WorldFAIR (D10.2) Agricultural Biodiversity Standards, Best Practices and Guidelines Recommendations: Tutorial

Although plant-pollinator datasets have become available worldwide, most of these datasets are published as supplementary files of research articles in a diversity of formats (WorldFAIR Deliverable 10.1, Trekels et al. 2023). In these cases, the FAIR principles (Findable, Accessible, Interoperable, and Reusable data, Wilkinson et al. 2016) are not fulfilled, which limits data retrieval and their use in subsequent integrative studies. Especially for datasets published as interaction networks, information regarding each interaction and species traits is still sparse, despite the efforts of numerous initiatives (Salim et al. 2022). 

Currently, the most used standard to share biodiversity data is Darwin Core (DwC, https://dwc.tdwg.org), which is a set of terms that allow capturing information about events, taxa and their occurrence in nature. The standard is extensible, so that particular information can be captured under discipline-specific terms. For plant-pollinator interactions in particular, a vocabulary of terms has been recently proposed by the Brazilian Network of Plant-Pollinator Interactions (REBIPP, https://www.rebipp.org.br, Salim et al. 2022). Thus, REBIPP terms can be used together with DwC to standardise plant-pollinator datasets and to make them accessible on different platforms, such as the REBIPP database.

The aim of this tutorial is to facilitate the standardisation of any spreadsheet containing plant-pollinator interaction data, and sharing the final product in the REBIPP platform. A standardised dataset can be shared in other platforms as well, such as GloBI (https://www.globalbioticinteractions.org) and GBIF (https://www.gbif.org/new-data-model) (see WorldFAIR Deliverables 10.2 and 10.3 for more information). The process of cleaning and standardising the data is done with OpenRefine (https://openrefine.org), a free, open source program useful for transforming biodiversity data en masse. Plant-pollinator databases may differ considerably in the level of detail of the information they contain and in how this information is presented, but we expect that every user will be able to standardise their own data by reproducing some of the steps detailed herein.

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WorldFAIR is funded by the EC HORIZON-WIDERA-2021-ERA-01-41 Coordination and Support Action under Grant Agreement No. 101058393.