Abstract
Motivation: Computer Aided Identification systems provide users with the resources to relate morpho-anatomic observations with taxa names and to subsequently access other knowledge about the organisms. They have the ability to manage descriptive data and make identifications through interactive keys. They are essential for both authors and users of biodiversity information. Xper2 version 2.0 is one of the most user-friendly tools in its category and provides a complete environment dedicated to taxonomic management.
Availability: Xper2 software can be freely downloaded at http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/softwares/xper2
Contact: [email protected]
1 INTRODUCTION
Linnaeus wrote that naming is the first stage of knowledge. Indeed, names of taxa are the main access keys to biological information (Polaszek, 2005). They link the real world of living organisms and the conceptual world proposed by systematists through the description and characterization of taxa. Identifying life forms is crucial for all activities related to biology and their taxonomic descriptions are more than necessary in the study of Biodiversity (Godfray, 2002; Lebbe and Vignes, 1991, 1998). Systematists inventory, study and structure biological diversity as precisely as possible (Matile et al., 1987). All this information may be summarized into knowledge bases to perform identification of specimens for new inventories and monitoring surveys, phylogenetic analyses, as well as biogeographic and ecological studies. A significant increase of this kind of digitized information should be expected in a near future. The deep social and scientific impact of web 2.0 stimulates sharing of digital data and proposals of ‘cybertaxonomy’ projects to study global biodiversity and climate changes. The generalization and the integration of knowledge-base management systems into current taxonomic work may be the next revolution in taxonomy. International projects are already opening the way of this new, delocalized taxonomy.
2 WHAT IS XPER2?
Xper2 is a management system for storage, editing, analysis and on-line distribution of descriptive data. It dynamically creates interactive keys for identifying specimens (Fig. 1). Xper2 does not require any special computer skills. It is written in Java and available on Windows™ Mac™ or Linux in French, English or Spanish versions. It has a user-friendly and intuitive interface aimed at professional taxonomists as well as naturalists who merely want to identify specimens using a ready-made application. Xper2's users are taxonomists, teachers, fauna and flora experts (for biodiversity monitoring or survey) and ecologists. Formalization of knowledge is the main difficulty for taxonomists. How to structure and organize different types of data? How to keep the scientific sources of the data in order to maintain traceability? Xper2 is designed to manage this rich and heterogeneous information. Divided into four modules, Xper2 allows taxonomists to either access the descriptive environment, the taxonomic description module, the management tools or the free access key:
descriptive model: creation and editing of a standardized description (structured into characters, states, groups and logical dependencies);
taxonomic editor: characteristics of the taxon, i.e. its name, descriptions, comments and pictures;
management tools (see Section 3.4); and
free access key: creation of interactive identification keys (IIK).
A screenshot of the identification module (Genets and Oyans knowledge base).
3 NEW FUNCTIONALITIES
3.1 Import/export structural descriptive data
Many international research programs focus on the establishment of standard formats for data and knowledge exchange. Xper2 implements the structured descriptive data (Hagedorn et al.2006), the exchange format for taxonomic descriptions that has emerged from the work of the Biodiversity Information Standards (TDWG, http://www.tdwg.org, formerly known as taxonomic database working group). Xper2 can seamless import/export data from/to SDD, following international recommendations.
3.2 Nexus export
Xper2 extends the descriptive morpho-anatomic work and the taxonomic expertise of taxonomists into phylogenetic studies. A knowledge base can be exported in nexus format and directly be run in most phylogeny programs such as PAUP*.
3.3 HTML export
Xper2 provides users with a user-friendly tool to instantly format the knowledge base in a set of HTML files according to a defined cascading style sheet provided by the application. These pages include a form for each taxon displaying its complete description, pictures and any additional comments. By this way, monographies can be easily computed and published in order to serve the entire community. As an example, a website on monitor lizards (http://lis-upmc.snv.jussieu.fr/varanID) has been created by a naturalist group from the Paris Museum.
3.4 An accurate knowledge representation and more tools to analyze descriptive data
Xper2 offers solutions to control and prevent inconsistencies via a check base function. Furthermore, analyzing descriptive data is one of the most important taxonomists' tasks and Xper2 gives tools to carry it out:
Xper2 is able to manage uncertainty by selecting several descriptor-states and using logical operators (logical AND, logical XOR, logical NOT).
Mismatch threshold: one can define a different threshold according to his expertise level when performing identification.
Instant comparison of all taxa in a matrix summarizing descriptions.
4 FORTHCOMING DEVELOPMENTS
Management of extended descriptor types are under development. This includes management of numerical data, hierarchical or structured descriptor states, computed values, or any other user-declared type (Chalubert and Vignes, 2006). Associated tools allowing writing descriptions or diagnoses in natural language or proposing different kinds of similarity index among taxa will be implemented in future versions.
5 AVAILABILITY
Xper2 is a versatile tool for editing and using taxonomic descriptions. It is free of charge and can be downloaded at http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/softwares/xper2. A mailing-list facility provides users with any help or advice that may be needed. Authors choose how they want to use or publish their knowledge base: distributed on CD (i.e. Mascarene Corals identification tool, Conruyt et al., 2000) or online publication (e.g. XperBotanica—a project to identify the flora of France, http://lis-upmc.snv.jussieu.fr/xperbotanica).
6 CONCLUSION
Many international projects such as GBIF, EDIT, BIOTA, Catalogue of Life, Encyclopedia of Life, Key2Nature, etc. have a common purpose: sharing knowledge and providing free web access to Biodiversity Information (Bisby et al., 2002; Ramsey and Janzen, 2002; Tillier and Roberts, 2006). In this context of collaborative work, Xper2 fits with current taxonomists' practices and gathers functionalities to perform a suitable e–taxonomy!
ACKNOWLEDGEMENTS
The authors thank B. Pavie, C. Gallut and A. Chalubert for their contribution to the initial Xper2 version in Java. They thank all the Xper2 users and especially Fabienne Audebert, Ôna Maiocco, Philippe Gaubert and David Caron for their bases and also members of the EDIT project for their comments on the software. They are also very grateful to Dr Kurt Liittschwager for comments and style improvement.
Funding: Xper2 development has been partially funded by the BioInfo 2002 grant of the CNRS and by the French Ministère for Research and New Technology (No. 04L370—Project Xper Botanica, 2005–07).
Conflict of interest: none declared.
REFERENCES
Author notes
Associate Editor: Alex Bateman
