JERICO Community Practices
https://repository.oceanbestpractices.org/handle/11329/362
2024-03-28T16:43:58ZJERICO-S3 D6.4 - WP6 - Best practices & recommendations for plankton imaging data management. Version 1.1.
https://repository.oceanbestpractices.org/handle/11329/2360
JERICO-S3 D6.4 - WP6 - Best practices & recommendations for plankton imaging data management. Version 1.1.
Martin-Cabrera, Patricia; Irisson, Jean-Olivier; Lombard, Fabien; Rühl, Saskia; Möller, Klas O.; Lindh, Markus; Creach, Veronique; Stemmann, Lars; Schepers, Lennert
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.
2023-01-01T00:00:00ZJERICO-S3 D6.3 - Data Management Best practices report for physical and BGC platforms. Version 2.0.
https://repository.oceanbestpractices.org/handle/11329/2359
JERICO-S3 D6.3 - Data Management Best practices report for physical and BGC platforms. Version 2.0.
Voynova, Yoana; Corgnati, Lorenzo; Zarokanellos, Nikolaos; Charcos, Miguel; Anastasopoulou, Gerasimi; Perivoliotis, Leonidas
This document provides information on the data management best practices for three widely used platforms for the data collection in the coastal zone: HF-Radars, ocean gliders and FerryBoxes. The existing standards and best practices from marine community efforts were reviewed and compiled by specific JERICO-S3 partners (CNR for HF-Radars, SOCIB for Gliders and Hereon for FerryBoxes) all selected due to their long experience, and expertise.
The provided best practices and standards in this report regard the processing steps from the acquisition to the data delivery for each platform, the best practices concerning the data processing, the quality control and quality assurance (both in NRT and DM), the upcoming issues and vulnerabilities of the data management encountered in each platform, training materials and contacts, as well as examples of data management plans. The implementation of the best practices described in this document is expected to increase the data FAIRness, facilitating the data integration into the relevant European Data aggregators, such as the Copernicus Marine, the EMODnet and the SeaDataNet.
2022-01-01T00:00:00ZJERICO-S3 D.5.5 - WP5 - Report on the functional homogenization tools that will support the implementation of best practices within the JERICO-RI. Version 1.0.
https://repository.oceanbestpractices.org/handle/11329/2358
JERICO-S3 D.5.5 - WP5 - Report on the functional homogenization tools that will support the implementation of best practices within the JERICO-RI. Version 1.0.
Mantovani, Carlo; Charcos, Miguel; Corgnati, Lorenzo; Fernández, Juan Gabriel; Frontera, Biel; Notario, Xisco; Pearlman, Jay; Reyes, Emma; Solabarrieta, Lohitzune; Zarokanellos, Nikolaos
This document describes a series of functional tools available for the JERICO-RI community supporting the harmonized management of mature coastal observing platforms as described in JERICO-S3 D5.2, namely Mooring, FerryBox, High Frequency Radar, Underwater Glider.
They include tools entirely designed and realized within JERICO-S3 and tools that have received a substantial contribution from JERICO-S3 discussions, deliverables, workshops, and have been developed in a collaborative framework with other projects.
Tools span from software routines for data management and data Quality Control to web applications for joint management of platform issues to methods and guidelines for structuring practices documentation and assessing their maturity level.
After the introduction, a main section contains the descriptions of each tool according to a uniform scheme.
First, a table is provided summarizing key information like the tool’s purpose, scope of applicability, the link to the tool itself and to its documentation.
Then, the tool and its features are described with a minimum level of detail. A second paragraph highlights the added value and contribution deriving from actual and/or previous work in JERICO projects, aimed at supporting the tool development. The contribution could be in terms of best practices, deliverables, workshops, surveys, etc.
The last paragraph is dedicated to the foreseen and potential use of the tool in a wider context and/or as a component or framework for other tools.
2023-01-01T00:00:00ZJERICO-S3 D5.4 – WP5 - Recommendation for Multiplatform implementation of a biogeochemical NRT observatory. Version 2.1.
https://repository.oceanbestpractices.org/handle/11329/2357
JERICO-S3 D5.4 – WP5 - Recommendation for Multiplatform implementation of a biogeochemical NRT observatory. Version 2.1.
