Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

Pooter, D. De; Appeltans, Ward; Bailly, Nicolas; Bristol, S.; Deneudt, K.; Eliezer, Menashè; Fujioka, Ei; Giorgetti, Alessandra; Goldstein, Philip; Lewis, Mirtha; Lipizer, Marina; Mackay, Kevin; Marín, María Rosa; Moncoiffé, Gwenaëlle; Nikolopoulou, Stamatina; Provoost, Pieter; Rauch, Shannon; Roubicek, A.; Torres, Carlos R.; Putte, Anton P. Van de; Vandepitte, L.; Vanhoorne, B.; Vinci, Matteo; Wambiji, Nina; Watts, D. J.; Salas, Eduardo; Hernández, F.

doi:10.3897/bdj.5.e10989

Cited by 66 publications

(56 citation statements)

References 16 publications

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“…OBIS‐ENV‐DATA is an adaptation of the Darwin Core Archive (DwC‐A) scheme specifically designed for sample‐based marine biological data. This format allows to package taxonomic and environmental data, together with sampling related information, in a single, self‐contained dataset (De Pooter et al , ). In the OBIS‐ENV‐DATA standard, the DwC‐A file consists of an Event core linked to two extensions namely: Occurrence extension and ExtendedMeasurementOrFact extension (eMoF).…”

Section: Dataset Location and Formatmentioning

confidence: 99%

LifeWatch observatory data: Zooplankton observations in the Belgian part of the North Sea

Mortelmans

Goossens

Martínez

et al. 2019

Geoscience Data Journal

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Through regular sampling surveys, the Flanders Marine Institute (VLIZ) is generating a long‐term data series for the Belgian coastal water and sandbank system, a designated site in the Long Term Ecological Research (LTER) network. The data series is built from sampling activities initiated in 2012 in the framework of the LifeWatch marine observatory. Nine nearshore stations are sampled monthly, with an additional eight offshore stations sampled seasonally. This paper presents the generated data series for zooplankton densities and size measurements, analysed using a ZooScan plankton imaging device together with the ZooProcess and Plankton Identifier software packages. To date 673.017 biological particles have been collected and identified. The collection and processing of the 2012–2018 dataset is described, along with its data curation and quality control. Yearly versions of the data are published in a standardized format together with environmental parameters, accompanied by an extensive metadata description and labelled with digital identifiers for traceability. The data are published under a CC‐BY 4.0 license, allowing use of the data under the condition of providing the reference to the original source.

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Section: Dataset Location and Formatmentioning

confidence: 99%

LifeWatch observatory data: Zooplankton observations in the Belgian part of the North Sea

Mortelmans

Goossens

Martínez

et al. 2019

Geoscience Data Journal

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“…The Ocean Biogeographic Information System (OBIS) began in 2000 as the repository for data from the Census of Marine Life. Since that time, OBIS has expanded its goals beyond simply hosting data to supporting more aspects of marine conservation (Pooter et al 2017). In order to accomplish those goals, the OBIS secretariat in partnership with its European node (EurOBIS) hosted at the Flanders Marine Institute (VLIZ, Belgium), and the Intergovernmental Oceanographic Commission (IOC) Committee on…”

Section: Introductionmentioning

confidence: 99%

Outcomes of the International Oceanographic Data and Information Exchange Ocean Biogeographic Information System OBIS-Event-Data Workshop on Animal Tagging and Tracking

Benson¹,

Appeltans²,

Bajona³

et al. 2018

BISS

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The Ocean Biogeographic Information System (OBIS) began in 2000 as the repository for data from the Census of Marine Life. Since that time, OBIS has expanded its goals beyond simply hosting data to supporting more aspects of marine conservation (Pooter et al. 2017). In order to accomplish those goals, the OBIS secretariat in partnership with its European node (EurOBIS) hosted at the Flanders Marine Institute (VLIZ, Belgium), and the Intergovernmental Oceanographic Commission (IOC) Committee on International Oceanographic Data and Information Exchange (IODE, 23rd session, March 2015, Brugge) established a 2-year pilot project to address a particularly problematic issue that environmental data collected as part of marine biological research were being disassociated from the biological data. OBIS-Event-Data is the solution that was developed from that pilot project, which devised a method for keeping environmental data together with the biological data (Pooter et al. 2017). OBIS is seeking early adopters of the new data standard OBIS-Event-Data from among the marine biodiversity monitoring communities, to further validate the data standard, and develop data products and scientific applications to support the enhancement of Biological and Ecosystem Essential Ocean Variables (EOVs) in the framework of the Global Ocean Observing System (GOOS) and the Marine Biodiversity Observation Network of the Group on Earth Observations (GEO BON MBON). After the successful 2-year IODE pilot project OBIS-ENV-DATA, the IOC established a new 2-year IODE pilot project OBIS-Event-Data for Scientific Applications (2017-2019). The OBIS-Event-Data data standard, building on Darwin Core, provides a technical solution for combined biological and environmental data, and incorporates details about sampling methods and effort, including event hierarchy. It also implements standardization of parameters involved in biological, environmental, and sampling details using an international standard controlled vocabulary (British Oceanographic Data Centre Natural Environment Research Council). A workshop organized by IODE/OBIS in April brought together major animal tagging and tracking networks such as the Ocean Tracking Network (OTN), the Animal Telemetry Network (ATN), the Integrated Marine Observing System (IMOS), the European Tracking Network (ETN) and the Acoustic Tracking Array Platform (ATAP) to test the OBIS-Event-Data standard through the development of some data products and science applications. Additionally, this workshop contributes to the further maturation of the GOOS EOV on fish as well as the EOV on birds, mammals and turtles. We will present the outcomes as well as any lessons learned from this workshop on problems, solutions, and applications of using Darwin Core/OBIS-Event-Data for bio-logging data.

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“…Nkem et al, 2006;Pinkerton et al, 2010). Initiatives such as the OBIS-ENV-DATA pilot project, established to combine biological, physical and chemical data sets within the same repository, are a major step forward in this direction (De Pooter et al, 2017), being similar to the approach of the research programme Antarctic Near-shore and Terrestrial Observing System (ANTOS; www.scar.org/ssg/life-sciences/antos, last access: 20 September 2017). The US Long Term Ecological Research Sites of the McMurdo Dry Valleys (terrestrial) and Palmer Station on the Antarctic Peninsula (marine), and the French Long Term Ecological Research PROTEKER observatory at the Kerguelen Islands, are examples of long-term field observations of physical processes and ecosystem change.…”

Section: Background and Justificationmentioning

confidence: 99%

Cross-disciplinarity in the advance of Antarctic ecosystem research

et al. 2018

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Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

Cited by 66 publications

References 16 publications

LifeWatch observatory data: Zooplankton observations in the Belgian part of the North Sea

LifeWatch observatory data: Zooplankton observations in the Belgian part of the North Sea

Outcomes of the International Oceanographic Data and Information Exchange Ocean Biogeographic Information System OBIS-Event-Data Workshop on Animal Tagging and Tracking

Cross-disciplinarity in the advance of Antarctic ecosystem research

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