Minimum Information Standards

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The minimum information standard is a set of guidelines for reporting experimental data derived by relevant method in biosciences. If followed, it ensures that the data can be easily verified, analysed and clearly interpreted by wider scientific community. Keeping with these recommendations also facilitates the foundation of structuralized databases, public repositories and development of data analysis tools.[1][2]

The individual minimum information standards are brought by the communities of cross-disciplinary specialists focused on the problematic of the specific method used in experimental biology. The standards then provide specifications what information about the experiments (meta data) is crucial and important to be reported together with the resultant data to make it comprehensive.[1][2] The need for this standardization is largely driven by the development of high troughput experimental methods that provide tremendous amounts of data. The development of minimum information standards of different methods is since 2008 being harmonized by "Minimum Information about a Biomedical or Biological Investigation" (MIBBI) project. More information about the MIBBI initiative and the MIBBI Foundry can be found below and on the MIBBI homepage or biosharing homepage[3]

MI Standards[edit]

MIAME, gene expression microarray[edit]

Minimum Information About a Microarray Experiment (MIAME) describes the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment and is aimed at facilitating the dissemination of data from microarray experiments.

MIAME contains a number of extensions to cover specific biological domains

MIAME-env, environmental genomics[edit]

MIAME-nut, nutrional genomics[edit]

MIAME-tox, toxogenomics[edit]

MIAME-Plant, plant[edit]

MINI: Minimum Information about a Neuroscience Investigation[edit]

MINI: Electrophysiology[edit]

Electrophysiology is a technology used to study the electrical properties of biological cells and tissues. Electrophysiology typically involves the measurements of voltage change or electrical current flow on a wide variety of scales from single ion channel proteins to whole tissues. This document is a single module, as part of the Minimum Information about a Neuroscience investigation (MINI) family of reporting guideline documents, produced by community consultation and continually available for public comment. A MINI module represents the minimum information that should be reported about a dataset to facilitate computational access and analysis to allow a reader to interpret and critically evaluate the processes performed and the conclusions reached, and to support their experimental corroboration. In practice a MINI module comprises a checklist of information that should be provided (for example about the protocols employed) when a data set is described for publication. The full specification of the MINI module can be found here.[4]

MIARE, RNAi experiment[edit]

Minimum Information About an RNAi Experiment (MIARE) is a data reporting guideline which describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results.

MIACA, cell based assay[edit]

Advances in genomics and functional genomics have enabled large-scale analyses of gene and protein function by means of high-throughput cell biological analyses. Thereby, cells in culture can be perturbed in vitro and the induced effects recorded and analyzed. Perturbations can be triggered in several ways, for instance with molecules (siRNAs, expression constructs, small chemical compounds, ligands for receptors, etc.), through environmental stresses (such as temperature shift, serum starvation, oxygen deprivation, etc.), or combinations thereof. The cellular responses to such perturbations are analyzed in order to identify molecular events in the biological processes addressed and understand biological principles. We propose the Minimum Information About a Cellular Assay (MIACA) for reporting a cellular assay, and CA-OM, the modular cellular assay object model, to facilitate exchange of data and accompanying information, and to compare and integrate data that originate from different, albeit complementary approaches, and to elucidate higher order principles. Documents describing MIACA are available and provide further information as well as the checklist of terms that should be reported.

MIAPE, proteomic experiments[edit]

The Minimum Information About a Proteomic Experiment documents describe information which should be given along with a proteomic experiment. The parent document describes the processes and principles underpinning the development of a series of domain specific documents which now cover all aspects of a MS-based proteomics workflow.

For more details on this topic, see Minimum Information About a Proteomics Experiment.

MIMIx, molecular interactions[edit]

This document has been developed and maintained by the Molecular Interaction worktrack of the HUPO-PSI (www.psidev.info) and describes the Minimum Information about a Molecular Interaction experiment.

MIAPAR, protein affinity reagents[edit]

The Minimum Information About a Protein Affinity Reagent has been developed and maintained by the Molecular Interaction worktrack of the HUPO-PSI (www.psidev.info)in conjunction with the HUPO Antibody Initiative and a European consortium of binder producers and seeks to encourage users to improve their description of binding reagents, such as antibodies, used in the process of protein identification.

MIABE, bioactive entities[edit]

The Minimum Information About a Bioactive Entity was produced by representatives from both large pharma and academia who are looking to improve the description of usually small molecules which bind to, and potentially modulate the activity of, specific targets in a living organism. This document encompasses drug-like molecules as well as hebicides, pesticides and food additives. It is primarily maintained through the EMBL-EBI Industry program (www.ebi.ac.uk/industry).

MIGS/MIMS, genome/metagenome sequences[edit]

This specification is being developed by the Genomic Standards Consortium

MIFlowCyt, flow cytometry[edit]

Minimum Information about a Flow Cytometry Experiment[edit]

The fundamental tenet of any scientific research is that the published results of any study have to be open to independent validation or refutation. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) establishes the criteria to record information about the experimental overview, samples, instrumentation and data analysis. It promotes consistent annotation of clinical, biological and technical issues surrounding a flow cytometry experiment by specifying the requirements for data content and by providing a structured framework for capturing information.

More information can be found at:

  • The Flow Informatics and Computational Cytometry Socienty (FICCS) MIFlowCyt wiki page.
  • The Bioinformatics Standards for Flow Cytometry MIFlowCyt web page.

