Difference between revisions of "Diversity Workbench"

Revision as of 18:56, 8 August 2023

Introduction

The modularized Diversity Workbench (= DWB) represents a virtual research environment for multiple scientific purposes with regard to management and analysis of life and environmental sciences data. The framework is appropriate to store different kinds of bio- and geodiversity data, taxonomies, terminologies, and facilitates the processing of ecological, molecular biological, observational, collection and taxonomic data. It is capable and flexible enough to be applied as data storage unit for institutional data repositories. The DWB is set up on a xml-enabled relational database system. Cients of every database of the Workbench are used as stand-alone applications and provide supporting functions to clients of corresponding databases. This results in a high flexibility with regard to the conceptual design, enabling sophisticated user administration and a rapid setup of project-specific and user-adapted entry forms. Further, it facilitates the dynamic integration of web services and external data resources.

The DWB is work in progress, aiming at developing a set of information models and application components that collaborate through agreed software interfaces. That is, each component of the Workbench applications uses services from other applications, but at the same time does not need to know about the internal design and implementation of them (encapsulation principle). The goal is increased reuse and collaboration across project and national borders.

Currently, three institutions with DWB editors and DWB staff for software development are involved:

• the Bavarian Natural History Collections with the SNSB IT Center,
• the University of Bayreuth, Mycology and Ecoinformatics,
• and the Museum für Naturkunde Berlin – the MfN since 2013 in replacement of the Julius Kühn-Institut Berlin.

Software tools for collecting, organising, transforming and accessing bio- and geodiversity information

For each component of the Diversity Workbench (DWB) we aim at providing a comprehensive documentation of the application and the information model online. The framework for these components is currently still under development as we continue to learn about the necessary components and the best approach to the modularization of bio- and geodiversity information. A draft paper distributed by G. Hagedorn in 2002 provided first insight into the framework concept.

History and projects

The start of the DWB was in 1999 with first discussions and design of concepts for a RDMS framework and workbench on diversity information (domain registration "diversityworkbench.net" in 2000). In an initial phase during the BMBF programme BIOLOG-IT with the GLOPP project (2000 until 2003) prototypic implementations were realised in Microsoft Access. The prototype applications are still available. With the exception of DeltaAccess/DiversityDescriptions they are by now largely obsolete.

Between 2003 and 2008 further applications were set up as part of the GBIF-D Mycology project using .Net technology and JAVA. Since 2006 the software development is continued as one of the general tasks of the SNSB IT Center. Starting with 2009 some advanced IT concepts and technical developments became part of the DiversityMobile/ IBF project, since 2010 certain GBIF relevant DWB-tools are optimized within the joint research project GBIF-D, Kompetenzzentren innovativer Datenmobilisierung. DWB applications and services are used by the Global Plants Initiative in Munich, since 2007, by the German Barcode of Life project, since 2011, by the Integrative Pilzforschung project, since 2013 and by several DFG funded research infrastructure projects, namely BiNHum, since 2012, IDES, since 2012, MOD-CO, since 2014 and ARAMOB with ARAMOB DFG project Wiki, since 2017.

Starting with autumn 2013, the Flora von Bayern initiative relies on DWB databases as software suite to realise data pipelines for occurrence and observation data from the past and now for the future. It is run at the SNSB IT Center. Thus, all current Bavaria-wide IT infrastructure projects are working closely together. With 2018 the DWB involvement is extended to run new services useful for nature conservation. A discrete DWB network installed at the SNSB is building the IT backbone of the Coordination office for flora conservation in Bavaria. The cooperative project Flora Silvae Gabretae – Flora des Böhmerwaldes – Květena Šumavy started in 2019. The action is mobilizing plant occurrence and species conservation data for the DWB network and is optimizing data processing for a common Bavarian-Czech data network and IT infrastructure. The funding period of the two projects, i.e. the Coordination office for flora conservation in Bavaria and the Bavaria-Czech project on the flora of the Bohemian forest, ended in 2022. At the same time the project Coordination office for the Bavarian flora started and took over responsibility on the existing DWB data network infrastructure including new research aspects in the field of collection-related data science.

