title: 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 Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently.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.
authors.affiliation: Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Serge
authors.initials: S
authors.lastname: Casaregola
authors.affiliation: All-Russian Collection of Microorganisms, IBPM RAS, Pushchino, Russia.
authors.forename: Alexander
authors.initials: A
authors.lastname: Vasilenko
authors.affiliation: IRCCS AOU San Martino IST, Largo R. Benzi 10, 16132 Genoa, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Romano
authors.affiliation: The Centraalbureau voor Schimmelcultures (CBS) Fungal Biodiversity Centre, Utrecht, The Netherlands.
authors.forename: Vincent
authors.initials: V
authors.lastname: Robert
authors.affiliation: All-Russian Collection of Microorganisms, IBPM RAS, Pushchino, Russia.
authors.forename: Svetlana
authors.initials: S
authors.lastname: Ozerskaya
authors.affiliation: Jacobs University Bremen, Bremen, Germany ; Max Planck Institut for Marine Microbiology, Bremen, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Kopf
authors.affiliation: Jacobs University Bremen, Bremen, Germany ; Max Planck Institut for Marine Microbiology, Bremen, Germany.
authors.forename: Frank O
authors.initials: FO
authors.lastname: Glöckner
authors.affiliation: CABI, Bioservices, Egham, Surrey TW20 9TY UK.
authors.forename: David
authors.initials: D
authors.lastname: Smith
keywords: Culture collection; Information Technology; Microbial domain Biological Resource Centre; Microorganism