MISFISHIE, In Situ Hybridization and Immunohistochemistry Experiments[edit]

MIAPA, Phylogenetic Analysis[edit]

Criteria for Minimum Information About a Phylogenetic Analysis were described in 2006. [5]

MIAO, ORF[edit]

MIAMET, METabolomics experiment[edit]

MIAFGE, Functional Genomics Experiment[edit]

MIRIAM, Minimum Information Required in the Annotation of Models[edit]

The Minimal Information Required In the Annotation of Models (MIRIAM), is a set of rules for the curation and annotation of quantitative models of biological systems.

MIASE, Minimum Information About a Simulation Experiment[edit]

The Minimum Information About a Simulation Experiment (MIASE) is an effort to standardize the description of simulation experiments in the field of systems biology.

CIMR, Core Information for Metabolomics Reporting[edit]

External links[edit]

MIBBI Minimum Information for Biological and Biomedical Investigations[edit]

A ‘one-stop shop’ for exploring the range of extant projects, foster collaborative development and ultimately promote gradual integration.

FGED Society[edit]

FGED Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of data generated by functional genomics experiments using DNA microarray and other genome-scale technologies.

HUPO-PSI HUPO Protein Standards Initiative[edit]

The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification.

FuGE Functional Genomics Experiment[edit]

FuGE provides a model of common components in functional genomics investigations. It can be extended to develop modular data formats and provides a consistent framework to capture complete lab workflows.

MSI The Metabolomics Standards Initiative[edit]

MSI has be appointed by the Metabolomics Society to monitor, coordinate and review the efforts of working groups in specialist areas that will examine standardization and make recommendations.

MIACA, Minimum Information About a Cellular Assay[edit]

Minimum Information About a Cellular Assay (MIACA) is a data reporting guideline which describes the minimum information that should be reported about a Cellular Assay Experiment to enable the interpretation of results, and the exchange and integration of data and information.

MIARE, Minimum Information About an RNAi Experiment[edit]

Minimum Information About an RNAi Experiment (MIARE) is a data reporting guideline which describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results.

MIFlowCyt, Minimum Information about a Flow Cytometry Experiment[edit]

Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) is a data reporting guideline which describes the minimum information that should be reported about a flow cytometry experiment to enable the interpretation of the results.

Nature Community Consultation[edit]

Standards papers under consideration for publication in Nature Biotechnology.

BioSharing catalogue[edit]

References[edit]

  1. ^ a b Lee, Jamie A.; Spidlen, Josef; Boyce, Keith; Cai, Jennifer; Crosbie, Nicholas; Dalphin, Mark; Furlong, Jeff; Gasparetto, Maura; Goldberg, Michael; Goralczyk, Elizabeth M.; Hyun, Bill; Jansen, Kirstin; Kollmann, Tobias; Kong, Megan; Leif, Robert; McWeeney, Shannon; Moloshok, Thomas D.; Moore, Wayne; Nolan, Garry; Nolan, John; Nikolich-Zugich, Janko; Parrish, David; Purcell, Barclay; Qian, Yu; Selvaraj, Biruntha; Smith, Clayton; Tchuvatkina, Olga; Wertheimer, Anne; Wilkinson, Peter; Wilson, Christopher; Wood, James; Zigon, Robert; Scheuermann, Richard H.; Brinkman, Ryan R. (1 October 2008). "MIFlowCyt: The minimum information about a flow cytometry experiment". Cytometry Part A 73A (10): 926–930. doi:10.1002/cyto.a.20623. PMC 2773297. PMID 18752282. 
  2. ^ a b Brazma, Alvis; Hingamp, Pascal; Quackenbush, John; Sherlock, Gavin; Spellman, Paul; Stoeckert, Chris; Aach, John; Ansorge, Wilhelm; Ball, Catherine A.; Causton, Helen C.; Gaasterland, Terry; Glenisson, Patrick; Holstege, Frank C.P.; Kim, Irene F.; Markowitz, Victor; Matese, John C.; Parkinson, Helen; Robinson, Alan; Sarkans, Ugis; Schulze-Kremer, Steffen; Stewart, Jason; Taylor, Ronald; Vilo, Jaak; Vingron, Martin (30 November 2001). "Minimum information about a microarray experiment (MIAME)—toward standards for microarray data". Nature Genetics 29 (4): 365–371. doi:10.1038/ng1201-365. PMID 11726920. 
  3. ^ Taylor, Chris F (2008). "Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project". Nature Biotechnology (26): 889–896. 
  4. ^ Gibson, Frank, Overton, Paul, Smulders, Tom, Schultz, Simon, Eglen, Stephen, Ingram, Colin, Panzeri, Stefano, Bream, Phil, Sernagor, Evelyne, Cunningham, Mark, Adams, Christopher, Echtermeyer, Christoph, Simonotto, Jennifer, Kaiser, Marcus, Swan, Daniel, Fletcher, Marty, and Lord, Phillip. Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2008.1720.1> (2008)
  5. ^ Leebens-Mack, J.; Vision, T.; Brenner, E.; Bowers, J. E.; Cannon, S.; Clement, M. J.; Cunningham, C. W.; Depamphilis, C.; Desalle, R.; Doyle, J. J.; Eisen, J. A.; Gu, X.; Harshman, J.; Jansen, R. K.; Kellogg, E. A.; Koonin, E. V.; Mishler, B. D.; Philippe, H.; Pires, J. C.; Qiu, Y. L.; Rhee, S. Y.; Sjölander, K.; Soltis, D. E.; Soltis, P. S.; Stevenson, D. W.; Wall, K.; Warnow, T.; Zmasek, C. (2006). "Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)". OMICS: A Journal of Integrative Biology 10 (2): 231. doi:10.1089/omi.2006.10.231.  edit