NAR Molecular Biology Database Collection entry number 1182

Database Description

The Bioportal currently integrates data from 55 Biological Resource Centres (BRCs) that cover all earth's continents and range from small niche-specific research collections to large general-purpose service collections into an integrated strain database that underpins the Bioportal (Dawyndt et al., 2005). Information extracted from three taxonomic reference databases together with their type strains is incorporated as well. This integration process has currently lumped over 690,000 strain numbers into about 310,000 equivalence classes that represent different strains of Bacteria, Archaea, filamentous fungi, yeasts, Algae and Protozoa. Through the online interface of the Bioportal, organisms can be searched by strain number, taxonomic name (optionally restricted to type strains of these species), INSDC accession number, full text or combinations of the previous search parameters. Query results redirect the user on-the-fly to the online catalogues of the different culture collections that have a given strain that matches the query in their holdings. Additional pointers allow the user to navigate the downstream information available on these organisms, thereby rendering superfluous the need to browse a multitude of autonomous and heterogeneous information sources. For each organism, a list of all sequences deposited in the INSDC databases is given as a separate view. This overview is dynamically compiled irrespective of the strain numbers assigned to different cultures of the same organism during the sequence deposition process, solving possible Babel-like confusions. Sequence records are linked out to the corresponding records in the INSDC databases and the SILVA database. Similarly, another view assembles all scientific publications on a given organism, with links to the PubMed and DOI repositories whenever available. Finally, the integrated history and geographic views allow simple inspection of strain authenticity and availability.


Dawyndt, P., Vancanneyt, M., De Meyer, H., Swings, J. (2005) Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources. IEEE Transactions on Knowledge and Data Engineering, 17(8), pp. 1111-1126.

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