An Information System for European culture collections: the way forward

Abstract

Culture collections contain indispensable information about the microorganisms preserved in their repositories, such as taxonomical descriptions, origins, physiological and biochemical characteristics, bibliographic references, etc. However, information currently accessible in databases rarely adheres to common standard protocols. The resultant heterogeneity between culture collections, in terms of both content and format, notably hampers microorganism-based research and development (R&D). The optimized exploitation of these resources thus requires standardized, and simplified, access to the associated information. To this end, and in the interest of supporting R&D in the fields of agriculture, health and biotechnology, a pan-European distributed research infrastructure, MIRRI, including over 40 public culture collections and research institutes from 19 European countries, was established. A prime objective of MIRRI is to unite and provide universal access to the fragmented, and untapped, resources, information and expertise available in European public collections of microorganisms; a key component of which is to develop a dynamic Information System. For the first time, both culture collection curators as well as their users have been consulted and their feedback, concerning the needs and requirements for collection databases and data accessibility, utilised. Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible. Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently. Moreover, complex searches are rarely possible in online databases thus limiting the extent of search queries. Curators also consider that overall harmonization-including Standard Operating Procedures, data structure, and software tools-is necessary to facilitate their work and to make high-quality data easily accessible to their users. Clearly, the needs of culture collection curators coincide with those of users on the crucial point of database interoperability. In this regard, and in order to design an appropriate Information System, important aspects on which the culture collection community should focus include: the interoperability of data sets with the ontologies to be used; setting best practice in data management, and the definition of an appropriate data standard.

Keywords: Culture collection; Information Technology; Microbial domain Biological Resource Centre; Microorganism.

Fig. 1

The “Extended Query Form” interface of CABRI. The SRS standard interface allows multiple query conditions to be set combined with boolean operators for each indexed data field. The query form for CABRI bacteria catalogues is shown. A possible response to a query would then return, e.g., all strains of the genus Phyllobacterium (field Name), isolated from Ardisia crispa (field Isolated_from) in Germany (field Geographic_origin)

Fig. 2

The “Advanced search” interface of StrainInfo. The query form for all the data in StrainInfo is shown. A possible response to a query would then return, e.g., all strains of the genus Debaryomyces (field Taxonomic name), isolated from dairy products and their environment (field full text)

Fig. 3

The “Advanced search” interface of WDCM with the request Isolation Source. The result of the request for Isolation Source for the entire content of the GCM (http://gcm.wfcc.info/strains.jsp) 02/02/2015

Fig. 4

Schematic representation of the main tasks of the construction of the MIRRI-IS. For simplicity’s sake, the hypothesis of an inter-operable interface linking all individual CC databases was chosen (see Proposed solutions for increased interoperability between the existing databases section)