2016
Plant Biology Europe EPSO / FESBP 2016 Congress (2016-06-26-2016-06-30) Prague (CZE). 2016.
08 Aug 2016 Contribution to a European roadmap for data standardisation in Plant Science at URGI-INRAPommier, C. ; Alaux, M. ; Dzale Yeumo, W. E. ; Cornut, G. ; Durand, S. ; Flores, R.-G. ; Kimmel, E. ; Letellier, T. ; Michotey, C. ; Mohellibi, N. ; Quesneville, H. ; Adam-Blondon, A.-F.
A roadmap on data standards in plant science has been developed by an ERA-CAPs ad hoc expert working groups. It underlines the main problems that are to be faced in order to make the data produced by plant researchers more accessible and re-usable. The expert working group proposes to foster by different means the community-based development of ad hoc standards for data and experiments, their support by common infrastructures and their enforcement by broad-base incentives.
URGI-INRA has been involved in the last 6 years in several projects (e.g. FP7 TransPLANT) or initiatives (Wheat Initiative, Research Data Alliance) contributing (i) to the development of community recommendations for data standardisation (e.g. wheatis.org), (ii) data standards for phenotyping data (MIAPPE; http://cropnet.pl/phenotypes/?page_id=15 ), (iii) crop specific ontologies in the frame of the CropOntology ( www.cropontology.org ) aiming at facilitating the capture of the data produced in large projects with a standard and structured vocabulary. The recommendation are implemented in our information system by different means : forcing the collection of metadata or of ontology driven variables, extraction of data from GnpIS in standard formats (e.g. MIAPPE compatible Isa-Tab format for phenotypic data). We are actively promoting the standards in the French community using as levers large French scientific projects centered around species (Wheat, Maize, Rapeseed, SunFlower, Pea and Sugar Beet) or infrastructures such as Phenome (the French node of the European Plant Phenotyping Network, EPPN) or our network of Plant Biological Resources Centers. We are also contributing to the BreedingAPI initiative, which objective is to design a standard Application Programming Interfaces for plant genetics and breeding.
The objective is to continue these efforts in the frame of on going projects such as Elixir-Excelerate, OpenMinTED or IFB Plant node (Elixir French node). In addition, we will focus on the identification of biological material (compliant with DivSeek objectives), contribute to the mapping of our crop ontologies to reference ontologies in collaboration with the Planteome project and start to develop FAIR compliant API.
Creation date: 30 Sep 2016
eZ PublishPublication supervisor: A-F. Adam-Blondon
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