Edition 15 - May, 2004

Towards a global infrastructure for microbial information

On 27-28 October 2003, an expert workshop “Towards a Global Infra-structure for Microbial Information” was held in Brussels. It was co-organised and co-funded by the Global Biodiversity Information Facility (GBIF), the World Federation for Culture Collections(WFCC), and the Belgian Coordinated Collections of Microorganisms (BCCM), the Belgian Biodiversity Information Facility (BeBIF), and the Belgian Biodiversity Platform (BBPF). It gathered 58 experts in biodiversity and microbial information from 13 countries.

The workshop was organised in the context of two international initiatives: the Global Biodiversity Information Facil-ity (GBIF) and the OECD Task Force on Biological Resources Centres (BRCs). The mission of the GBIF (http://www.gbif.org) is to make the world’s primary data on biodiversity freely and universally available via the Internet. Functionally, the GBIF encourages, coordinates, and supports the development of worldwide access to the vast amount of biodiversity data. In the near term, the GBIF devel-opments are focussing on species and specimen-level data. In the long term, molecular, genetic, ecological, and eco-system-level databases will be able to be linked to the system, which will facilitate and enable data mining of unprecedented utility and scientific merit.

In addition, the Organisation for Economic Co-operation and Development (OECD) decided in 1998 to test support for Bio-logical Resources Centres (BRC) as a key component of the scientific and techno-logical infrastructure of the life sciences and biotechnology. To do this, the OECD set up a task force on BRCs that conclud-ed that “Biological resources centres are an essential part of the infrastructure underpinning life sciences and biotechnol-ogy. They consist of service providers and repositories of the living cells, genomes of organisms, and information relating to heredity and the functions of biologi-cal systems. BRCs contain collections of culturable organisms (e.g. micro-organ-isms, plant, animal and human cells), replicable parts of these (e.g. genomes, plasmids, viruses, cDNAs), viable but not culturable organisms, cells and tissues, as well as databases containing molecular, physiological and structural information relevant to these collections and related bioinformatics.” Microbial Resources Centres (MRCs) are thus a type of BRC.Recently, the OECD Ministers, at their meeting on 29-30 January 2004 held under the auspices of the Committee on scientific and Technological Policy (CSTP), agreed to endorse efforts to es-tablish a framework for a Global Biological Resource Centre Network (GBRCN) by 2006. The GBRCN will, among other things, improve international access to biological material and data in a comple-mentary way to the GBIF. Indeed, the GBRCN will likely concern itself prima-rily with the collection and maintenance of high quality biological materials. The GBIF provides access to data on biologi-cal diversity but does not concern itself with the collection and maintenance of the biological material itself. Nonetheless, care needs to be taken to ensure that, in establishing a GBRCN, the work of the GBIF or other existing international bod-ies is not duplicated.

Prof. Jean Swings, WFCC President and Dr. Larry Speers, GBIF Secretariat, Electronic Catalogue of Names of Known Organisms (ECAT), Programme Officer

In this international context, the main objectives of this workshop were to define standards and protocols for sharing microbial information, i.e., to determine: which microbial data the MRCs want to share with the GBIF and, within the fu-ture GBRCN, how to share it, and which data the MRCs want to access from the GBIF. Therefore, the workshop had two main themes:

• scientific data on bacteria/archeae and fungi/yeasts,
• information technology.

Before the workshop, a preparatory electronic conference on these two main themes took place in September 2003 on the forum server at the Belgian Federal Science Policy (http://forum.belspo.be/bccm).The workshop started on 27 October with several presentations and demon-strations:

• Introduction to the World Federation for Culture Collections (J. Swings);
• Introduction to the World Data Centre for Microorganisms (H. Sugawara);
• Introduction to the GBIF, its data model and network (D. Hobern);
• The Catalogue of Life and Species 2000 (P. Kirk);
• Introduction to fungal data (P. Kirk);
• Introduction to bacterial data (G. Garrity);
• Analysis of microbial data (L. Vauterin);
• BCCM introduction to the manage-ment of collection data (A. Ndimubandi & P. Dawyndt);
• Introduction to the Belgian Biodiversity Information Facility - BeBIF (P. Mergen);
• Conclusions of the electronic confer-ence (P. Mergen).

The workshop continued with discus-sions groups on the different themes. The workshop contributed to the development of the GBIF general data model, which matches the requirements of the MRCs with special focus on fungi/yeasts and bacteria/archeae microbial information. The first data set that the MRCs will share with the GBIF was selected: the Minimal Data Set that was adopted by the OECD Task Force on BRCs. This data set was originally created by the European projects MINE (Microbial Information Network Europe) and CABRI (Common Access to Biological Resources and Information, http://www.cabri.org).
The participants agreed to test the use of the GBIF network and data exchange standards to make an index of the MRCs core data available for searching. The GBIF currently uses the Darwin Core XML schema for data exchange with DIGIR technology (http://digir.sourceforge.net) within its network. This schema, which consists of 48 general fields, can be used initially to exchange microbial information with the GBIF even though it lacks many of the fields needed by the microbial Minimal Data Set. The temporary solution is to put the additional information in the “Notes” concept in a structured way. In the second stage, the Access to Biological Collection Data (ABCD) XML schema, which offers many more possibilities and fields and is now under development, will be reviewed by experts in microbial data in order to make it match the requirements of the MRCs. The ABCD schema is being developed by the Task Group on Access to Biological Collection Data, a joint CODATA (http://www.codata.org) and TDWG initiative (http://www.tdwg.org) supported by the GBIF and the BioCase project (http://www.biocase.org). It is likely that the ABCD schema will be adopted by GBIF in the near future.The workshop participants agreed to make trials of mapping the microbial data, including additional information on sequences and literature, against the Dar-winCore and ABCD schemas. Shortly after the workshop the Belgian node of the GBIF, the Belgian Biodiversity Information Facility (BeBIF, http://www.be.gbif.net) project, initiated this testing phase, which is open to any culture col-lection worldwide.
By sharing data with the GBIF, the MRCs will also help the GBIF to produce lists of names for microbial species for its program, Electronic Catalogue of Names of Known Organisms (ECAT).The final outcomes of the lessons learned at this workshop and of the tests of data mapping will be presented at the 10th International Congress for Culture Col-lections (ICCC-10, 10-15 October 2004, Tsukuba, Japan, http://www.ics-inc.co.jp/iccc10). In the meantime, more infor-mation on the workshop and the testing phase can be found on the e-conference site at http://forum.belspo.be/bccm.

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