19th International CODATA Conference
Category: Poster

A collaborative tool for biologists - the Berlin Model Internet taxonomic editor

Marc Geoffroy (m.geoffroy@bgbm.org), Anton Güntsch, Jinling Li & Walter G. Berendsohn
Freie Universität Berlin, Botanic Garden and Botanical Museum Berlin-Dahlem, Department of Biodiversity Informatics and Laboratories, Germany

In systematic biology, the creation of collaborative publications such as floras, checklists, and database driven taxonomic web information systems is often hindered by a missing infrastructure for exchanging and sharing information entities (e.g. bibliographic references) which the contributors need to agree on. Nomenclatural and bibliographic references, author abbreviations as well as the syntax of taxonomic names may differ between experts even if referring to the same objects. Traditionally, such data conflicts have to be resolved by a central project secretariat searching for duplicates within the incoming data sets and replacing the data items considered incorrect. This task is highly time consuming, and often frustrating as it has to be carried out every time new data sets are coming in to be resolved and integrated.

The Berlin Model Internet taxonomic editor aims at minimizing this effort by offering a software tool to carry out editing directly on a shared taxonomic database over the World Wide Web. With this, changes on common objects (e.g. bibliographic reference titles) are visible for all other taxonomists working on the same product. Furthermore, new objects (e.g. new author teams) entered into the system can be re-used immediately. Being built on the Berlin Model (http://www.bgbm.org/biodivinf/docs/bgbm-model/), a comprehensive taxonomic data model, the system allows for processing alternative and even conflicting taxonomies for the same group thus preserving taxonomic concepts (taxa as circumscribed by a reference) and facts linked to them properly.

The system is entirely implemented with software components running on a central server (Cold Fusion and Java). Taxonomists working with only need a JavaScript enabled World Wide Web Browser, which is installed on most computers anyway. The editor comprises modules for browsing and re-arranging taxonomies, editing names and references, editing factual data, as well as management of relations between taxonomic concepts. Security is ensured with a database controlled login system. Additionally, a suite of software tools has been implemented supporting the central database maintenance and publication of its content on the Web.