Plant A+: Taking plant omics data through annotation, acquisition and analysis to application


Within the EOSC-Life project, EMPHASIS, together with 13 ESFRI projects from the Health & Food sector, is developing a digital platform for cooperation across disciplinary boundaries in order to make data available and usable in accordance with FAIR principles.

EOSC-Life has been funding the so-called “Demonstrator” projects, scientific and technical pilot projects that provide concrete scientific use-cases and guide and structure the work done in EOSC-Life to build an open digital and collaborative space for biological and medical research.

The EOSC-Life demonstrator "Plant A+", funded in the first open call, is a collaboration of EMPHASIS with ISBE and ELIXIR. The objective of the Plant A+ project is to cross data from different domains: phenomics, genetics and environmental data and develop tools to integrate, analyse and visualize these data in a FAIR manner. Nowadays, mother genomes are available and shared and a high amount of phenotypic data is produced daily. This project aims to improve data harmonisation and standards to better re-use and integrate existing data in plant science.

Within Plant A+, this demonstrator has developed a series of interesting tools that should improve best practices and FAIR data sharing in plant sciences:

FAIRdom SEEK 

The FAIRdom SEEK tool was developed to bring data harmonisation and standards by capturing FAIR metadata to handle both genomic and phenomics data. With FAIRdom SEEK, each dataset entry includes biological material description, plant phenotyping ontologies and methods, phenotyping dataset and experiments location but also allows for custom metadata to be added depending on the need.

More about FAIRdom SEEK

FAIRdom SEEK software

pISA-tree

Complementary to FAIRdom SEEK, pISA-tree was developed.  pISA-Tree is a system of batch files that creates a standard directory tree and automatically guides the user through required metadata inputs and is more adapted to the needs in small labs. 

Link to pISA-tree

Gene Expression Plotter

Another tool was developed to facilitate the analysis and the visualisation of gene expression data. This tool, which is already publicly available via github, makes RNA sequencing expression data and data visualisation available via the browser. It facilitates sharing and exploration of the data and provides non-technical researchers with powerful visualisation tools to quickly analyse and generate graphical data representation.

 Gene Expression Plotter

 

Participants:

INRA (Cyril Pommier)

FZJ/EMPHASIS (Asis Hallab, Björn Usadel, Constantin Eiteneuer)

UNIMAN (Stuart Owen)

NIB (Kristina Gruden)

 

Publications:

Papoutsoglou et al (2020) Enabling reusability of plant phenomic datasets with MIAPPE 1.1.

New Phytologist URL: https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16544