MIAPPE

Minimum Information About a Plant Phenotyping Experiment

MIAPPE is an open, community driven project to harmonize data from plant phenotyping experiments. MIAPPE comprises both a conceptual checklist of metadata required to adequately describe a plant phenotyping experiment, and software to validate, store and disseminate MIAPPE-compliant data. We welcome contributions from anyone interested in plant phenotyping data.

Development of MIAPPE is an open process, so if you would like to do more than just comment, and to participate in the ongoing development, please let us know via miappe-feedback@ebi.ac.uk.

MIAPPE v1.1

MIAPPE version 1.1 was officially released on 10th January 2019, following consideration of responses to two requests for comments. Major developments over v1.0 include:

  • The extension of MIAPPE’s scope to accommodate woody plants as an additional use-case.
  • The specification of a data model for MIAPPE, to facilitate its implementation in various formats and enable its automatic validation.
  • Compatibility of the MIAPPE logical standard with common frameworks for representing these data types, namely ISA-Tools and the Breeding API (BrAPI).
  • The enrichment of MIAPPE, with the provision of clear definitions and examples for all fields.
We are currently writing a paper describing the new version for publication. All those who contributed to the work will be asked if they wish to participate as authors in the near future. Meanwhile, improvements can be suggested via miappe-feedback@ebi.ac.uk. Work is now commencing on the next version of MIAPPE, v2.0. Development is at an early stage and all contributions are welcome.

Background

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.

MIAPPE was originally been developed in the context of the transPLANT, European Plant Phenotyping Network and ELIXIR-EXCELERATE projects, but we are keen to work with anyone interested in contributing to, reviewing or using the standard, or developing new tools.