Minimum Information Standards

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Minimum Information (MI) standards or reporting guidelines specify the minimum amount of meta data (information) and data required to meet a specific aims or aims. Usually the aim is to provide enough meta data and data to enable the unambiguous reproduction and interpretation of an experiment. MI guidelines are normally informal human readable specifications that inform the development of formal data models (e.g. XML or UML) or knowledge models such as an ontology), and data exchange formats (e.g. FuGE, MAGE-ML, MAGE-TAB, MGED-Ontology).

MI standards are developed by working bodies of practitioners working in a particular scientific domain. The MI standards listed below are all from the life sciences, largely driven by the development of high throughput experimental technologies.

These MI standards groups have been brought together in 2007 to form the "Minimum Information about a Biomedical or Biological Investigation" (MIBBI) umbrella community. More information about the MIBBI initiative and the MIBBI Foundry can be found below and on the MIBBI homepage: http://mibbi.sourceforge.net/.

Contents 1 MI Standards 1.1 MIAME, gene expression microarray 1.1.1 MIAME-env, environmental genomics 1.1.2 MIAME-nut, nutrional genomics 1.1.3 MIAME-tox, toxogenomics 1.1.4 MIAME-Plant, plant 1.2 MIARE, RNAi experiment 1.3 MIACA, cell based assay 1.4 MIAPE, proteomic experiments 1.4.1 MIAPE CC, reporting requirements for column chromatography 1.4.2 MIAPE CE, reporting requirements for capillary electrophoresis 1.4.3 MIAPE MS, reporting requirements for mass spectrometry 1.4.4 MIAPE SP, reporting requirements for sample preparation and handling 1.4.5 MIAPE GE, reporting requirements for gel electrophoresis 1.4.6 MIAPE GI, reporting requirements for gel informatics 1.4.7 MIMIX, reporting requirements for molecular interaction experiments 1.5 MIGS/MIMS, genome/metagenome sequences 1.6 MIFlowCyt, flow cytometry 1.6.1 Minimum Information about a Flow Cytometry Experiment 1.7 MISFISHIE, In Situ Hybridization and Immunohistochemistry Experiments 1.8 MIAPA, Phylogenetic Analysis 1.9 MIAO, ORF 1.10 MIAMET, METabolomics experiment 1.11 MIAFGE, Functional Genomics Experiment 1.12 MIRIAM, Minimum information requested in the annotation of biochemical models 1.13 CIMR, Core Information for Metabolomics Reporting 2 References 3 External links 3.1 MIBBI Minimum Information for Biological and Biomedical Investigations 3.2 MGED The Microarray Gene Expression Data Society 3.3 HUPO-PSI HUPO Protein Standards Initiative 3.4 FuGE Functional Genomics Experiment 3.5 MSI The Metabolomics Standards Initiative 3.6 MIACA, Minimum Information About a Cellular Assay 3.7 MIARE, Minimum Information About an RNAi Experiment 3.8 MIFlowCyt, Minimum Information about a Flow Cytometry Experiment 3.9 Nature Community Consultation

[edit] MI Standards

[edit] 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

[edit] MIAME-env, environmental genomics

[edit] MIAME-nut, nutrional genomics

[edit] MIAME-tox, toxogenomics

[edit] MIAME-Plant, plant

[edit] 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.

[edit] 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.

[edit] MIAPE, proteomic experiments

Minimal Information About a Proteomic Experiment documents describe information which should be given along with a proteomic experiment.

[edit] MIAPE CC, reporting requirements for column chromatography

[edit] MIAPE CE, reporting requirements for capillary electrophoresis

[edit] MIAPE MS, reporting requirements for mass spectrometry

[edit] MIAPE SP, reporting requirements for sample preparation and handling

[edit] MIAPE GE, reporting requirements for gel electrophoresis

This module identifies the minimum information required to report the use of n-dimensional gel electrophoresis in a proteomics experiment, in a manner compliant with the aims as laid out in the MIAPE Principles document. These reporting guidelines cover gel manufacture and preparation, running conditions, visualization techniques such as staining, the method of image capture and a technical description of the image obtained. They do not explicitly cover sample preparation, but do require the recording of which samples were loaded onto a gel. They do not include spot detection or other analyses of gel images, nor do they include protein identification procedures. Items falling outside the scope of this module may be captured in complementary modules, which can be obtained from the MIAPE website.

[edit] MIAPE GI, reporting requirements for gel informatics

[edit] MIMIX, reporting requirements for molecular interaction experiments

[edit] MIGS/MIMS, genome/metagenome sequences

This specification is being developed by the Genomic Standards Consortium

[edit] MIFlowCyt, flow cytometry

[edit] 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:

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

[edit] MISFISHIE, In Situ Hybridization and Immunohistochemistry Experiments

[edit] MIAPA, Phylogenetic Analysis

[edit] MIAO, ORF

[edit] MIAMET, METabolomics experiment

[edit] MIAFGE, Functional Genomics Experiment

[edit] MIRIAM, Minimum information requested in the annotation of biochemical models

MIRIAM, the Minimal Information Requested In the Annotation of Models, is a set of rules for curating quantitative models of biological systems.

[edit] CIMR, Core Information for Metabolomics Reporting

[edit] References

[edit] External links

[edit] MIBBI Minimum Information for Biological and Biomedical Investigations

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

[edit] MGED The Microarray Gene Expression Data Society

(MGED) Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments.

[edit] HUPO-PSI HUPO Protein Standards Initiative

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

[edit] FuGE Functional Genomics Experiment

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.

[edit] MSI The Metabolomics Standards Initiative

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.

[edit] MIACA, Minimum Information About a Cellular Assay

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.

[edit] MIARE, Minimum Information About an 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.

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

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.

[edit] Nature Community Consultation

Standards papers under consideration for publication in Nature Biotechnology.