Project deliverable Open Access
Miguel, Célia; Pommier, Cyril; Finkers, Richard; Coppens, Frederik; Bolser, Dan
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 unlocking the full potential of a multi-omics approach to plant science, the overarching goal of this workpackage is to make plant data 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 coautoring most of them. Their use has been demonstrated by exemplary application to data from diverse species published in public repositories.
Building from this previous work (Deliverable 7.1) we have now implemented anarchitecture for supporting access to distributed datasets annotated according to the developed standards. This architecture uses the Breeding API (BrAPI, www.brapi.org ), an API for accessing data relevant for plant breeding developed by the international plant community.
We have implemented 7 API endpoints over datasets held at the several ELIXIR nodes participating in the Plants Use Case, thereby publicly exposing these datasets and making them accessible and contributing for their interoperability and re-use. We further contributed to the evolution of BrAPI specification by working on the alignment with the MIAPPE ( www.miappe.org ) standard for plant phenotypic data, based on the experience with our exemplar data sets, and the needs of the Use Case. This work represents an important intermediate step towards the full implementation of an ELIXIR Plant Data Lookup Service currently under development.