On Minimum Reporting Requirements and Standard Formatting of Plant Phenotypic Data

In recent years increasing efforts have been directed at characterising crop plants' phenotypes, not only morphological traits measured in field or greenhouse experiments, or adaptation to environment and diseases, but also results of gene action at transcript, protein or metabolite level, or chromatin features. Due to the widely acknowledged need for a systems biology approach and fast development of high-throughput measurement protocols, both traditional and new “omics” data are being collected in large experiments with factorial structure, often including repeated measurements in time. Although the laboratory protocols for different traits require different data collection schemes and device-specific preprocessing algorithms, at some point the data have to be gathered for clearly identified “samples” or “experimental units” to allow its integration into knowledge about the system under study. The understanding of the structure of information is crucial to reasonably exchange the data between researchers, databases and data analysis tools. To allow this, we are developing recommendations concerning metadata and annotation methods for datasets containing phenotypic observations. We do this with recognition of standardization achievements in other areas of “omics” studies, such as transcriptomics, proteomics, or metabolomics, which, however, as domain-specific generally do not allow for inclusion of morphological, yield-related, quality or resistance traits. We propose the “Minimum Information about Plant Phenotypic Experiments” (MIAPPE) checklist, based on existing “Minimum Information” recommendations, and the implementation of this standard as a file format based on the ISA-TAB structure, which has been successfully applied in other biomedical domains.
The presented standards and recommendations are being developed under the auspices of the transPLANT* project (a European partnership promoting data integration in plant sciences) and will be used by the transPLANT consortium to build and refine tools for data exchange, information retrieval and integrated data analysis of phenotypic data.

* The transPLANT project is funded by the European Commission within its 7th Framework Programme under the thematic area “Infrastructures”, contract number 283496.