The GFBio project started with the end of 2013 and is going to extend the user services of the Diversity Workbench on demand of biological and environmental research communities and projects in Germany. DWB is one of the two platforms/ workbenches recommended by the GFBio consortium and the GFBio e.V. for data producers in biodiversity research projects. The DWB applications installed at GFBio data centers are technically documented. GFBio has the DFG mandate to work on business models as well as on standard technical solutions for sustainable research data management.

Starting with autumn 2019, the DWB team in München is working on the implementation of a "Progressive Web Application (PWA)" DiversityNaviKey to interactively identify items and item groups (often biological taxa) from datasets with structured characteristics.

The DWB tools for research data management (early in the data life cycle) and data transformation are producing FAIR++ data objects (in the sense of Harjes et al. 2020). The DFG-recommended tools are currently set up, extended and maintained by the SNSB in its role as NFDI e.V. and GFBio e.V. partner institution. Thus, the DWB is part of the services that the NFDI4Biodiversity consortium provides from 2021 onwards.

Financial support

Financial support for timely and thematically restricted DWB projects was/ is granted by the:

• Bayerisches Staatsministerium für Wissenschaft und Kunst (StMWK)
• Bundesministerium für Bildung und Forschung (BMBF)
• Deutsche Forschungsgemeinschaft (DFG) with the Scientific Library Services and Information Systems (LIS) programme and the National Research Data Infrastructure (NFDI)
• EU Commission with the Fifth and Seventh Framework Programmes (EU FP5, EU FP7) (EU projects Species 2000 europa and 4D4Life)
• EU Commission with the EU ETC INTERREG V program of the European Regional Development Fund
• Bayerisches Landesamt für Umwelt (LfU)
• World Wildlife Fund for Nature Deutschland (WWF-DE)

Persons involved

Diversity Workbench editors and software engineers are continuously modelling and implementing DWB tools in C#. Furthermore, there are a number of persons from outside this DWB core group who are contributing with new concepts and are setting up special scripts and interfaces to extend the functionalities of DWB networks and databases. For further information see About DWB.

Features

The features of the Diversity Workbench concept were analysed in 2011 (see Diversity Workbench Performance). In 2018, GFBio published the description "DWB in 10 questions". The DWB tools are subject of national and international data collections and Surveys on Working Tools for Biodiversity Informatics and Virtual Research Environments. The Diversity Workbench is appropriate to serve as database backbone and data management system for bio- and geodiversity research projects and is therefore listed as Research Infrastructure in the DFG RIsources Portal. The SNSB IT Center and GFBio e.V. offer user help desk and services in this context, see About DWB.

Diversity Workbench Software is available under GNU General Public License 3.0 – GPLv3.

Information models

• Information models

Software for download

• Software

Technical support, training and outreach

• Technical support, training and outreach

User and data statistics

The numbers below are rough estimations about the general use of DWB data management software at data repositories together with the amount of DWB single identificable data records (digital objects) – status as of January 2021.

• 350-400 DWB users have active accounts and use DWB client software, see DWB introduction – 44th DWB Workshop
• 12 server instances with more than 100 DWB database installations are technically administrated by the SNSB IT Center, approx. 10 further DWB instances are known running on other research data networks in Germany
• 30-40 organisations use DWB client software together with hosting and data curation services of the SNSB IT Center for partner organisations and projects
• 25-30 major third-party funded research projects as well as institutional collection infrastructure projects created and continue to create and manage DWB data records, including the projects listed here
• 26 million DWB identificable data records are managed in internal data networks
  • 20 million identificable data records in DiversityCollection
  • 0.2 million identificable data records in DiversityDescriptions
  • 0.5 million identificable data records in DiversityTaxonNames
  • 5 million identificable data records in other DWB core applications
• 23 million DWB identificable data records are published as FAIR data objects via various research data networks and via the DWB cloud services, see also DWB introduction – 40th DWB Workshop

Workshops

• 44 workshops with 630 participants at the SNSB IT Center, see here

The Diversity Workbench pages were first published 2000-11-15, moved from static html to a JSP-Wiki 2006-02-07 and ported to the current MediaWiki 2008-09-05.