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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Web initiative aims to help clear name confusion

“The first part of knowledge is getting the names right.”   Chinese proverb quoted in Evolution of Insects, Grimaldi and Engel, 2005.

Species names are the primary entrance for accessing biological knowledge about organisms. However, the tangled bank of nomenclature created by 250 years of diverse communities of taxonomic specialists working largely in isolation challenges those seeking knowledge. It can be difficult to know what is already known. Identifying even well-studied organisms in backyards, such as North American ants for example, may require graduate-level training. As taxonomic knowledge moves increasingly onto the web, tools that enable non-specialists and specialists alike to access biological knowledge of organisms are beginning to be developed. In my view, the solution will be a combination of information science tools enabling access to biological literature together with a universal library of standardized genetic sequences, ie DNA barcodes, and simple technologies for barcode sequencing. 

An exciting development in taxonomic information science is https://www.ubio.orguBio (Universal Biological Indexer and Organizer) www.ubio.org, “an initiative within the science library community to join international efforts to create and utilize a comprehensive and collaborative catalog of known names of all living (and once-living) organisms. The Taxonomic Name Server (10,699,999 NameBank records so far) catalogs names and classifications to enable tools that can help users find information on living things using any of the names that may be related to an organism.” 

The uBio site provides a sophisticated and enjoyable illustrated introduction (excerpt at right) to the variety of challenges in retrieving information using organism names. Another feature is Nomenclator Zoologicus, a searchable list of the names of genera and subgenera in zoology from the tenth edition of Linnaeus 1758 to the end of 2004, developed with Zoological Society of London. uBio is helping organize and index Encyclopedia of Life (“a web page for every species”) and Biodiversity Heritage Library (1.124 million pages digitized and on the web so far). 

I close with an example from birds. Some taxonomic confusion reflects the struggle to integrate older works that use outdated taxon names or species limits with modern knowledge. Other discordances reflect lack of consensus among current experts. Given the intensity of scientific study and public interest in birds, it is surprising there is no single authoritative world checklist, especially since most of the differences at the species level reflect minor disagreements about generic assignment, a few cases of splitting/lumping, or differences in spelling. As one step until there is an expert consensus checklist, for those interested in birds, we have prepared an “ABBI Name Lookup” (Excel, 8 MB) file for harmonizing specimen lists that recognizes 2,462 synonyms, alternate and misspellings, and extinct species.

This entry was posted on Friday, November 16th, 2007 at 11:59 pm 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.

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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.