Resource Identification for a Biological Collection Information Service in Europe Results of the Concerted Action Project

[Contents] [BioCISE Home |  The Survey | Collection catalogue | Software | Standards and Models]

The BioCISE collection catalogue

Anton Güntsch

Pp. 53-58 in: Berendsohn, W. G. (ed.), Resource Identification for a Biological Collection Information Service in Europe (BioCISE). - Botanic Garden and Botanical Museum Berlin-Dahlem, Dept. of Biodiversity Informatics.

Introduction

Unit-level collection data (see box in Chapter III) are a primary source for the derivation of new knowledge in life sciences, and the unit itself provides the possibility to verify existing scientific statements (Cotterill 1999, Lane 1996). Unfortunately, a common access system for collection information on the World Wide Web is far from being implemented. Over 90% of Europe's collections still do not publish unit-level data, in most cases because the collection is not electronically catalogued (see Chapter VII). The design of a unified interface for those collection information systems willing to publish their information through data networks is hindered by the diversity of information models and data standards in use.

Several initiatives try to overcome these obstacles by standardising interfaces to collection databases and developing appropriate and convenient user interfaces. The European Natural History Specimen Information Network (ENHSIN 2000), the International Species Information System of zoological gardens (ISIS 1999), and the German Botanical Garden Information System SYSTAX (Hoppe et al. 1996), are examples of different approaches.

Cataloguing biological collections

A first step on the way to a common access system for the hundreds of millions of collection objects held by European private and public institutions is the development of a catalogue providing collection information on various levels of abstraction.

The term collection information is here understood to cover information describing entire collections or sub-collections instead of single collection objects (units, fig. 10). Collection information covers categorizations and descriptive keywords (e.g. taxonomic and geographic), content and storage characteristics, as well as IPR statements and administrative properties. The Collection Description Working Group (Powell 1998) compiles a detailed list of meta information attributes to describe collections of any kind (including documents, art collections, etc.) based on the well-known Dublin Core (Anon. 1998).

Figure 10: Collection-level vs. unit-level information

The BioCISE collection catalogue (http://www.bgbm.org/BioCISE/database/) is based on the results of the BioCISE survey (see Chapter VII). It realizes a simple variant of such an information system by offering data from the following information areas:

• · Collection holders: Address, URL, and a free text self-portrayal
• · Collections: Broad collection category and free text description
• · Collection databases: Detailed description of systems in use including statements on information models, data quality, software features, status of data acquisition, and online accessibility
• · Collection databasing expertise: Names and specialties of collection information system experts, contact information

A simple user interface (fig. 11) allows querying the system by country or broad collection category (plants, animals, fungi, fossils, micro-organisms, and other).

Figure 11: User interface of the BioCISE collection catalogue

Prototype networking in the BioCISE collection catalogue

Biological collection catalogues already exist in some countries and for some thematic areas. These systems are community-driven, part of long-term projects, or supported by established organizations. A European information service should not duplicate their efforts, but rather help to enhance accessibility and feedback to them.

The BioCISE catalogue demonstrates a federation of catalogues which is based on a simple technique originating from the co-operation with the BIODIV project. (Güntsch & Vander Velde 1998). BIODIV - "Biodiversity Resources in Belgium" - is a Belgian initiative for cataloguing biodiversity resources on the World Wide Web. BIODIV cyclically transfers a file containing a core set of data fields necessary to establish the link from the BioCISE collection catalogue. In detail, these attributes are: Laboratory, department, and institution holding the collection, city and country, and collection categories derived from a defined set of keywords. As location, name and keywords are relatively stable, transfer intervals of 6 months are sufficient. The initial workload for the participating network consists of creating a query, which produces the transfer file; the workload for the updates is negligible.

Figure 12: Co-operation of BIODIV and BioCISE

To populate the BioCISE project database, the data in the transfer files are transformed to a SQL script, which maps the keywords used in the source (e.g. BIODIV) to those valid for the BioCISE collection catalogue, thus allowing for a common view on local and networked data. Whenever users of the BioCISE collection catalogue select a Belgian collection, they will be directed immediately to the BIODIV system to receive the latest information. The transformation process is automated by a Java application, which requires a minimum effort of reprogramming for the incorporation of new thematic or local networks. The regular incorporation of updated transfer files in the BioCISE catalogue takes a few minutes each, provided that the transfer files are "well-formed". Fig. 12 summarizes the mechanism.

The collaboration between BIODIV and BioCISE served as a prototype for several similar co-operations, which were established in 1999 (table 1).

Table 1: Networks collaborating with the BioCISE collection catalogue

BIODIV. The national network "Biodiversity Resources in Belgium" has the aim to develop an inventory with information on Belgian institutions, specialists, collections, projects, and literature concerned with Biodiversity. The information is largely captured through online questionnaires.

NatureWeb. The Austrian "Networking Initiative for Natural History Collections and Observation Information Exchange" was initiated in 1998. One of the project's aims is to compile an online collection catalogue, which currently includes information on 98 collections.

Polish Herbaria. The Institute of Botany of the Polish Academy of Science compiled an extensive overview of Polish herbaria. Collection-level information on herbaria are accessible through a simple clickable map. The State Committee for Scientific Research supported the development.

Index Herbariorum. The Herbaria of the World, Part I, last printed as the 9th edition, is a much relied upon standard reference for botanists, which is now also available as a World Wide Web database. It contains information on about 3000 public herbaria and nearly 9000 staff members world-wide. The abbreviation assigned to the collection is an acknowledged TDWG standard.

CABRI. "Common Access to Biotechnological Resources and Information" was an EU financed project which has now been taken over by the participants. Its aim is to make catalogue databases of various organism types and genetic material accessible through a common interface. CABRI also developed standards and procedures to ensure the highest possible data quality (see Chapter VI). Although CABRI is focused on unit related data, collection-level information on the participating collections is provided as a "side effect" and included into the BioCISE collection catalogue. 

IPGRI. The Directory of Germplasm Collections held by the International Plant Genetic Resources Institute maintains an information system on ex situ germplasm collections, providing meta-information for more than 5 million objects worldwide. 

Although the BioCISE collection catalogue was originally designed as a simple inventory of European collections it turned out to be a valuable tool especially to get updated contact information and collection descriptions. Nevertheless, this is a prototype. It does not fulfil several criteria, which are essential for a proper Information Service: scalability, wide range of query parameters, accuracy (and non-redundancy) of results, ease of maintenance, and feedback to participating networks. The willingness of networks to participate, however, was very encouraging - the networks in the Catalogue are indeed all that had been approached.

© BioCISE Secretariat. Email: biocise@, FAX: +49 (30) 841729-55
Address: Botanischer Garten und Botanisches Museum Berlin-Dahlem (BGBM), Freie Universität Berlin, Königin-Luise-Str. 6-8, D-14195 Berlin, Germany