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

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).The authors thank, among others, Rosario Oliveira, Maria Joao Vieira, Idalina Machado, Nuno Cerca, Mariana Henriques, Pilar Teixeira, Douglas Monteiro, Melissa Negri, Susana Lopes, Carina Almeida, Alexandrina Rodrigues, Tom Coenye, Paul Stoodley and Helder Lopes, for submitting their data and participating in the aforementioned standardisation initiatives. The financial support from the Institute of Biotechnology and Bioengineering Center of Biological Engineering (IBB-CEB), the Fundacao para a Ciencia e Tecnologia (FCT) and European Community fund FEDER (Program COMPETE), projects PTDC/SAU-ESA/646091/2006/ and FCOMP-01-0124-FEDER-007480, and the PhD grant of Ana Margarida Sousa (SFRH/BD/31065/2006) are also gratefully acknowledged