King, Andrew; Marty, Sabine; Roden, Nicholas; Frigstad, Helene; Coppola, Laurent; Ntoumas, Manolis; Frangoulis, Constantin; Cantoni, Carolina; Zarokanellos, Nikolaos; Seppälä, Jukka
This Deliverable provides recommendations for multiplatform implementation of near real-time biogeochemical observations within the JERICO-S3 coastal observing framework. Near real-time sensor-based observations of the biogeochemical Essential Ocean Variables (EOVs) – dissolved oxygen, inorganic carbon, dissolved organic matter, and nutrients – are described in the first section of the Main Report. This is followed by five examples from JERICO-S3 Integrated Regional Sites (IRS) and Pilot Supersites (PSS) where multiplatform biogeochemical observations have been carried out, and how multiplatform observations have been performed. The main recommendations, due in part to the high degree of difficulty in making high quality biogeochemical observations, include utilising a well-constrained (near) real-time quality control (QC) system informed by existing datasets and model outputs, validate/compare observations made by complementary observing platforms (including other autonomous platforms, remote sensing products, etc.; i.e., multiplatform approach), and finally validation via traditional oceanographic (research vessel-based) sampling and laboratory analytical techniques.
2023-01-01T00:00:00ZDeliverable D.5.3, WP5: Report on the Key Platform Performance Indicators and Key Integration Performance Indicators developed for the JERICO-RI. Version 3.0.
https://repository.oceanbestpractices.org/handle/11329/2356
Deliverable D.5.3, WP5: Report on the Key Platform Performance Indicators and Key Integration Performance Indicators developed for the JERICO-RI. Version 3.0.
Nair, Rajesh; Pearlman, Jay; Coppola, Laurent; Mader, Julien; Mantovani, Carlo
This document reports on the development of Key Platform Performance Indicators and Key Integration Performance Indicators for assessing the performances of the observing platforms of the JERICO-RI, including the level of their integration at the network level. The activity forms part of Work Package 5 (“Harmonisation of integrated Multiplatform & Multidisciplinary systems“) of JERICO-S3, specifically, Task 5.4 (“Performance Monitoring for the operation and integration of JERICO-RI platforms”), which gathers together the approaches and recommendations of 9 partners of the project.
2022-01-01T00:00:00ZJERICO-S3 Deliverable 5.2. Electronic Handbook for Mature Platforms: Mooring - HF Radar - FerryBox – Glider. Version 1.1.
https://repository.oceanbestpractices.org/handle/11329/2344
JERICO-S3 Deliverable 5.2. Electronic Handbook for Mature Platforms: Mooring - HF Radar - FerryBox – Glider. Version 1.1.
Mantovani, Carlo; Pearlman, Jay; Simpson, Pauline; Corgnati, Lorenzo; Ntoumas, Manolis; Zarokanellos, Nikolaos D.; Voynova, Yoana G.; Möller, Klas Ove
Mantovani, Carlo; Pearlman, Jay; Simpson, Pauline
Harmonization across monitoring of coastal Europe has been an emphasis of the JERICO projects. The monitoring resources span geography, diversity of sensors and platforms, and the availability of local resources. With the growing importance of sustainability and understanding of the impacts of human activity on the sea, having a comprehensive and holistic perspective on the coastal seas is essential. This has been expressed through the Marine Strategy Framework Directive1 (MSFD) , https://ec.europa.eu/environment/marine/eu-coast-and-marine-policy/marine-strategy-framework-directive/index_en.htm and other European documents as well as national imperatives.
Coastal monitoring has been supported by national and project resources. Creating a harmonized European-wide Research infrastructure for coastal observing and information is a primary goal of JERICO [Farcy, et al, 2019]. Harmonization encompasses many actions. An important one is that data are collected according to commonly-accepted procedures and are interoperable. For this, a series of best practices is evolving for methods used in data collection and, more broadly, in the creation of decisionable information.
JERICO has been motivating the creation of best practices for over a decade and has documented procedures in all aspects of coastal observations. These procedures come in many forms (e.g., standard operating procedures or manuals) with varying levels of acceptance and maturity. In some cases, there may be multiple procedures to achieve the same objective, with the result that the selection of the best procedure is unclear.
This report addresses some of these challenges by introducing a refined scale of best practice maturity levels. These levels cover two key objectives: the status of the methods documentation and the degree to which the methods have been widely and effectively implemented. This is done through “A Best Practices Maturity Model for Methods and their Applications'', which is introduced for the first time (see the Introduction for more information). The report then collects the best practice documents of JERICO and looks at their levels of maturity.
This report addresses best practices in the context of four mature JERICO observation networks: moorings, high frequency radar coastal monitoring, ferry boxes and underwater gliders. These systems are described in detail, covering the platform, the sensors and, with the exception of the moorings, the data management. With this background, the best practices related to each of the systems are given. The practices that exist are important for interoperability and trust in the data, but there are gaps in practices and these will need to be identified and addressed.
2023-01-01T00:00:00ZBest practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures. Version 1.
https://repository.oceanbestpractices.org/handle/11329/1917
Best practices and recommendations for plankton imaging data management: Ensuring effective data flow towards European data infrastructures. Version 1.
