Minimum Information About a Plant Phenotyping Experiment
Plant phenotyping data is diverse, dispersed and increasingly plentiful owing to the application of new automated techniques. While various initiatives have explored how to describe plant traits (e.g. the Plant Trait Ontology) and phenotypes, description of the experimental design that provides the context for phenotypic observations is not well-standardized. A basic description of the materials used and the experiment performed is needed to support data discovery and data mining applications. MIAPPE – the Minimal Information About a Plant Phenotyping Experiment – is in development to address these needs.
MIAPPE is a Minimum Information (MI) standard for plant phenotyping. It defines a list of attributes that might be necessary to fully describe a phenotyping experiment, following the model originally established for microarray data. Not all of the elements listed in an MI must be reported in each case. An MI document should rather be considered as a checklist, and consulted by a person describing or depositing the data to ensure the inclusion of all important data characteristics, i.e. what is meaningful for the interpretation and potential replication of the research.
MIAPPE is a logical standard - but there are specific implementations of tools designed to support its use and application, for example, in the ISA-tools framework. We are working with the developers of the Plant Breeding API (BRAPI) to ensure the compliance of BRAPI with the MIAPPE standard, and to coordinate future developments. A workshop to develop an RDF-implementation will be held later this year (details to be posted shortly).
Please follow the links to:
- The current version (April 2016) of MIAPPE in PDF format.
- The MIAPPE opinion paper: Towards recommendations for metadata and data handling in plant phenotyping.
- A recent paper describing the implementation of MIAPPE: Measures for interoperability of phenotypic data: minimum information requirements and formatting.
- The current implementation of the MIAPPE standard in ISA-Tab format.
- More information about the ISA-tab for phenotyping: concept and use; and more generally, about the Investigation-Study-Assay file format.
- An archive of previous versions of the MIAPPE specification and ISA-Tab configurations.
- A mapping of MIAPPE terms to the checklist for the submission of plant nucleic acid sequence to the European Nucleotide Archive (coming soon).
- The MIAPPE GitHub repository.
- A full list of Minimum Information Standards available, and the MIAPPE record, available on biosharing.org.
- Contact us as at firstname.lastname@example.org.