Minimum Information Standards

The minimum information standard is a set of guidelines for reporting data derived by relevant methods in biosciences. If followed, it ensures that the data can be easily verified, analysed and clearly interpreted by the 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 (metadata) 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-throughput 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.[3]

MI Standards

MIAME, gene expression microarray

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, including MIAME-env, MIAME-nut and MIAME-tox, covering environmental genomics, nutritional genomics and toxogenomics, respectively

MINI: Minimum Information about a Neuroscience Investigation

MINI: Electrophysiology

Electrophysiology is a technology used to study the electrical properties of biological cells and tissues. Electrophysiology typically involves the measurements of voltage change or electric 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

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

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

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

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

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

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

This specification is being developed by the Genomic Standards Consortium

MIFlowCyt, flow cytometry

Minimum Information about a Flow Cytometry Experiment

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:

MIAPA, Phylogenetic Analysis

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

MIRIAM, Minimum Information Required in the Annotation of Models

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

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

External links

References

  1. 1 2 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. Cite uses deprecated parameter |coauthors= (help)
  2. 1 2 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. Cite uses deprecated parameter |coauthors= (help)
  3. ↑ Taylor, Chris F (2008). "Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project". Nature Biotechnology 26: 889–896. doi:10.1038/nbt.1411.
  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.
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