EMODnet Biology datasets enriched with standardized associated media information
The Flanders Marine Institute (VLIZ) acts as the coordination and information platform for marine and coastal-related scientific research in Flanders and serves as an international contact point. The Flanders Marine Data Centre (VMDC) is the VLIZ division with the mission to provide technologies and tools to scientists and policymakers, making high-quality data and information accessible to a wide range of marine sciences, while implementing a FAIR (Findable, Accessible, Interoperable, and Reusable) and Open data policy. It is heavily involved in the development and management of international e-infrastructures and services: EMODnet and the EMODnet Biology thematic lot, EMOD-PACE, LifeWatch Species Information Backbone and data systems, World Register of Marine Species (WoRMS), Global Sea Level Observing System (GLOSS), Ocean Biodiversity Information System (OBIS), Marine Data Archive, Integrated Marine Information System, Marine Regions. VLIZ is a National Oceanographic Data Centre in the network of the IODE programme of IOC-UNESCO and a regular member of the International Science Council World Data System (ICSU-WDS).
Challenges faced by the user
Imaging instruments are increasingly used to record species occurrences, and to repeatedly measure ecological traits. Publishing this information in international biodiversity data portals, allows users to obtain detailed taxonomic characterisation of taxa observations, as well as quantitative information that is useful for ecological studies. 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 in a standard format. Overcoming this challenge allows for the integration and exchange of these datasets, enabling end users to analyse and visualise them more effectively. Therefore, to make these data as FAIR as possible, recommendations to users of imaging instruments on how to format their data for submission to biodiversity international data portals following the OBIS-ENV-DATA format, a Darwin Core (DwC) based approach to standardise biodiversity data, are needed.
How does EMODnet support the user
The first steps to develop the guidelines on how to report imaging data (focusing on the specific case of plankton imaging) in a standardised manner, were to look at the different data outputs generated by the imaging instruments, identify the common metadata elements and map these to the DwC terms used in the OBIS-ENV-DATA format. Several additional DwC terms that were not commonly used in this format, were identified and a recommendation provided on how to populate them. Various meetings with EMODnet Biology data managers were necessary to discuss the appropriate use of the terms and how to populate them using existing controlled vocabularies. Their input was necessary as well for the creation of new controlled vocabularies specific to imaging metadata and how to fit these within the OBIS-ENV-DATA format. Thus, intensive interactions and feedback from the global marine plankton community and EMODnet Biology team were a significant part of this work. This collaboration, led to the development of the Best practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures (Cabrera et al., 2022). In this document, EMODnet Biology contributed with their expertise to the description on how to report plankton imaging data following the biodiversity data standards and formats.
Impact of EMODnet
As a result of this work, and to showcase how to apply the best practices to a dataset that includes this associated media information, the Explore Your Shore dataset, available via EMODnet Biology was updated. In particular, three additional DwC terms were included: IdentificationVerificationStatus, identificationReferences, and associatedMedia. With these new terms, users can have access to the images that are linked to the biological occurrences. When applied in a plankton imaging dataset, users will have the possibility to publish manually validated datasets or datasets produced by fully automated plankton identification workflows. This was possible again thanks to the technical team of EMODnet Biology, that added the terms to the databases and their workflows. In the future it is foreseen that plankton imaging data generators implement the recommendations and workflows presented in the best practices into their procedures, in order to share their data with EMODnet Biology, enriching the database with plankton imaging data derived from the different instruments.
Martin-Cabrera, P., Perez Perez, R., Irisson, J-O., Lombard, F., Möller, K.O., Rühl, S., Creach, V., Lindh, M., Stemmann, L. and Schepers, L. (2022) Best practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures. Ostend, Belgium, Flanders Marine Institute, 31pp. DOI: http://dx.doi.org/10.25607/OBP-1742
Flanders Marine Institute (VLIZ), Belgium (2022): Explore Your Shore. https://doi.org/10.14284/563
This work received financial and technical support; and is based on zooplankton imaging data; all provided through the LifeWatch project, a Flemish contribution to the LifeWatch ESFRI by VLIZ. The Best practices were developed under the JERICO-S3 project that received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 871153.