Task 6.3

Task 6.3: Data management activities on selected biological and biogeochemistry sensor types 

M1-36 (Lead: CEFAS).

In the following tasks WP6 will work with experts active in the “less mature” communities for the selected sensors providing biological parameters. The work for each sensor type will follow basically the same approach. The JERICO-S3 experts will bring together the leading group of experts (workshops) will identify the existing best practices, opportunities for standards, gaps and missing data, and provide co-design/co-development input in closing the gaps. Dissemination of the results will be under task 6.2 and will work via the representatives of the sensor communities in JERICO-S3.

Subtask 6.3.1: Biological imagery data (VLIZ, Hereon, CNRS (LOV-Sorbonne), (SMHI) (M1-42)

Instruments for measuring in situ and high frequency plankton diversity are now equipped with camera systems that produce a live time-series stream of millions of images. There is a clear need for describing best practices and develop a strategy towards data management of biological imagery data, ensuring effective data flow towards European data infrastructures. In order to draw up data management best practices that have the community consensus, we need to engage with the scientific data users and the experts operating the sensors to (a) Develop standardised protocol descriptions and minimal technical metadata elements for effective re-use; Identify and extension of appropriate vocabularies; (b) Identify tools for data integration and platforms for thrust-worthy long-term archival; (c) Map sensor-specific formats to standardized data formats to be ingested by European data infrastructures; (d) Discuss on meaningful spatial and temporal data aggregation (D6.4).

Subtask 6.3.2: Use of biological sensors for acquiring diversity and functionality data of the phytoplankton communities, (M1-42) (CEFAS, CNRS (LOG-ULCO), CNRS (MIO), SMHI, SYKE, VLIZ, IFREMER

Within the research area of phytoplankton observations, several communities are applying novel technology biological sensors to acquire diversity and functionality data. In WP5 they will focus on the data acquisition and standards of practice. As part of WP6 the focus will be to agree on a framework of data management Best Practices so the data collected by the different sensors can be published to the European data aggregators (EMODNet Biology, SeaDataNet). By using agreed and harmonised metadata, ontologies and exchange formats a richer understanding of the temporal and spatial variability in marine productivity will be created. In order to fulfil the objectives, (a) appropriate vocabulary will be identified, (b) Best Practices including standardised output formats and archiving approaches for flow cytometry, multispectral fluorescence will be defined in collaboration with European infrastructures (EMODNet Biology and SeadataNet, and at national and international levels.

NB: The data aspects and appropriate data flows towards EMODNet and ELIXIR for both the fast repetition rate fluorometry (FRRF) and DNA based approaches (omics) will be discussed as emerging technologies for plankton observation  (D6.5).

Subtask 6.3.3: Guidelines and strategy for carbonate systems data management, (M1-42) (IOW, FMI)
In the coastal seas high biological activity, river discharges, and variations in salinity create technical challenges for measuring various carbonate system components as well as modelling of carbonate system. The behaviour of carbonate system differs in ≠ coastal areas, even within regional seas. To understand the role of coastal seas in carbon-fluxes, and to provide data to study the impacts of climate change we need to develop a data management structure for carbonate systems. The task includes: (a) collection of regional protocols for carbonate system measurements, (b) identification of gaps; provide coastal observing community recommendations on best practices on carbonate system observations, (c) interact with ICOS-OTC and SOCAT on knowledge and support for standardization of coastal ecosystem carbonate system observations  (published in D6.8).

Deliverables

Task 6.3: D6.4 Best Practices guidelines & strategy for biological imagery data management (M26)

Task 6.3: D6.5 Best Practices guidelines & strategy for bio. optical sensor and functionality data management (M26)

Task 6.3: D6.8 Best practices guidelines and strategy for coastal carbonate systems data management (M36)