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Biodiversity informatics lab: investment in computer hardware and software facilities

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Title Biodiversity informatics lab: investment in computer hardware and software facilities
Period 02 / 2003 - 12 / 2007
Status Completed
Data Supplier: Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)

Abstract

The Expert center for Taxonomic Identification (ETI Biodiversity Center) was founded in 1990 as a R&D institute in the field of 'bioinformatics'. In 1995 it acquired the NGO status under UNESCO. ETI's core tasks are: 1) to study scientific principles in taxonomy, ecology and biodiversity research relating to the processing, analysis, interpretation and presentation of (heterogeneous) data and to explore the possibilities of information and communication technology (ICT) for the development of algorithms and innovative software applications to support scientific research and education; 2) to stimulate international collaboration with respect to the above through international networks of specialists particularly in taxonomy, ecology and biodiversity, and through (inter)national concerted projects to support the science community with 'bio-algorithms' and (compatible) software tools for documentation, integration, analysis and dissemination (sharing) of scientific data based on the achievements of 250 years of distributed taxonomy; 3) to administrate a unitary taxonomy and to publish up-to-date taxonomically orientated biodiversity information systems ('electronic taxonomic monographs') and to facilitate worldwide availability of the information; 4) capacity building in biodiversity informatics by providing training, education and technical support to scientists and students, and by offering electronic publishing and multimedia laboratory facilities to science and education; 5) facilitate and underpin NL-BIF activities (national) and contribute to GBIF (international). Making quality information widely available on the web and electronic media is imperative to achieve a new approach in organising taxonomy. ETI is working at the interface of taxonomy, biodiversity sciences and ICT, a field currently referred to as 'biodiversity informatics'. It supports the national and international biodiversity community with data management and research tools and scientific CD-ROM publications. Some major achievements: * The Linnaeus II software for taxonomic data management and analysis is internationally accepted (presently ± 1,600 experts world-wide work with ETI) and a de facto standard for creating 'electronic taxonomic monographs'; * Over 50 high-quality taxonomic monographs were published on CD-ROM, and at present information on 226,000 taxa are stored in the World Biodiversity Database and accessible on-line; * The World Taxonomist Database set up under the Global Taxonomy Iniatiative now hold detailed information on more than 3,400 specialists and is the largest user driven taxonomic directory used; * A strong national embedding for taxonomic and biodiversity research and ICT development in the (national) Research School Biodiversity and research funding schemes (BIF 1996-1999, ICES-KIS II 1999-2002, NL-BIF 2002-2006) and strategic partnerships with e.g. ZMA and IBED, SARA, CWI, Institutes for Informatics, Amstel Institute; * A strong international embedding for concerted actions in biodiversity informatics R&D (e.g. European Molecular Biologogy Network (EMBnet), Fauna Europaea, European Network for Biodiversity Information (ENBI), Species 2000, Global Biodiversity Information Facility (GBIF), EUROCAT, PHLUKES), all especially focused on web-based developments; - In 2001 ETI was appointed as a focal point for the Netherlands' National GBIF Node (NL-BIF). Working with advanced up-to-date computer systems and software environments is conditional for ETI's research and output. The computer facilities include server machines and back-up devices, high bandwidth connections, heavy duty workstations for developing algorithms, software applications and information systems, workstations for compiling, combining, editing, analysing scientific information, digitalization equipment, and a multimedia laboratory (an open facility for ICT courses, guest researchers and students). In parallel with the financing of NL-BIF activities this investment plan concerns a period of five years: 2002-2006. Research facilitated by equipment supported by this investment grant will be carried out in national and international collaborative projects and encompass: - Version 3.0 (Internet compatible) for Linnaeus II software for biodiversity documentation (based on technology developed for Fauna Europaea, with NL-BIF en GBIF); - Algorithms and softwares for image analyses to support automated organism identification and 'smart' searches in image libraries (with PHLUKES, ICES-KIS II); - Algorithms and software supporting merger of information from databases with taxonomic (hierarchy) discrepancies, automated data validation procedures (ETI-WBD with SPECIES 2000 - SPICE); - Common access tools to link and query to heterogeneous biological databases (NL-BIF, ENBI, EUROCAT); - 'GRID' applications for fast searches through distributed heterogeneous databases to support data mining (with UvA, NL-BIF); - Web-based GIS applications on distributed taxonomic databases (ICES-KIS III, NL-BIF); - Server capacity, back-up facilities and high capacity bandwidth (incl NL-BIF).

Related organisations

Related people

Project leader Dr. P.H. Schalk

Classification

A31100 ICT equipment
D16100 Computer systems, architectures, networks
D16200 Software, algorithms, control systems
D16400 Information systems, databases
D21100 Bioinformatics, biomathematics, biomechanics
D22200 Biogeography, taxonomy
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