JERICO-S3 D6.4 - WP6 - Best practices & recommendations for plankton imaging data management. Version 1.1.

Abstract

Plankton imaging instruments are increasingly used to record species occurrences, and they are also able to repeatedly measure ecological traits. However, due to the extensive variety of instruments and the different formats of the data output, there are currently no guidelines and best practices available to store all the relevant data and information in a standard format. Overcoming this challenge will allow for the integration and exchange of these datasets, enabling end users to analyse and visualise them more effectively. To make these data as FAIR (Findable, Accessible, Interoperable, and Reusable) as possible and to share them with international biodiversity data portals, such as the European Marine Observation and Data Network (EMODnet Biology) and the international Ocean Biodiversity Information System (OBIS) Network, like EurOBIS (the European node of OBIS), best practices for the management of plankton imaging data are needed. Thus, the goal of this document is to provide recommendations to plankton imaging users on how to format their data following the OBIS-ENV-DATA format, a Darwin Core based approach to standardise biodiversity data, for submission to these international data portals. These best practices and recommendations are created by an expert working group in the framework of the JERICO-S3 project and by intensive interactions and feedback from the global marine plankton and OBIS community. This document provides (1) an introduction of the current landscape of plankton imaging instruments and the processing of their images, (2) a description of the data standards and format used in biodiversity and guidelines on how to use these, (3) a workflow from instrument to EMODnet Biology, and (4) a discussion on the data management issues identified. With the best practices presented here, it is possible to report a detailed taxonomic characterisation of plankton observations as well as quantitative information that is useful for ecological studies. This format allows biodiversity data portals to extend their scope beyond species occurrence data. Furthermore, proposing the use of more Darwin Core fields in this format, users now have the possibility to publish manually validated datasets, but also datasets produced by fully automated plankton identification workflows. The proposed data and file formats are simple and both human- and machine-readable to automatise workflows. This format will allow data generators to submit enriched plankton imaging datasets to the international biodiversity data portals, (Eur)OBIS and EMODnet Biology. We encourage plankton imaging data generators to implement these workflows into their pipelines, to share their data with the international data portals easily, enriching these databases with this valuable data.