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.
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.
MIAPPE v1.1 Proposal
A proposal has been made to extend the MIAPPE v1.0 specification. This document is now available here, in PDF and Google Docs formats. The proposal is now open for consultation, and we welcome contributions from anyone with interest in the field.
Feedback can be provided in a number of ways:
- Comment directly on the proposal in Google docs. We will try to leave comments up for as long as possible to facilitate discussion, but will harvest comments from the document if necessary to prevent it from becoming unwieldy.
- Read the document (as PDF, or in Google docs), and feedback via email. Please use miappe-feedback@ebi.ac.uk for this purpose.
- Feedback via our public github tracker, at https://github.com/MIAPPE/MIAPPE-checklist/issues. This will also be set up shortly.
We would like to encourage feedback by the end of January 2018, in order that we can prepared a revised proposal in accordance with the comments (and take further feedback prior to eventual ratification by the MIAPPE steering committee).
Please share this request with anyone who you know who might be interested in contributing. We request that individuals do not comment anonymously. All contributions will be discussed by the development team, and responded to in writing, and contributors will be credited on www.miappe.org. All contributors will also be invited to participate in the writing of a paper to publicise the final standard.
Responses to comments will be prepared by the development team via remote discussion (email and meetings). Development of MIAPPE is an open process, so if you would like to do more than just comment, and to participate in these meetings, please let us know via miappe-feedback@ebi.ac.uk