Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Patricia Martin-Cabrera (patricia.cabrera@vliz.be)
Received: 29 Aug 2022 | Published: 07 Sep 2022
© 2022 Patricia Martin-Cabrera, Ruben Perez Perez, Jean-Olivier Irrison, Fabien Lombard, Klas Ove Möller, Saskia Rühl, Veronique Creach, Markus Lindh, Lars Stemmann, Lennert Schepers
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Martin-Cabrera P, Perez Perez R, Irrison J-O, Lombard F, Ove Möller K, Rühl S, Creach V, Lindh M, Stemmann L, Schepers L (2022) Establishing Plankton Imagery Dataflows Towards International Biodiversity Data Aggregators. Biodiversity Information Science and Standards 6: e94196. https://doi.org/10.3897/biss.6.94196
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Over the last decade, plankton research has experienced extensive developments in automatic image acquisition for identifying and quantifying plankton species. This information is useful for the reporting of plankton occurrences and ecological data. Imagery instruments can vary in the way they sample (benchtop or in situ imagers) and the particle’s size range they target (see
The recommended data format follows the OBIS-ENV-DATA format (
Moreover, the OBIS-ENV-DATA format allows the ingestion of additional information thanks to the use of the Darwin Core (DwC) Extended Measurement Or Facts or eMoF extension in the DwC Event core. The eMoF stores biotic, abiotic and sampling measurements and facts that are related to the Event and Occurrence table. An important aspect of this extension is that it includes standardised terms and controlled vocabularies, such as the British Oceanographic Data Centre (BODC) vocabularies, to standardise parameters that are not covered by DwC. The advantages of these is to unambiguously report information and to include those measurements that cannot be reported in the Event and Occurrence table (e.g., reporting abundance or biomass of plankton), and that are crucial to investigate ecosystem functioning questions. As a consequence, biodiversity data aggregators can extend their scope beyond species occurrence data.
Fig.
Images are cropped and classified with software. This can be done in EcoTaxa, a web application that allows users to taxonomically classify images of individual organisms.
Data is formatted in OBIS-ENV-DATA format. This format can be exported from EcoTaxa through its API.
Data is submitted to EurOBIS via the IPT (Integrated Publishing Toolkit).
Data is quality controlled by the BioCheck tool.
Data in EurOBIS can flow to EMODnet Biology, OBIS and GBIF (Global Biodiversity Information Facility).
Plankton imagery instrument operators now have the possibility to format their data following the best practices and recommendations for plankton imagery data management (
The next steps are to disseminate these best practices, encouraging plankton imagery data generators to implement these workflows to share their data easily, enriching these data portals and encouraging cross collaborations to create data products covering broader geographic scales and plankton species.
imagery instruments, imagery data, Darwin Core, best practices
Patricia Martin-Cabrera
TDWG 2022
This work was supported by the JERICO-S3 project, that received funding from the European Union’s Horizon 2020 research and innovation programme, grant agreement no. 871153.
Flanders Marine Institute
Practical example of the data format proposed for plankton imagery data