BExIS – Biodiversity Exploratories Information System

Title: BExIS – Biodiversity Exploratories Information System
Authors: Birgitta Koenig-Ries, Andreas Ostrowski, Eleonora Petzold, Jens Nieschulze
Source: TDWG 2011 - Annual Conference
Place: New Orleans, USA
Date: 2011-10-01
Type: Conference Paper
Abstract:

The Biodiversity Exploratories Information System (BExIS) (https://exploratories.bgc-jena.mpg.de) is a virtual research environment for collaborative research. It has been developed as the data repository and information exchange platform of the Biodiversity Exploratories collaborative project (Exploratories, www.biodiversity-exploratories.de). This project started in 2006 and is funded by the German Science Foundation (DFG) as a long-term, interdisciplinary open research platform. The goal is to advance biodiversity research in Germany by a better understanding of the relationship between biodiversity of different taxa and levels, the role of land use and management for biodiversity, and the role of biodiversity for processes in the ecosystem. Currently, the Exploratories comprise around 40 subprojects from a wide range of disciplines ranging from soil science to remote sensing and from genetics to landscape geography, resulting in a spatial resolution from a few square centimetre (genomics) to entire landscapes (airborne remote sensing), a time resolution from ½ hour of automatic climatic data loggers to 5-year return cycle of forest inventories. All of these projects use BExIS. Additionally, BExIS is being used by a number of additional collaborative projects beyond the Exploratories including the DFG financed research units Kilimanjaro ecosystems under global change (KiLi, https://www.kilimanjaro.biozentrum.uni-wuerzburg.de) and The Jena Experiment (http://www.the-jena-experiment.de). Further installations are in preparation.

BExIS offers a web-based interface to a platform for storage and management of biodiversity data in a database. All metadata and primary data are handled with the document oriented native XML approach. BExIS uses IBM’s DB2 as relational Database Management System (DBMS) with pureXML, a native XML extension (http://www-01.ibm.com/software/data/db2/xml) .

BExIS supports highly flexible data structures and data syntax for primary data ensured by user-driven configuration during metadata creation. Thereby the user defines the data structure for primary data, more precisely the quantity, arrangement, and data type of variables. This allows different scientists to use their own diverse data structures while still sharing their data in one database.

It is possible to map BExIS project specific metadata schema to biodiversity metadata standards like DarwinCore with its TapirDotNETXml application, an extension of TapirDotNET (http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirDotNET). It provides an interface to the TDWG Access Protocol for Information Retrieval (TAPIR) and allows networking of BExIS data in data portals like GBIF or DataOne, and more generally the flow of data between repositories or ,e,g., towards data archives.

BExIS offers a variety of functions for visualization of data: it is viewable as scrollable tables, may be displayed against Google Maps and plotted via a statistics service.

BExIS is based on a service oriented architecture which allows for easy integration of external functionality and automatic data flows.  For instance, it provides a web service based interface to RServe (RServe, http://www.rforge.net/Rserve/doc.html).

BExIS also offers a function to merge multiple datasets, and the option to create views of defined subsets of structured data. It supports a number of usual file formats (Microsoft Excel and Access, ASCII, dBASE) for uploading, updating, downloading and sharing the data. BExIS can manage also unstructured data such as documents, pictures and GIS data.

Access to data and functionality are handled by fine grained authorization mechanisms, managing users, rights of data use, and roles.

BExIS provides further functionalities useful for projects, e.g., to organize and document field work, as well as blackboards and interactive charting of research plots and Wiki based communication platforms In addition, there are publication and event management tools for scientific work.

BExIS is freely available under a Creative Commons license for non-commercial use.