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CBOL Working Groups. David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu ; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938. CBOL’s Working Groups. Database: Designing/constructing the BARCODE data standards
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CBOL Working Groups David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938 South/Central America Regional Meeting, Campinas, Brazil, 19 March 2007
CBOL’s Working Groups • Database: Designing/constructing the BARCODE data standards • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Data Analysis: Beyond phenetic methods; population genetics perspective • Plants: Identify gene region(s) for barcoding
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
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
Digitizing Taxonomic Literature • CBOL’s catalytic efforts: • Library-Laboratory meeting in London, 2005, on electronic access to taxonomic literature • Led to formation of Biodiversity Heritage Library initiative • Industrial-scale digitization of pre-1923 taxonomic literature; free online access • OCR and Taxonomic Intelligence • Partner in Encyclopedia of Life informatics
CBOL’s Working Groups • Database: Designing/constructing the BARCODE data standards • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Data Analysis: Beyond phenetic methods; population genetics perspective • Plants: Identify gene region(s) for barcoding
CBOL Formalin Workshop • May 8-9, 2006 workshop in Washington, National Research Council • Literature survey of DNA recovery protocols from formalin-fixed specimens Chemists, biochemists, biophysicists, biomedical researchers • Create a new research agenda • Follow-on with SPNHC as major partner
CBOL’s Working Groups • Database: Designing/constructing the BARCODE data standards • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Data Analysis: Beyond phenetic methods; population genetics perspective • Plants: Identify gene region(s) for barcoding
CBOL’s Working Groups • Database: Designing/constructing the BARCODE data standards • DNA: Protocols for formalin-fixed and old museum specimens; Producing LIMS for dissemination • Data Analysis: Beyond phenetic methods; population genetics perspective • Plants: Identify gene region(s) for barcoding by December 2006
Progress toward Plant Barcode • Kress 2005 proposal for ITS and trnh-psbA • Kew Garden receives Sloan/Moore Foundation support, early 2005 • Phase 1 screens 100 genes across 50 sibling species pairs • Phase 2 tests of matK, rpcoC1, rpoB, ndhJ, and accD • Canadian proposal for rbcL • CBOL protocols for approving barcode regions
Wider Impacts of Barcoding • Catalyzing interoperability of databases • Barcode data standards link sequences, specimens, species names and publications • Improving information infrastructure • Digital library initiative in taxonomy • Expanding analytical toolbox for taxonomy • Renewing the mission of museums • DNA recovery from formalin-fixed specimens