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

Sousa, Ana Margarida ; Ferreira, Andreia ; Azevedo, Nuno ; Pereira, Maria Olivia ; Lourenco, Analia

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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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)


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Sousa, Ana Margarida ; Ferreira, Andreia ; Azevedo, Nuno ; Pereira, Maria Olivia ; Lourenco, Analia  (2012)  Computational approaches to standard-compliant biofilm data for reliable analysis and integration. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 9(3): Special Issue: Selected extended papers of the 6th International Conference on Practical Applications of Computational Biology and Bioinformatics, Salamanca, Spain, 2012

Online-Journal: http://journal.imbio.de/article.php?aid=203
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2012/5213



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