Species File Software: a powerful tool for taxonomic database development
What is Species File Software?
Construction of taxonomic databases requires considerable programming skill, a deep understanding of biological taxonomy, intimate familiarity with relevant nomenclatural codes, and knowledge of current standards proposed by the biodiversity informatics community. Such a combination of strengths is rarely found in a single individual and so, database development is best done by a team of information technology professionals and taxonomists working together. The Species File Development Group at the Illinois Natural History Survey represents just such a mix of talent, with nine full-time staff coming from an array of different professional backgrounds, including taxonomists, software specialists, web developers and computer programmers. Our group draws extensively on the skills and experience of these individuals, using their combined expertise to develop specialized software capable of tracking taxonomic names at all hierarchical levels, display geographic distributions, capture specimen data, host images, archive and play sound recordings and facilitate data mining. Moreover, Species File Software (hereafter referred to as SFS) encodes the nomenclatural regulations laid out in the Fourth Edition of the International Code of Zoological Nomenclature . This important feature makes SFS a powerful tool for the development of taxonomic databases within the scope of the animal kingdom.
SFS is both a database and a website, providing seamless data entry and immediate display of data, both through a web browser interface. Species Files (SF, public or private SFS units for a given taxon) effortlessly manage taxonomic information for taxa containing from 10 to 100,000 species. Species File stores and organizes these data and provides Species File curator(s) (taxonomists, biodiversity biologists, or highly motivated individuals with nontraditional training) with a means to manage and add more data as new species are described, new classification schemes are proposed, or taxonomic revisions are published. Some SFs include Orthoptera Species File (OSF: http://orthoptera.speciesfile.org), Mantodea Species File (MSF: http://mantodea.speciesfile.org), and Plecoptera Species File (PlecSF: http://plecoptera.speciesfile.org/). Currently, there are 24 SFs in various states of development. Development is currently underway for several other SFs. Although our efforts to date have been applied to insect taxa, SFS has been designed to handle the nomenclatural details of any animal taxon. SFS shares taxonomic information with the world through its web interface and with other organizations such as the Integrated Taxonomic Information Service (ITIS), Species 2000 Catalogue of Life (COL), Encyclopedia of Life (EOL), and the Global Biodiversity Information Facility (GBIF).
SFS targets its efforts to the support of both builders of SFs and users of SF information. Builders could include professional taxonomists/systematists who work on a genus, subfamily, family or other higher taxonomic category. These scientists understand the rules of nomenclature very well and are making valuable contributions to the knowledge of the group they study through new species descriptions, revisions of groups, and phylogenetic analyses that lead to better classification of the members in a group. There are other professionals who develop SFs, either in collaboration with a taxonomist or on their own. These SF collaborators are often highly skilled in the identification of members of a particular taxon, understand the Code, and are skilled at finding paper and electronic sources of taxonomic information. SFS depends upon both types of individuals to produce SFs.
Users of SFs include taxonomists, ecologists, conservation biologists, government biologists, and the general public. Most users come to our SFs to check on current usage of taxon names, to find literature references for a given taxon, to look for images and sound recordings, and to use our identification keys. Our SFs are often the primary or only source of reliable taxonomic information for a taxon, and as such, data aggregators such as the Catalogue of Life (COL), Encyclopedia of Life (EOL), Integrated Taxonomic Information System (ITIS), and the Global Biodiversity Information Facility (GBIF) come to us annually, or more frequently, to harvest taxon names and nomenclatural details for their databases.
Why use Species File Software?
There are several powerful features that make SFS an indispensable tool for storage and management of taxonomic information. First, development of a SF is done through a web interface. SF authors do not have to worry about software platform compatibility, server maintenance, backup schedules, troubleshooting of software, or any other problems that they would encounter if they were to build an application on their own. Additionally, SFS was programmed with the Code as a primary development guide with many data integrity checks and warnings that prevent mistakes from being made that violate the Code. SFS also meets or exceeds Darwin Core and Taxonomic Working Group (TDWG) standards for recording specimen data and geographic affiliations, respectively. More information specific to Species File Software development may be found at http://software.speciesfile.org.