title: BiofOmics: a Web platform for the systematic and standardized collection of high-throughput biofilm data.
abstract: BACKGROUND
  Consortia of microorganisms, commonly known as biofilms, are attracting much attention from the scientific community due to their impact in human activity. As biofilm research grows to be a data-intensive discipline, the need for suitable bioinformatics approaches becomes compelling to manage and validate individual experiments, and also execute inter-laboratory large-scale comparisons. However, biofilm data is widespread across ad hoc, non-standardized individual files and, thus, data interchange among researchers, or any attempt of cross-laboratory experimentation or analysis, is hardly possible or even attempted.
  
  
  RESULTS
  This paper presents BiofOmics, the first publicly accessible Web platform specialized in the management and analysis of data derived from biofilm high-throughput studies. The aim is to promote data interchange across laboratories, implementing collaborative experiments, and enable the development of bioinformatics tools in support of the processing and analysis of the increasing volumes of experimental biofilm data that are being generated. BiofOmics' data deposition facility enforces data structuring and standardization, supported by controlled vocabulary. Researchers are responsible for the description of the experiments, their results and conclusions. BiofOmics' curators interact with submitters only to enforce data structuring and the use of controlled vocabulary. Then, BiofOmics' search facility makes publicly available the profile and data associated with a submitted study so that any researcher can profit from these standardization efforts to compare similar studies, generate new hypotheses to be tested or even extend the conditions experimented in the study.
  
  
  CONCLUSIONS
  BiofOmics' novelty lies in its support to standardized data deposition, the availability of computerizable data files and the free-of-charge dissemination of biofilm studies across the community. Hopefully, this will open promising research possibilities, namely the comparison of results between different laboratories, the reproducibility of methods within and between laboratories, and the development of guidelines and standardized protocols for biofilm formation operating procedures and analytical methods.
authors: IBB--Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Braga, Portugal.
authors: Anália
authors: A
authors: Lourenço
authors: Andreia
authors: A
authors: Ferreira
authors: Nuno
authors: N
authors: Veiga
authors: Idalina
authors: I
authors: Machado
authors: Maria Olivia
authors: MO
authors: Pereira
authors: Nuno F
authors: NF
authors: Azevedo
mesh_terms: D001331:Automation; D018441:Biofilms; D019295:Computational Biology / Q000379:methods* / Q000592:standards*; D003625:Data Collection; D019992:Databases as Topic; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D020407:Internet; D009862:Online Systems; D011642:Publications; D012015:Reference Standards; D015203:Reproducibility of Results; D013045:Species Specificity