Project deliverable Open Access
Miguel, Célia; Pommier, Cyril; Finkers, Richard; Coppens, Frederik; Bolser, Dan; Ruiz, Manuel; Adam-Blondon, Anne-Françoise; Gruden, Kristina; Ramšak, Živa; Papoutsoglou, Evangelia; Faria, Daniel; Costa, Bruno; Chaves, Inês
High-throughput “omics” technologies are widely used and increasingly important to support plant biology research and breeding of diverse plant species for production of food, feed, fibre and other biomaterials, and bio-energy. Significant advances in plant science can be obtained from the integration of available genomic and genotyping data with diverse types of phenotyping data, including field or greenhouse experimental data, molecular, -omics and image data. Although most -omics data, and especially phenomic data, are being generated in increasing scale, either from public or private research institutes, the dispersion of datasets and metadata among multiple repositories and their often poor description and annotation, make their use and exploitation still challenging or even unapproachable.
To help unlock the full potential of a multi-omics approach to plant science, the overarching goal of this work package is to make plant data reusable and interoperable in accordance with the FAIR principles (i.e. Findable, Accessible, Interoperable and Re-usable). Hence, several standards have been built these past years for the annotation of data sets, and the ELIXIR plant community is co-authoring most of them. Their use has been demonstrated by exemplary application to data from diverse species published in public repositories (Deliverable 7.1). They are also the foundation of the ELIXIR Plant Data Search Service, FAIDARE, that gives access to distributed and standardized datasets. This service uses the Breeding API (BrAPI1), an API for accessing data relevant for plant breeding developed by the international plant community (Deliverable 7.2). It is based on a federation of plant phenotyping/genotyping data repositories, accessible through a single data discovery webportal2, that connects not only ELIXIR data repositories, but also any other Breeding API compatible database.
This work represents a major step towards plant FAIR data and a significant tool for the international plant community focused on plant breeding, either of crops or forest trees. Furthermore, with this deliverable we reach the main goal of WP7, to provide a distributed infrastructure to allow plant genotype-phenotype analysis based on the widest available public datasets, and we give an important contribution to address goal one of the ELIXIR-EXCELERATE project: Deliver world-leading data services for academia and industry.
ELIXIR-EXCELERATE D7.3 Implementation of BRAPI.pdf