Towards a Global Names Architecture: The future of indexing scientific names

Abstract

For more than 250 years, the taxonomic enterprise has remained almost unchanged. Certainly, the tools of the trade have improved: months-long journeys aboard sailing ships have been reduced to hours aboard jet airplanes; advanced technology allows humans to access environments that were once utterly inaccessible; GPS has replaced crude maps; digital hi-resolution imagery provides far more accurate renderings of organisms that even the best commissioned artists of a century ago; and primitive candle-lit microscopes have been replaced by an array of technologies ranging from scanning electron microscopy to DNA sequencing. But the basic paradigm remains the same. Perhaps the most revolutionary change of all - which we are still in the midst of, and which has not yet been fully realized - is the means by which taxonomists manage and communicate the information of their trade. The rapid evolution in recent decades of computer database management software, and of information dissemination via the Internet, have both dramatically improved the potential for streamlining the entire taxonomic process. Unfortunately, the potential still largely exceeds the reality. The vast majority of taxonomic information is either not yet digitized, or digitized in a form that does not allow direct and easy access. Moreover, the information that is easily accessed in digital form is not yet seamlessly interconnected. In an effort to bring reality closer to potential, a loose affiliation of major taxonomic resources, including GBIF, the Encyclopedia of Life, NBII, Catalog of Life, ITIS, IPNI, ICZN, Index Fungorum, and many others have been crafting a "Global Names Architecture" (GNA). The intention of the GNA is not to replace any of the existing taxonomic data initiatives, but rather to serve as a dynamic index to interconnect them in a way that streamlines the entire taxonomic enterprise: from gathering specimens in the field, to publication of new taxa and related data.

Keywords: Biodiversity Data; Carl Linnaeus; Charles Davies Sherborn; Global Names Index; Global Names Usage Bank; Taxonomy; ZooBank Biodiversity Library.

Figure 1.

In centuries past, months-long journeys aboard sailing ships were required for taxonomists to reach their destinations (left, Thomas Whitcombe). Today, almost any part of the world can be reached aboard modern aircraft (right, R. L. Pyle).

Figure 2.

Early taxonomists had only crude maps to plot the locations of their specimens; in this case the French Polynesian islands of Tahiti and Moorea (top, from Prévost D’Exiles 1746–1789). Today, highly accurate maps and satellite imagery can pinpoint particular locations within a few meters (bottom, Landsat).

Figure 3.

Highly trained artisans once labored to produce detailed hand-painted illustrations of specimens (top, from Jordan and Evermann 1903). Modern digital cameras can generate far more accurate and detailed images almost instantly and with minimal skill (bottom, R. L. Pyle). Both images depict Bodianus sanguineus Jordan and Evermann 1903.

Figure 4.

Carl Linnaeus used candle-lit microscopes with primitive optics to examine his specimens (left, H. Kingsbury). Modern technology allows us to generate high-resolution 3D CT scans of the internal structures of specimens without displacing a single scale (right top, Digimorph; Chromis abyssus), capture crisp images of tiny organisms through electron microscopy (right middle, NOAA; single-celled foraminifera), and read DNA sequences (right bottom, BOLD, unspecified taxon).

Figure 5.

Methods of collecting specimens from the field have advanced from earlier eras (left, from C.Delon, 1889) to modern high-tech equipment of today (right, Ken Corben).

Figure 6.

Despite many technological advancements in the tools of the taxonomic trade, the fundamental paradigm for the taxonomic enterprise remains almost unchanged from centuries ago (left, from Bates 1863; right Bishop Museum).

Figure 7.

At the start of modern zoological nomenclature, Linnaeus’ tenth edition of Systema Naturae contained almost 4,400 species-group names (left). By 1850, the number of species names for animals had reached nearly 430,000 – an increase of two orders of magnitude.

Figure 8.

The icons around the periphery represent examples of where biological data tagged with scientific names currently exist. The cluster of names in the center represent examples of distinct text-strings that have been used to represent the same species within different data sources.

Figure 9.

An example ZooBank page, illustrating several GNUB services: 1 user authentication 2 “fuzzy” searching of GNUB content 3 APIs and services 4 ZooBank registration 5 External Identifier cross-linking 6 BHL page linking 7 record editing capabilities 8 similar/related name discovery (via GNI’s name searching service); and 9 multi-lingual support. Not shown are services to manage user accounts, de-duplicate records, prototype reconciliation tools, services for journal publishers, and visualization tools for author publication history and other statistics.