Rockefeller University

Program for the Human Environment

The Barcode Blog

A mostly scientific blog about short DNA sequences for species identification and discovery. I encourage your commentary. -- Mark Stoeckle

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One biodiversity database to the next

Jumping between biodiversity databases is getting easier. For example, typing in “Atlantic cod” at Ocean Biogeographic Information System (OBIS) takes you to a Gadus morhua species page summarizing 616,444 records, a zoomable map of its geographic range based on specimen collection locations, and direct links to G. morhua pages in other databases, including, for example, Barcode of Life (BOLD), Encyclopedia of Life (EOL), Catalog of Life, World Register of Marine Species (WorMS), and Google images, among others. Having all that, inspired by Matt Damon’s character in The Bourne Ultimatum, we want to take more leaps–perhaps to G. morhua pages in Arkive, Biodiversity Heritage Library, FishBase, and/or GenBank?

Something new is having links to Encylopedia of Life species pages embedded in research articles (so far in some papers in PLoS ONE; for an example, see shark names in Ward-Paige et al 2010 PLoS ONE). Having direct links to literature sources is a wonderful enhancement of research articles, and I believe that species name links will be equally valuable, particularly for biodiversity literature, so I hope this catches on. Species name links have potential to increase the audience and impact of research papers, since many otherwise interested persons will not recognize scientific names or will be entirely unfamiliar with the organisms being studied.

This entry was posted on Wednesday, October 13th, 2010 at 11:23 am and is filed under General. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

One Response to “One biodiversity database to the next”

  1. Dr. Subhendu Chatterjee Says:
    October 21st, 2010 at 10:28 pm

    Yes, this is really important to include the species name apart from the scientific names only, as it is difficult for the otherwise generally interested people and readers to take the full advantage of bioversity literature. However, similarly this is also true that providing some species name is nearly impossible as the scientific name is all that they are identified with, for example, Synoicum castellatum. Thanks for sharing.

Contact: mark.stoeckle@rockefeller.edu

About this site

This web site is an outgrowth of the Taxonomy, DNA, and Barcode of Life meeting held at Banbury Center, Cold Spring Harbor Laboratory, September 9-12, 2003. It is designed and managed by Mark Stoeckle, Perrin Meyer, and Jason Yung at the Program for the Human Environment (PHE) at The Rockefeller University.

About the Program for the Human Environment

The involvement of the Program for the Human Environment in DNA barcoding dates to Jesse Ausubel's attendance in February 2002 at a conference in Nova Scotia organized by the Canadian Center for Marine Biodiversity. At the conference, Paul Hebert presented for the first time his concept of large-scale DNA barcoding for species identification. Impressed by the potential for this technology to address difficult challenges in the Census of Marine Life, Jesse agreed with Paul on encouraging a conference to explore the contribution taxonomy and DNA could make to the Census as well as other large-scale terrestrial efforts. In his capacity as a Program Director of the Sloan Foundation, Jesse turned to the Banbury Conference Center of Cold Spring Harbor Laboratory, whose leader Jan Witkowski prepared a strong proposal to explore both the scientific reliability of barcoding and the processes that might bring it to broad application. Concurrently, PHE researcher Mark Stoeckle began to work with the Hebert lab on analytic studies of barcoding in birds. Our involvement in barcoding now takes 3 forms: assisting the organizational development of the Consortium for the Barcode of Life and the Barcode of Life Initiative; contributing to the scientific development of the field, especially by studies in birds, and contributing to public understanding of the science and technology of barcoding and its applications through improved visualization techniques and preparation of brochures and other broadly accessible means, including this website. While the Sloan Foundation continues to support CBOL through a grant to the Smithsonian Institution, it does not provide financial support for barcoding research itself or support to the PHE for its research in this field.