Martin-Cabrera, Patricia; Perez Perez, Ruben; Irisson, Jean-Olivier; Lombard, Fabien; Möller, Klas Ove; Rühl, Saskia; Creach, Veronique; Lindh, Markus; Stemmann, Lars; Schepers, Lennert
Martin-Cabrera, Patricia
The best practices and recommendations for plankton imaging data management enable users 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.
2022-01-01T00:00:00ZDocument describing the biological data. JERICO-NEXT WP5, Deliverable D5.5, Version 3.
https://repository.oceanbestpractices.org/handle/11329/1548
Document describing the biological data. JERICO-NEXT WP5, Deliverable D5.5, Version 3.
Oset, P.
Integration of biological data(Task 5.2) in coastal observatories has been one of the key objectives of the JERICO-NEXT project. Biological data collection has taken place in the framework of JRAP1 and JRAP2 (planktonic and benthic communities) using both traditional and novel observing methodologies.The objective of this task is to provide an operational link between EMODnet Biology and JERICO-NEXT, and to make the JRAP1 and JRAP2 data discoverable by users and increase its FAIRness. All the biological data in the project has been described and is findable in the EMODnet Biology catalogue and through a map viewer interface. To ensure its reusability, dataset descriptions contain machine-readable licenses that have been agreed with the data providers. A considerable amount of these data is nowaccessible via EMODnet Biology through different mechanisms: a) links to local data systems or repositories; b) a download link to data files in the Marine Data Archive; c) direct download from EMODnet Biology or integrated in the EMODnet Biology download toolbox. The method chosen depends on the degree or the standardisation possibilities that the data outputs offer. Making the biological data from novel sensors interoperable remains a challenge due to a lack of mature standards for data types that are still in earlier stage of development. Significant improvements have been achieved in the framework of the Sea Data Cloud project to develop controlled vocabularies for Flowcytometry (FCM) data. During the length of the project, EMODnet Biology and OBIS have transitionedto a new data schema (Darwin Core OBIS-ENV) which brings more flexibility and allows the inclusion of new data types (both biotic and abiotic). The upgraded data schema has allowed for the integration of tests FCM datasets in EMODnet Biology which, together with new developments in the download toolbox, have made JERICO-NEXT data discoverable at the record levelin the EMODnet Biology portal.Despite these achievements, significant efforts are needed in terms of harmonisation throughout all the data management phases, definition of best practices and development of semantic standards for these new data types. This is the only way to ensure thatwe can exploit the monitoring capabilities of these novel observation methodologies with the appropriate certainty. These should be priorities during the next phase of JERICO-RI. However, it also needs to be recognised that putting data management into practice and opening the data is a resource consuming activity, both at the end-side of the chain (i.e. data aggregators or repositories), but also for data collectors and scientists at the initial steps. Data management needs to be appropriately funded throughout all these different stages to avoid potential bottlenecks, which might hinder the actual publication of data.
2019-01-01T00:00:00ZQA best practices and protocols on QC for radial and total HF radar data (INCREASE WP3, D3.1).
https://repository.oceanbestpractices.org/handle/11329/1538
QA best practices and protocols on QC for radial and total HF radar data (INCREASE WP3, D3.1).
This document is the deliverable D.3.1 from INCREASE WP3. In the last months, there has been intense exchange within the European HFR experts for the definition of standards QA and QC procedures. This progress has been achieved in collaboration with JERICO-Next project and has been shared and supported by the HF radar community through INCREASE project efforts (INCREASE HFR Experts Workshop, September 2016). In this context, WP3 will make a step forward, focusing on the practical aspects linked to their implementation to real data. The main goal of this deliverable is to provide a demonstration on the application of these procedures, which will be the basis for the development of INCREASE HFR basic products (M3.1).
2017-01-01T00:00:00ZWhite paper on dissolved oxygen measurements: scientific needs and sensors accuracy.
https://repository.oceanbestpractices.org/handle/11329/1524
White paper on dissolved oxygen measurements: scientific needs and sensors accuracy.
Coppola, Laurent; Salvetat, Florence; Delauney, Laurent; Machoczek, Detlev; Karstensen, Johannes; Sparnocchia, Stefania; Thierry, Virginie; Hydes, David; Haller, Michael; Nair, Rajesh; Lefevre, Dominique
The objective here is to review the practical accuracy and the precision of the existing oxygen sensors used in oceanography. The idea is to review all oxygen sensors mounted on fixed and lagrangian platforms (mooring, CTD profiler, glider, ARGO floats) used on coastal observatories. This report synthetizes the past experiences and recommendations for a better use of oxygen sensors in order to improve the quality of the oxygen data for scientific exploitations.
2013-01-01T00:00:00Z