Barcode Index Numbers (BINs)
The Barcode Index Number System is an online framework that clusters barcode sequences algorithmically, generating a web page for each cluster. Since clusters show high concordance with species, this system can be used to verify species identifications as well as document diversity when taxonomic information is lacking.
This system consists of three parts:
- A clustering algorithm employing graph theoretic methods to generate operational taxonomic units (OTUs) and putative species from sequence data without prior taxonomic information.
- A curated registry of barcode clusters integrated with an online database of specimen and taxonomic data with support for community annotations.
- An Annotation framework that allows researchers to review and critique the taxonomic identifications associated with each BIN and notify data owners of errors.
The BIN framework can greatly expedite the evaluation and annotation of described species and putative new ones while reducing the need to generate interim names, a non-trivial issue in barcoding datasets. The BIN algorithm has been effectively tested on a broad set of taxonomic groups and shows potential for applications in species abundance studies and environmental barcoding. The registry employs modern URI and web service functionality enabling integration with other databases.
COI sequences over 500bp will be evaluated for inclusion into BINs if they meet the quality standards. Sequences over 300bp will be considered for membership into an existing BIN, but will not create or split BINs.
Ratnasingham S, Hebert PDN (2013) A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System. PLoS ONE 8(8): e66213. DOI:10.1371/journal.pone.0066213
BIN pages display aggregated data in several sections described and illustrated below.
BIN page example
BIN page definitions for the illustration below.
Back to Top
|1. BIN Details
||BIN details include BIN identifiers (URI and DOI), the member count, and distributional information. Also, nearest neighbour BIN details are provided ,along with the nearest member and the taxonomy of that record.
||The taxonomy of the public data is visible for the BIN, with highlighting to indicate taxonomy concordance and discordance. NEW! For each taxon, logged in users can search the records that they have access to by clicking on the magnifying glass icon.
||Via the Add Tags & Comments button, BIN pages support community vetting though annotation of individual data elements (taxonomy, images, collection sites and attribution). Please see the Annotation section for more details.
|4. Distance Distribution
||A histogram provides the distribution of distances between sequences within the BIN and against the nearest neighbour sequence.
|5. Associated Publications
||List of the publications that contain sequences from the BIN.
|6. Dendrogram of Sequences
||For BINs with 3 - 150 members, a circle tree is displayed which also includes the nearest neighbour. Hovering over taxon names on the circular tree highlights the terminal branch. A PDF version of the tree is available for download for all BINs with more than 2 members.
|7. Haplotype Network
||The interactive diagram allows for investigation of the haplotypes in the BIN cluster along species and geographical splits. Hovering over a haplotype node in the diagram reveals details on which species or geographical information are grouped. The larger the node, the more sequences in the haplotype. The thicker the line between nodes, the more closely related those two haplotypes are.
|8. Collection and Owner Data
||A list of the collection countries and number of specimens collected per country followed by a list of the owners of the public and private sequences contained within a BIN. NEW! For each country, logged in users can search the records that they have access to by clicking on the magnifying glass icon.
|9. BIN Barcode Compliance
||BINs are marked as compliant if they contain at least one sequence that meets Barcode Compliance standards.
|10. Specimen Images
||Displays all images for records clustered in the BIN, with license information available for each.
|11. Sampling Sites
||Displays a map of the collection sites based on GPS coordinates.
||Lists the institutions where specimens are deposited and sequenced, along with photographers, collectors, taxonomists, and funding sources. NEW! For each Specimen Depository, logged in users can search the records that they have access to by clicking on the magnifying glass icon.