Minimum information standards
Minimum information standards are sets of guidelines and formats for reporting data derived by specific high-throughput methods. Their purpose is to ensure the data generated by these methods can be easily verified, analysed and interpreted by the wider scientific community. Ultimately, they facilitate the transfer of data from journal articles (unstructured data) into databases (structured data) in a form that enables data to be mined across multiple data sets.
MIAME for microarray experiments
The typical example of a minimum information standard is the ‘Minimum Information about a Microarray Experiment’ (MIAME), developed by the Functional Genomics Data Society (FGED; originally the Microarray Data Society). The community that ultimately became FGED had representatives from labs generating microarray data (academic and industrial), data repositories, microarray manufacturers and journal publishers. Many journals and funding agencies now require authors reporting on microarray-based transcriptomics experiments to comply with the MIAME standard.
Figure 7 A schematic representation of the six kinds of data captured in MIAME; adapted from the original publication (6).
Figure 7 key
Experiment: the set of hybridisation experiments as a whole
Array: each array used and each element (spot, feature) on the array
Sample: samples used, extract preparation and labelling
Hybridisation: procedures and parameters
Data: images, quantification and specifications
Normalisation: types, values and specifications of controls
White boxes: represent external links
Minimum information standards typically have two parts. Firstly, there is a set of reporting requirements - typically presented as a table or a checklist. Secondly, there is a data format. Information about an experiment needs to be converted into the appropriate data format for it to be submitted to the relevant database. In the case of MIAME, the data format is provided in spreadsheet format (MAGE-TAB). Some of the communities that maintain minimum information standards also provide tools to help experimental researchers to annotate their data. For example, Annotare helps researchers to construct MIAME-compliant annotation files based on the MAGE-TAB format.
BioSharing.org provides a list of minimum information standards, tagged as reporting guidelines or models/formats.