Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces.

The minimum information about a biofilm experiment (MIABiE) initiative has arisen from the need to find an adequate and scientifically sound way to control the quality of the documentation accompanying the public deposition of biofilm-related data, particularly those obtained using high-throughput devices and techniques. Thereby, the MIABiE consortium has initiated the identification and organization of a set of modules containing the minimum information that needs to be reported to guarantee the interpretability and independent verification of experimental results and their integration with knowledge coming from other fields. MIABiE does not intend to propose specific standards on how biofilms experiments should be performed, because it is acknowledged that specific research questions require specific conditions which may deviate from any standardization. Instead, MIABiE presents guidelines about the data to be recorded and published in order for the procedure and results to be easily and unequivocally interpreted and reproduced. Overall, MIABiE opens up the discussion about a number of particular areas of interest and attempts to achieve a broad consensus about which biofilm data and metadata should be reported in scientific journals in a systematic, rigorous and understandable manner.

[1]  Anália Lourenço,et al.  BiofOmics: A Web Platform for the Systematic and Standardized Collection of High-Throughput Biofilm Data , 2012, PloS one.

[2]  Andreia Ferreira,et al.  Computational approaches to standard-compliant biofilm data for reliable analysis and integration , 2012, J. Integr. Bioinform..

[3]  Lennart Martens,et al.  The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.

[4]  Shreyas Karnik,et al.  CAMP: a useful resource for research on antimicrobial peptides , 2009, Nucleic Acids Res..

[5]  J. Wingender,et al.  Metagenome Survey of Biofilms in Drinking-Water Networks , 2003, Applied and Environmental Microbiology.

[6]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , 2022 .

[7]  Bernhard O. Palsson,et al.  A road map for the development of community systems (CoSy) biology , 2012, Nature Reviews Microbiology.

[8]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[9]  Shannon McWeeney,et al.  MIFlowCyt: The minimum information about a flow cytometry experiment , 2008, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[10]  Raphael Gottardo,et al.  Comparability and reproducibility of biomedical data , 2012, Briefings Bioinform..

[11]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[12]  Corie Lok Literature mining: Speed reading , 2010, Nature.

[13]  Lennart Martens,et al.  PRIDE Inspector: a tool to visualize and validate MS proteomics data , 2011, Nature Biotechnology.

[14]  J. Banfield,et al.  Community Proteomics of a Natural Microbial Biofilm , 2005, Science.

[15]  Jillian F. Banfield,et al.  Community Proteomics of a Natural Microbial Biofilm , 2005 .

[16]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[17]  É. Yergeau,et al.  Metatranscriptomic Analysis of the Response of River Biofilms to Pharmaceutical Products, Using Anonymous DNA Microarrays , 2010, Applied and Environmental Microbiology.

[18]  Paul Stoodley,et al.  Bacterial biofilms: from the Natural environment to infectious diseases , 2004, Nature Reviews Microbiology.

[19]  D. Allison,et al.  The Biofilm Matrix , 2003, Biofouling.

[20]  S. Stepanović,et al.  A modified microtiter-plate test for quantification of staphylococcal biofilm formation. , 2000, Journal of microbiological methods.

[21]  J. Ellenberg,et al.  High-throughput fluorescence microscopy for systems biology , 2006, Nature Reviews Molecular Cell Biology.

[22]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[23]  David S. Wishart,et al.  DrugBank 3.0: a comprehensive resource for ‘Omics’ research on drugs , 2010, Nucleic Acids Res..

[24]  Zhiyong Lu,et al.  Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II , 2012, Database J. Biol. Databases Curation.

[25]  Computational approaches to standard-compliant biofilm data for reliable analysis and integration. , 2012, Journal of integrative bioinformatics.

[26]  Hans De Meyer,et al.  Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources , 2005, IEEE Transactions on Knowledge and Data Engineering.

[27]  Thorsten Henrich,et al.  Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE) , 2008, Nature Biotechnology.

[28]  H. Ceri,et al.  The Calgary Biofilm Device: New Technology for Rapid Determination of Antibiotic Susceptibilities of Bacterial Biofilms , 1999, Journal of Clinical Microbiology.

[29]  Werner Ceusters,et al.  A Unified Framework for Biomedical Terminologies and Ontologies , 2010, MedInfo.

[30]  Nigel W. Hardy,et al.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.

[31]  H. Flemming,et al.  The biofilm matrix , 2010, Nature Reviews Microbiology.

[32]  Ni Li,et al.  Gene Ontology Annotations and Resources , 2012, Nucleic Acids Res..

[33]  Martin A Hamilton,et al.  Comparative evaluation of biofilm disinfectant efficacy tests. , 2007, Journal of microbiological methods.

[34]  H. Nelis,et al.  Comparison of multiple methods for quantification of microbial biofilms grown in microtiter plates. , 2008, Journal of microbiological methods.

[35]  R. Maxwell,et al.  NMR metabolomics of planktonic and biofilm modes of growth in Pseudomonas aeruginosa. , 2007, Analytical chemistry.

[36]  John M. Hancock,et al.  Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data , 2009, BMC Bioinformatics.