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Schindel   i evobio norman ok - jun 11
 

Schindel i evobio norman ok - jun 11

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DNA Barcode Data Standards presentation at the iEvoBio (Informatics for Evolutionary Biology) meeting in Norman, OK, 22 June 2011

DNA Barcode Data Standards presentation at the iEvoBio (Informatics for Evolutionary Biology) meeting in Norman, OK, 22 June 2011

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    Schindel   i evobio norman ok - jun 11 Schindel i evobio norman ok - jun 11 Presentation Transcript

    • The BARCODE Data Standard as a Cross-Cultural Bridge
      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
    • Gaining Large Scale Through Standards
      Are our data meant only for small segregated communities of practice or bigger audiences?
      Accelerate progress, Economies of scale
      Re-use and new use of data, synthesis, comparative analysis
      Shared hardware and software
      Standardized protocols, easier training and technical assistance
      Applications by non-specialists (regulatory agencies, citizen scientists, K-12 classroom)
    • www.e-biosphere09.org
    • Species Identification Matters
      Basic research:
      One more character set, but digital and calibrated
      Standardized yardstick for measuring variability and divergence
      Objective comparison across taxa, distance
      Links to Linnean names
      Triage by non-specialists for species discovery
      Ecology of juveniles, gut contents, fecal matter
      Shallow phylogenies showing history of community assemblages
      Subject to weaknesses of any single character (convergence, pseudogenes, introgression, etc.)
    • Species Identification Matters
      Applied research/regulation by non-specialists
      Agricultural pests/beneficial species
      Endangered/protected species
      Disease vectors/pathogens
      Environmental quality indicators
      Invasive species (e.g., in ballast water)
      Managing for sustainable harvesting
      Consumer protection, ensuring food quality
      Fidelity of seedbanks, culture collections
    • 6
    • Small ribosomal RNA
      The Mitochondrial Genome
      D-Loop
      DNA
      mtDNA
      Cytochrome b
      ND1
      ND6
      ND5
      COI
      ND2
      COI
      L-strand
      H-strand
      Typical Animal Cell
      ND4
      ND4L
      COII
      ND3
      COIII
      ATPase subunit 8
      ATPase subunit 6
      Mitochondrion
      An Internal ID System for All Animals
    • Non-COI regions for other taxa
      Land plants:
      Chloroplast matK and rbcL approved Nov 09
      70-75% resolvingability, higher in angiosperms
      Non-coding plastid and nuclear regions being explored
      Fungi:
      CBOL Working Group met this week in Amsterdam
      Agreed to recommend ITS; 72% effective
      Protists:
      CBOL Working Group July meeting, Berlin
    • How Barcoding Works
      PHASE 1: Build a barcode reference library:
      Well-identified specimen
      Tissue subsample
      DNA extraction, PCR amplification
      DNA sequencing
      Data submission to GenBank
      PHASE 2: Identify unknowns:
      Any unidentified juvenile, adult, fragment, product
      Tissue sample, DNA, sequencing
      Comparison with sequences in reference library
    • Barcode of Life Community
      1,264,000 specimens already barcoded from 104,500 species
      Networks, Projects, Organizations
      • Promote barcoding as a global standard
      • Build participation
      • Working Groups
      • BARCODE standard
      • International Conferences
      • Increase production of public BARCODE records
    • Barcode of Life Data Systems (BOLD)
      University of Guelph
      Workbench with 1.27M records, 105K species/OTUs
    • BARCODE Record Flow Chart
      Key
      Mirroring
      Update Channel
      Private Records
      USER
      /GenBank
    • BARCODE Records in GenBank
    • Submission of BARCODE Records to EBI and DDBJ
    • BARCODE Records in INSDC
      Voucher Specimen
      Species Name
      Specimen Metadata
      GeoreferenceHabitatCharacter setsImagesBehaviorOther genes
      Indices - Catalogue of Life - GBIF/ECAT
      Nomenclators - Zoo Record - IPNI - NameBank
      Publication links - New species
      Barcode Sequence
      Trace files
      Primers
      Other Databases
      Literature(link to content or citation)
      PhylogeneticPop’n GeneticsEcological
      Databases - Provisional sp.
    • Linkout from GenBank to BOLD
    • Linkout from GenBank to Taxonomy
      ISBER: 13 May 2009
    • Link from GenBank to Museums
      ISBER: 13 May 2009
    • Darwin Core TripletStructured Link to Vouchers
      Institutional Acronym
      Collection Code
      Catalog ID
      :
      :
    • Structured Link to Vouchers
      :
      :
      NHM
      LEP
      123456
      :
      :
      personal
      DHJanzen
      SRNP12345
    • NCBI’s Biorepository List
      Compiled from Index Herbariorum, literature sources, GenBank submissions
      6,936 records
      1,177 records with non-unique acronyms
      517 homonymous acronyms
      374 shared by two records
      143 shared by three records
    • CBOL/GBIF/NCBI Registry of Biorepositories
      www.biorepositories.org
    • Accessibility
      Formal naming
      Collaborative consensus-building of taxon concepts (CATE)
      Sharing of non-BARCODE data (ScratchPads)
      BARCODE data release with provisional nomenclature (PLoS)
      Specimen data release (GBIF)
      Comparisons, concept validation
      Taxon concept formation, refinement
      Collecting events, specimens
      Specimen clustering
      Two Taxonomic Research Processes
    • Long-term data curationof BARCODE records
      Data records assembled in BOLD
      Community feedback
      Compliant with BARCODE standards?
      Update records (audit trail of species names retained)
      Data records released on INSDC
      IDs consistent with other records?
      GenBank adds BARCODE flag
      CBOL control of BARCODE flag
      Data records published in BOLD