The document discusses the Barcode of Life project and database. It began in 2003 with the goal of creating a global reference library of DNA barcode sequences linked to specimens and species names. The Barcode of Life Database was established as a community workbench. Sequence data is submitted to GenBank and undergoes quality checks before being added to the barcode database. Challenges include ensuring high quality data with links to specimens and taxonomic identifications.

1. Ilene Mizrachi
November 30, 2011
Fourth International Barcode
of Life Conference
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

2. Barcode Project -2003 and beyond
 Barcode of Life project was initiated at in 2003
 INSDC would be the repository for raw and assembled
sequence data
 INSDC adopts new source fields to accommodate
Barcode metadata requirements
 Barcode of Life Database (BOLD) established as a
community workbench and sequencing center
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

3. What is a Barcode?
 A global reference library of DNA barcode sequences
that is integrated with other systems of biodiversity
information (e.g., databases of
specimens, species, biogeographic information).
 Mechanism to link DNA sequences to vouchered
specimens and valid species names.
 A reserved BARCODE keyword was adopted for data
that met strict barcode standards
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

4. Barcode Standard
 Formally described species or a provisional label for an unpublished species
 Voucher specimen identifier, preferably in a biorepository using a structured
field
 Country-Code using the controlled vocabulary used by GenBank;
 Sequence from a gene region specified by the CBOL
 COI for animals
 matK and rbcL for plants
 ITS for fungi
 Contain at least 75% contiguous, high quality bases from within the approved
region
 Electropherogram trace files for bidirectional sequencing runs
 Sequences of all forward and reverse primers
 Strongly recommended data elements
 GPS coordinates
 Name of the identifier
 Name of the collector
 Date of collection
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

5. Compliant Barcode Record

6. Barcode records in GenBank
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

7. Life of an iBOL
Record

8. Submissions from BOLD
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

9. Data Sharing Works
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

10. http://www.ncbi.nlm.nih.gov/WebSub/?tool=barcode

11. QA checks at GenBank
To ensure that the sequence data is of high quality, the
following checks are run:
 Barcode data element compliance
 Consistency checks such as:
 reported latitude-longitude falls within cited country
 collection date has already occurred
 Sequence quality checks
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

12. Compliance tool
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

13. Checking Sequence Quality
• Trim primer sequences
• Check congruence between
fwd and reverse reads
• Align sequences to check for
gaps
• Translate sequences to check
for internal stops
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

14. Updates Are Critical
 Primary data repository – sequence records owned by
submitter
 Submitter is responsible for providing additional data
and metadata as it becomes available:
 Publication
 Sequence
 Taxonomy
 Voucher
 Third party updates are welcome!
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

15. Challenges
 If Reference Barcodes are to be used for species
identification, phylogenetics, ecological
forensics, conservation, and macro-analysis of
biodiversity patterns, then the minimal requirement
should be (a) high quality sequence (b) link to
specimen and (c) taxonomic identification
 Need to support rapid data release including
preliminary taxonomic classifications similar to “Fort
Lauderdale Principles” of genomics community
 Data updated asynchronously at BOLD and in
GenBank. Need to continue work on update channel
 Need to work with communities to devise strict QA
tests for plant and fungal Barcodes
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

16. Acknowledgements
 Taxonomy Group  GenBank Group
 Scott Federhen  Susan Schafer
 Conrad Schoch  Michael Fetchko
 Lu Sun
 Carol Hotton  Software Support
 Detlef Leipe  Colleen Bollin
 Kamen Todorov
 Vasuki Gobu
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA