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The BARCODE Data Standard: CBOL’s Partnership with the International Nucleotide Sequence Database Collaboration (INSDC). David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu ; http://www.barcoding.si.edu
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The BARCODE Data Standard:CBOL’s Partnership with the International Nucleotide Sequence Database Collaboration (INSDC) 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
Infrastructure of Taxonomy:Fragmented, Disconnected • Collections and databases of specimens • Seedbanks, culture/cell line collections • Compilations of taxonomic names • Floristic and faunistic surveys/inventories • Monographs, Taxonomic revisions • Data repositories (gene sequences, characters, images, trees) • The (undigitized) Taxonomic Literature
Linking Logical Categories (2):Naming and defining species Holotype specimens
Linking Logical Categories (3):Establishing species boundaries Species concept beyond holotype - Paratype series - Typological versus population thinking - Genetic lineages - BSC (hard to apply)
Linking Logical Categories (4):Interpreting species boundaries • Other assigned specimens: • Species philosophy of original author • Interpretation of user
Databases of Names, Specimens, Species Distributions Museum databases of associated data Databases of species occurrences and distribution (OBIS) Authority files of taxonomic names
DNA Barcodes:A Key Variable for Biodiversity Informatics Museum databases of associated data Databases of species occurrences and distribution (OBIS) Authority files of taxonomic names
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 • Data Analysis: Beyond phenetic methods; population genetics perspective • (Plants: Initiated discussions of plant barcode gene region(s))
BARCODE Data Standards • Consultations with GenBank, ITIS, museum database developers, GBIF, ISIS, from 2004 • Consensus results of Front Royal meeting • GBIF ITIS GRIN • NBII Species2000 IPNI • ICZN ZooRecord OBIS • GenBank Proposed to International Nucleotide Sequence Database Collaboration (EMBL, DDBJ) • Approved by CBOL and INSDC mid-2005
Reserved Keyword “BARCODE” • GenBank reviews records against standard • Adds keyword “BARCODE” in annotation field • Can be removed by CBOL
Requirements • Species name selected from authority • Sequence from COI or other barcode region approved by CBOL • Structured link to voucher specimen • Online access to metadata • Trace files and quality scores • Primer sequences and names • Minimum sequence length (500bp for COI) • Geographic locality
Recommended fields, added to INSDC at CBOL’s request • Latitude and longitude • Name of the identifier • Name of the collector • Date of collection
New Data Fields Latitude/Longitude Collection date Collector’s name Identifier’s name
BARCODE Records in INSDC Specimen Metadata Voucher Specimen Species Name 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.
Structured link to Vouchers Specimen Metadata Voucher Specimen Species Name 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.
What constitutes a voucher? • Long-term reference tied to BARCODE • Corroborates the species identification • Provides additional tissue • CBOL relies on community decisions: • Full specimen? • Parts for morphologic features (e.g., feather?) • Frozen tissue? • E-Vouchers for large specimens, destructive samples, catch-and-release?
Structured Voucher IDs Linking to Vouchers
Voucher Specimen ID • Based on Darwin Core • Eventually will be replaced by GUID • Triplet: Institution Acronym : Collection : Specimen # NMNH : FISH : 123456 • CBOL, GBIF and NCBI discussing global registry of: • Institutional acronyms • Collection codes • “Pre-accession” specimen IDs
Link to Species Names Specimen Metadata Voucher Specimen Species Name 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.
NCBI Taxonomy BrowserThe good, the bad, and the ugly • Species names provided by submitters • Checked against compilations • Linkout to Catalogue of Life, other sources • Names not found added to Taxonomy Browser • Submitters informed of errors but not forced to make corrections
Authoritative Species Lists • Catalogue of Life • Species lists compiled by barcoding projects • FISH-BOL from FishBase, CoF • MBI mosquito catalog • Nomenclators • NameBank • New names in publications • Eventually, central registries (e.g., ZooBank)
Provisional Species ID • Uncertain identifications • Species complexes • Newly discovered variants • Ecogenomic samples • Need general guidelines to ensure: • Globally unique, • Stable, retrievable • Can’t be confused with valid species name
BARCODE Records in INSDC Specimen Metadata Voucher Specimen Species Name 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.
Connecting taxonomic articles Improving links to taxonomic journals
Links to Taxonomic Literature • Library-Laboratory meeting in London, 2005, on electronic access to taxonomic literature • Led to formation of Biodiversity Heritage Library initiative • Proactive steps with PubMed to add taxonomic journals to online abstracts • Aggressive negotiation with publishers of barcoding papers • Involvement in Encyclopedia of Life
Long-term data curationof BARCODE records Data records assembled 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
Acknowledgements Robert Hanner, University of Guelph, Chair of CBOL’s Database Working Group Scott Federhen, NCBI Taxonomy Browser Donald Hobern, Head of Informatics, GBIF