Barcode Data Standard

Introduction

The Barcode Data Standard was established by the Consortium of the Barcode of Life soon after the first scientific paper by Dr. Paul Hebert was published that proposed the method of DNA Barcoding. You can find a link to the official data standard document on the CBOL website at: http://www.barcodeoflife.org/sites/default/files/DWG_data_standards-Final.pdf.

_images/data_standard_link.png

The data standard consists of several required and strongly recommended elements that have to do either with specimen metadata or sequence data. We will go through each element, give a brief explanation, and try to highlight any commonly seen mistakes.

Specimen Metadata
Text from Standard
GenBank Field Required or Recommended?
“a unique identifier for the voucher
specimen using a structured field
specified by CBOL and NCBI”
specimen_voucher Required
“the name of a formally described
species or a provisional label for
an unpublished species”
organism Required
“Country-Code using the controlled
vocabulary used by GenBank”
country Required
“Latitude and longitude”
lat_lon Strongly recommended
“Name of the identifier”
identified_by Strongly recommended
“Name of the collector”
collected_by Strongly recommended
“Date of collection”
collection_date Strongly recommended
Sequence Metadata
Text from Standard
GenBank Field Required or Recommended?
“Come from a gene region
accepted by CBOL as an effective
barcode” ... “Include the name of
the region used”
gene Required
“the sequences of all forward and
reverse primers used”
PCR_primers Required
“the names of the forward and
reverse primers”
PCR_primers Strongly recommended
“trace files for the forward and
reverse sequencing runs
submitted to the NCBI Trace
Archive or the Ensembl Trace
Server”
NCBI Trace Archive Required
“at least 75% contiguous, high
quality bases from within the
approved barcode region”
nucleotide_sequence Required

Specimen metadata

Collection metadata

Country – Required
The GenBank field name “Country” is slightly confusing – not just because the INSDC country controlled vocabulary list (http://www.insdc.org/country.html) includes oceans and seas in addition to countries – but because the country name is often concatenated with a colon to provide more specific location information about where a specimen was collected.
Latitude and Longitude – Strongly Recommended
The geographical coordinates of the location of where a specimen was collected are stored in the “lat_lon” field in decimal format. GenBank uses the specific format “d[d.dddd] N|S d[dd.dddd] W|E”. An example of this is “38.891262 N 77.026093 W” for the Smithsonian Natural History Museum.
Collector Name – Strongly Recommended
The name of the person(s) or institute that collected the specimen. GenBank does not provide any guidance on how to structure name (“Give Name Surname” vs. “Surname, Given Name”) or how to group multiple names, but at least be consistent.
Collection Date – Strongly Recommended

The date(s) on which the specimen was collected. Date ranges are supported by providing two collection dates from among the supported value formats, delimited by a forward-slash character.

Here are the supported value formats, with examples:

  • “DD-Mmm-YYYY”: 01-Jan-2016
  • “Mmm-YYYY”: Jan-2016
  • “YYYY”: 2016
  • “YYYY-MM-DD”: 2016-01-01
  • “YYYY-MM”: 2016-01

Voucher metadata

Specimen Voucher – Required

The specimen voucher field is the most important portion of the Barcode Data Standard, because it serves as the bridge between genetic data and specimen data. This field is even more important for plants, because the plant barcode consists of more than one gene region. The two sequences that make up a plant barcode are published as two separate GenBank records, so a unique specimen voucher field is the only thing that asserts that these sequences came from the same individual.

Not only is a unique identifier required for the specimen voucher, but it also needs to be in a specific format. It is very easy to miss since this format is specified in a footnote, but the data standard document specifies that the voucher specimen identifier should use a triplet structure based on elements of the Darwin Core (DwC) separated by a colon:

institutionCode:collectionCode:catalogNumber

To ensure that specimen voucher identifiers are unique and traceable, CBOL maintains the Global Registry of Biorepositories (GRBio.org), which is a community-curated directory of all biological collections in natural history museums, herbaria, and other biorepositories.

Organism – Required
The scientific name of the organism that provided the sequenced genetic material. The text from the data standard reads “the name of a formally described species or a provisional label for an unpublished species”, which allows for the exception of allowing for organism names only identified to the Order or Family level. It is recommended by GenBank to give provisional names the values of the specimen voucher for reproducibility reasons.
Identifier Name – Highly Recommended
The name of the person(s) or institute that identified the specimen. Just as with Collector Name, GenBank does not provide any guidance on how to structure name (“Give Name Surname” vs. “Surname, Given Name”) or how to group multiple names, but at least be consistent.

Sequence metadata

Nucleotide Sequence – Required
This is the DNA sequence of the barcode record.
PCR Primer Sequence(s) – Required

This refers to the sequences for the PCR primers used to amplify the DNA Barcode region. All sequences should be presented in 5’>3’ order.

Fill this in with complicated examples of cocktail primers vs. multiple pcr attempts.

PCR Primer Name(s) – Highly Recommended
This refers to the “common names” of the primer sequences. Unfortunately this field is optional, and the vast majority of BARCODE keyword records do not have primer names listed.
Trace Files – Required
Trace files for the forward and reverse sequencing runs must be submitted to the NCBI Trace Archive or the Ensembl Trace Server.