. BoLD Data System • Developed/hosted by Univ. Guelph • Workbench for most barcode projects • Laboratory Information Management System (LIMS) for assembling data • Management and Analysis System • Identification system for matching unknowns to reference records • Uploading to GenBank Data Analysis Working Group, Paris, 6 July 2006

  8. Data Analysis Working Group, Paris, 6 July 2006

  9. IDS – Identification System Data Analysis Working Group, Paris, 6 July 2006

  10. Linkage to Mapping System Data Analysis Working Group, Paris, 6 July 2006

  11. CBOL’s Working Groups • Database: Designing/constructing the Barcode Section of GenBank • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Plants: Identify gene region(s) for barcoding • Data Analysis: Beyond phenetic methods; population genetics perspective Data Analysis Working Group, Paris, 6 July 2006

  12. Barcode Data Standards • Consensus results of Front Royal meeting • GBIF  ITIS  GRIN • NBII  Species2000  IPNI • ICZN  ZooRecord  OBIS • Structured link to voucher specimen • Species name selected from authority • Online access to metadata • Trace files and quality scores • Minimum sequence length Data Analysis Working Group, Paris, 6 July 2006

  13. BARCODE Records in INSDC Specimen Metadata Voucher Specimen Species Name GeoreferenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalog of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Databases - Provisional sp. Barcode Sequence Trace files Primers Other Databases Literature(link to content or citation) PhylogeneticPop’n GeneticsEcological Data Analysis Working Group, Paris, 6 July 2006

  14. History of Data Analysis WG • Initial meeting at First Barcode Conference, London, February 2005 • Planning meetings: • DIMACS, Rutgers, NJ in September 2005 • National Museum of Natural History, Paris in September 2005 • Submission of Program of Work to CBOL • Paris Workshop Prospectus, Call for Participation, Technical Challenges • Grant support from ESF, NSF, CBOL Data Analysis Working Group, Paris, 6 July 2006

  15. Milestones for 2008 2006 2007 2008 Q1 Q2 Q3 Q4 Q1 Q2 Q3 Q4 Q1 Q2 Database: 100K records 200K records 500K records Formalin Study Advanced Lab Protocols DNA WG: Plant Barcode Announced Plant WG: International Conference Demonstrator System Launched Data Analysis WG: Data Analysis Protocols and S/W BoLI Data Portal Launched Data Standards Extended DB Interoperability Database WG: Campaigns: Regional Groups Operational First Data Releases 10K birds30K fish

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