Computational approaches to standard-compliant biofilm data for reliable analysis and integration

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doi doi:10.2390/biecoll-jib-2012-203
submission July 02, 2012
published July 24, 2012
NCBI PubMed PubMed ID 22829574

Ana Margarida Sousa, Andreia Ferreira, Nuno Azevedo, Maria Olívia Pereira and Anália Lourenço

Correspondence should be addressed to:
Anália Lourenço
IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga - PORTUGAL
se.ogivu@nullailana


Abstract

The study of microorganism consortia, also known as biofilms, is associated to a number of applications in biotechnology, ecotechnology and clinical domains. Nowadays, biofilm studies are heterogeneous and data-intensive, encompassing different levels of analysis. Computational modelling of biofilm studies has become thus a requirement to make sense of these vast and ever-expanding biofilm data volumes. The rationale of the present work is a machine-readable format for representing biofilm studies and supporting biofilm data interchange and data integration. This format is supported by the Biofilm Science Ontology (BSO), the first ontology on biofilms information. The ontology is decomposed into a number of areas of interest, namely: the Experimental Procedure Ontology (EPO) which describes biofilm experimental procedures; the Colony Morphology Ontology (CMO) which characterises morphologically microorganism colonies; and other modules concerning biofilm phenotype, antimicrobial susceptibility and virulence traits. The overall objective behind BSO is to develop semantic resources to capture, represent and share data on biofilms and related experiments in a regularized fashion manner. Furthermore, the present work also introduces a framework in assistance of biofilm data interchange and analysis – BiofOmics (http://biofomics.org) – and a public repository on colony morphology signatures – MorphoCol (http://stardust.deb.uminho.pt/morphocol).

Reference

Ana Margarida Sousa, Andreia Ferreira, Nuno Azevedo, Maria Olívia Pereira and Anália Lourenço. Computational approaches to standard-compliant biofilm data for reliable analysis and integration. Journal of Integrative Bioinformatics, 9(3):203, 2012. Online Journal: http://journal.imbio.de/index.php?paper_id=203
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