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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 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
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
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
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
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
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
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
IDS – Identification System Data Analysis Working Group, Paris, 6 July 2006
Linkage to Mapping System Data Analysis Working Group, Paris, 6 July 2006
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
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
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
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
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