National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USANational Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

BARCODE SEQUENCE DATAFLOW INTO GENBANK

Ilene MizrachiNovember 30, 2011

Fourth International Barcode of Life Conference

National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

Barcode Project -2003 and beyondBarcode of Life project was initiated at in

2003 INSDC would be the repository for raw and

assembled sequence dataINSDC 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

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

Barcode Standard Formally described species or a provisional label for an unpublished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

Compliant Barcode Record

National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

Barcode records in GenBank

Life of an iBOL Record

National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

Submissions from BOLD

National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

Data Sharing Works

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

National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

QA checks at GenBankTo ensure that the sequence data is of high quality, the following checks are run:Barcode data element complianceConsistency checks such as:

reported latitude-longitude falls within cited country

collection date has already occurredSequence quality checks

National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

Compliance tool

National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

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

Updates Are CriticalPrimary data repository – sequence records

owned by submitter Submitter is responsible for providing

additional data and metadata as it becomes available:PublicationSequenceTaxonomyVoucher

Third party updates are welcome!

National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA

ChallengesIf 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

AcknowledgementsTaxonomy Group

Scott FederhenConrad SchochLu SunCarol HottonDetlef Leipe

GenBank GroupSusan Schafer Michael Fetchko

Software SupportColleen BollinKamen TodorovVasuki Gobu