Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii

More and more phenomic data are produced in high throughput phenotyping facilities or in collaborative networks like EPPN, ICIS or CGIARS. Those data are highly heterogeneous and include phenotypic traits, hyperspectral image, NIRS, raw or derived alphanumeric data produced at different time and physical scales.

Phenomic data sharing, integration and analysis are therefore major challenges which can be eased by several standards, with ontologies like the Crop Ontology or file format like ISA TAB for phenotyping.

ISA Tab is a zip archive file handling both raw and elaborated data, annotated by rich ontology driven metadata. It is an implementation of the “Minimum Information about Plant Phenotypic Experiments” (MIAPPE) checklist. It has been integrated in several information systems in the transPLANT project (European Commission 7th Framework, “Infrastructures”, contract 283496.).

One of them is the IPGPAS Bii Data Manager instance, which allows for storage and access to formatted phenotypic datasets. Another is GnpIS, an INRA information system for plant and their bio aggressors which integrates and links genomic, genetic and phenomic.

GnpIS Phenotypes data is accessible through Ephesis, which integrates multifactorial phenotyping Trial for any plant species, at any scale with ontology variables. Ephesis allows the set-up of multi trial data sets which can be exported as ISA TAB for analysis either to decipher genotypes to environmental constraints or to prepare association studies.

Thanks to the transplant implementations, we will be able to gather the necessary feedback to improve ISA TAB for Phenotyping format and ease its use by the international community.