Developing Data Interoperability using standards: A Wheat Community use case
The International Wheat Initiative (IWI) has identified easy access and interoperability of all wheat-related data as a top priority for the wheat research community (and agriculture in general), which is in line with FAIR (findable, accessible, interoperable, re-usable) data principles.
Interoperability - - understood as a the ability of two or more systems to cooperate to exchange and interpret shared data/information - - is a growing concern for different research communities - - as the need to interpret the deluge of (managed, published, and reused) data obtained through high-throughput technologies grows ...
To face the challenge of data interoperability in wheat research community, members of the Wheat Data Interoperability Working Group (WG)
- - one of the WGs of the Research Data Alliance (RDA) and the only WG of the Agriculture Data Interoperability Interest Group (IGAD) - -
This joint effort of the Wheat Research Community is presented in the recently published article :
Dzale Yeumo E, Alaux M, Arnaud E et al. Developing data interoperability using standards: A wheat community use case [version 1]. F1000Research 2017, 6:1843 (doi: 10.12688/f1000research.12234.1),
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A community-driven approach for data interoperability guidelines design, validation, publishing and adoption - - described in detail in the aforementioned article - - is generalizable to other (agricultural) domains.
In particular, built on existing standards and practices, the Wheat Data Interoperability Guidelines present a selected set of recommendations on how to publish and manage data types identified by the wheat research community as the most important for the coming years, such as:
sequence variants :
genome annotations :
germplasm data :
gene expression analysis measures the abundance of the mRNA molecules, and gives us insight into the regulation of the genes of interest.
The Wheat Data Interoperability Guidelines of the WDI-WG are intended for data producers, data managers, data consumers, and software developers.
The adoption of this guidelines - - that constitute a key building block for FAIR data sharing infrastructures - - will facilitate the depositing of data within well recognized repositories in addition to make them easily understandable and reusable.
- International Wheat Information System (WheatIS) - a single-access web base system to access to the available data resources and bioinformatics tools to support the wheat research community
- AgroPortal : a common unique repository of standard vocabularies and ontologies relevant for wheat. As of today, AgroPortal's Wheat group contains 20 ontologies of the 23 identified by the WDI-WG.
- IGAD Data Experts shared their Knowledge & Expertise at the RDA-IGAD Pre-Meeting in Montreal
- Dzalé Yeumo E, Fulss R, Alaux M, et al.: Wheat Data Interoperability Guidelines, Ontologies and User Cases. Recommendations from the RDA Wheat Data Interoperability Working Group. EUDAT B2Share.2017
- Subirats I, Cooper L, Shrestha R, et al.: Towards a Comprehensive Overview of Ontologies and Vocabularies for Research on Wheat. Zenodo. 2015