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(Welcome to the Species File Software Help Wiki)
(Welcome to the Species File Software Help Wiki)
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== Welcome to the Species File Software Help Wiki ==
 
  
 
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This is the brief context/mission statement.
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'''Welcome to the Species File Software Help Wiki'''.  Mission statement here.  
 
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  <div style="float:left; border:1px solid green; margin-left:15%; padding:2em;"> [[Overview]] </div>
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  <div style="float:left; border:1px solid green; margin-left:15%; padding:2em;"> [[Services]] </div>
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  <div style="float:left; border:1px solid orange; margin: 1em; padding:1em;"> Portal 1 </div>
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Revision as of 10:48, 14 April 2012


Welcome to the Species File Software Help Wiki. Mission statement here.

Overview
Services
Tools
 
Portal 1
Portal 2
Portal 3
 


Biodiversity informatics: a brief introduction

The current biodiversity crisis, with its accelerated rates of extinction and habitat loss, brings the importance of documenting global biodiversity sharply into focus. With the vast majority of species still undescribed and many becoming extinct before they are discovered, the huge task of describing, documenting and storing information about the diversity of life is one of the greatest challenges facing modern biology. Taxonomists, ecologists and conservationists all agree on the paramount importance of this endeavor and over the past 20 years, efforts to overcome some of the limitations imposed by the ‘taxonomic impediment’ have led to much greater use of information technology at all stages in the process of biodiversity research. This trend reflects concurrent advances in information science which, together with the urgent need for powerful web-based tools to facilitate the compilation and storage of biological data, led to the development of a new multidisciplinary effort with the goal of providing the informatics infrastructure needed to support modern biodiversity research initiatives. The result was biodiversity informatics; a new discipline built on a foundation of taxonomic, biogeographic and ecological data stored in digital format and utilizing modern computer techniques to facilitate the collection, organization and use of these data in basic research.

Biodiversity informatics is defined as the application of informatics techniques to the management, presentation and dissemination of information concerning biological diversity. Moreover, the widespread use of taxonomic databases in recent years has fueled the development of novel informatics-based tools for the discovery, exploration and analysis of biodiversity data. Consequently, biodiversity informatics initiatives are much more than just data management engines, having now become powerful analytical tools in their own right, essential for the adequate exploration and documentation of biological diversity and the utility of the resulting data. Today, biodiversity informatics is a dynamic and fast-growing field incorporating aspects of taxonomy, systematics, ecology and genomics within the broader frameworks of conservation biology and information science. This interface between the biological and computer sciences heralds a new phase in the development of biodiversity research, providing not only wider access to relevant data, but new ways in which to use it. Thus, biodiversity informatics represents an invaluable set of resources not only for taxonomists, ecologists and conservationists, but also for government policy makers, non-governmental organizations, and the public.

Taxonomic databases: the backbone of biodiversity informatics

At the heart of biodiversity informatics are taxonomic databases – digital repositories developed for the storage of detailed information about biological taxa and designed to maximize efficiency in terms of data management and information retrieval. Such repositories contain information organized by taxonomic name and are routinely used to produce biological checklists for formal publication and in the management of biological collections. With the advent of biodiversity informatics, taxonomic databases took on a central role in the effort to consolidate our knowledge of biological diversity. Such databases constitute the essential infrastructure underpinning the operation of web-based species information systems, frequently providing both the data itself and a means by which to manage it. This fundamental function of taxonomic databases makes their development, maintenance and cross-system integration a top priority within the biodiversity informatics community.

The ultimate goal of a taxonomic database should be to accurately model all relevant data concerning the organisms of interest within the overall scope of the system and its intended usage. Modeling taxonomic hierarchies in such databases is relatively intuitive given the relational schema employed by almost all database systems. Moreover, taxonomic databases can be designed to incorporate the rules of nomenclature as laid out in the relevant International Codes and are extremely flexible in terms of the types of data they can handle. For example, in addition to encoding taxon identifiers (e.g. valid scientific name, author, date of publication, etc.) a taxonomic database may frequently incorporate other valuable information, such as specimen data, synonyms, literature citations and taxonomic notes. Furthermore, a wide range of biological attributes can also be documented, such as geographic distribution, ecology and conservation status (e.g. threatened, vulnerable etc.) along with various digital media including images, sound recordings and videos. The great flexibility offered by taxonomic databases makes the construction of data-rich repositories straightforward and rapid, thereby facilitating the collection, organization and long-term management of biodiversity data – the essential first steps of any biodiversity informatics initiative.

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 custodian(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 Code 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.


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