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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 [email protected]; 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 (1): Specimens, Names, Opinions Voucher Specimen ?? Journal Publication Species Name Linking Logical Categories (2): Naming and defining species Voucher Specimen Journal Publication Holotype specimens Species Name Linking Logical Categories (3): Establishing species boundaries Voucher Specimen ?? Journal Publication Species concept beyond holotype - Paratype series - Typological versus population thinking - Genetic lineages - BSC (hard to apply) Species Name Linking Logical Categories (4): Interpreting species boundaries Voucher Specimen Other assigned specimens: •Species philosophy of original author •Interpretation of user ?? Journal Publication Species Name Databases of Names, Specimens, Species Distributions Voucher Specimen Museum databases of associated data Databases of species occurrences and distribution (OBIS) Journal Publication Species Name Authority files of taxonomic names DNA Barcodes: A Key Variable for Biodiversity Informatics Voucher Specimen Museum databases of associated data Databases of species occurrences and distribution (OBIS) Barcode Sequence Journal Publication Species Name 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 – NBII – ICZN ITIS Species2000 ZooRecord GRIN IPNI 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 Keyword in GenBank BARCODE Records in INSDC Specimen Metadata Georeference Habitat Character sets Images Behavior Other genes Other Databases Phylogenetic Pop’n Genetics Ecological Voucher Specimen Barcode Sequence Trace files Primers Literature (link to content or citation) Species Name Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Databases - Provisional sp. Structured link to Vouchers Specimen Metadata Georeference Habitat Character sets Images Behavior Other genes Other Databases Phylogenetic Pop’n Genetics Ecological Voucher Specimen Barcode Sequence Trace files Primers Literature (link to content or citation) Species Name Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species 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? Where’s the voucher? 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 Georeference Habitat Character sets Images Behavior Other genes Other Databases Phylogenetic Pop’n Genetics Ecological Voucher Specimen Barcode Sequence Trace files Primers Literature (link to content or citation) Species Name Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Databases - Provisional sp. Species names in INSDC NCBI Taxonomy Browser The 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 NCBI Taxonomy Browser NCBI Taxonomy Browser Some names have no other source Other names linked to GBIF and Catalogue of Life… …and primary data source 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 Georeference Habitat Character sets Images Behavior Other genes Other Databases Phylogenetic Pop’n Genetics Ecological Voucher Specimen Barcode Sequence Trace files Primers Literature (link to content or citation) Species Name Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species 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 curation of BARCODE records Data records assembled Community feedback Data records released on INSDC Update records (audit trail of species names retained) IDs consistent with other records? GenBank adds BARCODE flag CBOL control of BARCODE flag Compliant with BARCODE standards? 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