Minimum Information About a Microarray Experiment - MIAME

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. [Brazma et al., Nature Genetics]

The six most critical elements contributing towards MIAME are:

  1. The raw data for each hybridisation (e.g., CEL or GPR files)
  2. The final processed (normalised) data for the set of hybridisations in the experiment (study) (e.g., the gene expression data matrix used to draw the conclusions from the study)
  3. The essential sample annotation including experimental factors and their values (e.g., compound and dose in a dose response experiment)
  4. The experimental design including sample data relationships (e.g., which raw data file relates to which sample, which hybridisations are technical, which are biological replicates)
  5. Sufficient annotation of the array (e.g., gene identifiers, genomic coordinates, probe oligonucleotide sequences or reference commercial array catalog number)
  6. The essential laboratory and data processing protocols (e.g., what normalisation method has been used to obtain the final processed data)

For more details, see MIAME 2.0.

MIAME does not specify a particular format, however, obviously the data are more usable, if it is encoded in a way that the essential information specified by MIAME can be accessed easily. FGED recommends the use of MAGE-TAB format, which is based on spreadsheets, or MAGE-ML.

MIAME also does not specify any particular terminology, however for automated data exchange the use of standard controlled vocabularies and ontologies are desirable. FGED recommends the use of MGED Ontology for the description of the key experimental concepts, and where possible ontologies developed by the respective community for describing terms such as anatomy, disease, chemical compounds etc (see OBO page for more detail).

MIAME In Practice

The public repositories ArrayExpress at the EBI (UK), GEO at NCBI (US) and CIBEX at DDBJ (Japan) are designed to accept, hold and distribute MIAME compliant microarray data.

There is a number of software tools supporting MIAME requirements under development.

Open letter to the scientific journals about submitting MIAME compliant data [RTF 14kb] [HTML 12kb].

These journals require MIAME compliant data as a condition for publishing microarray based papers.

ArrayExpress service to journals [PDF 508kb].

MIAME extensions or related activities

FGED Sponsors