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

The Ocean Biogeographic Information System (OBIS) is the world's most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.Fil: De Pooter, Daphnis. Flanders Marine Institute; BélgicaFil: Appeltans, Ward. UNESCO-IOC; BélgicaFil: Bailly, Nicolas. Hellenic Centre for Marine Research, MedOBIS; GreciaFil: Bristol, Sky. United States Geological Survey; Estados UnidosFil: Deneudt, Klaas. Flanders Marine Institute; BélgicaFil: Eliezer, Menashè. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Fujioka, Ei. University Of Duke. Nicholas School Of Environment. Duke Marine Lab; Estados UnidosFil: Giorgetti, Alessandra. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Goldstein, Philip. University of Colorado Museum of Natural History, OBIS; Estados UnidosFil: Lewis, Mirtha Noemi. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Lipizer, Marina. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Mackay, Kevin. National Institute of Water and Atmospheric Research; Nueva ZelandaFil: Marin, Maria Rosa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Moncoiffé, Gwenaëlle. British Oceanographic Data Center; Reino UnidoFil: Nikolopoulou, Stamatina. Hellenic Centre for Marine Research, MedOBIS; GreciaFil: Provoost, Pieter. UNESCO-IOC; BélgicaFil: Rauch, Shannon. Woods Hole Oceanographic Institution; Estados UnidosFil: Roubicek, Andres. CSIRO Oceans and Atmosphere; AustraliaFil: Torres, Carlos. Universidad Autonoma de Baja California Sur; MéxicoFil: van de Putte, Anton. Royal Belgian Institute for Natural Sciences; BélgicaFil: Vandepitte, Leen. Flanders Marine Institute; BélgicaFil: Vanhoorne, Bart. Flanders Marine Institute; BélgicaFil: Vinci, Mateo. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Wambiji, Nina. Kenya Marine and Fisheries Research Institute; KeniaFil: Watts, David. CSIRO Oceans and Atmosphere; AustraliaFil: Klein Salas, Eduardo. Universidad Simon Bolivar; VenezuelaFil: Hernandez, Francisco. Flanders Marine Institute; Bélgic

The Experimental MJO Prediction Project

Weather prediction is typically concerned with lead times of hours to days, while seasonal-to-interannual climate prediction is concerned with lead times of months to seasons. Recently, there has been growing interest in 'subseasonal' forecasts---those that have lead times on the order of weeks (e.g., Schubert et al. 2002; Waliser et al. 2003; Waliser et al. 2005). The basis for developing and exploiting subseasonal predictions largely resides with phenomena such as the Pacific North American (PNA) pattern, the North Atlantic oscillation (NAO), the Madden-Julian Oscillation (MJO), mid-latitude blocking, and the memory associated with soil moisture, as well as modeling techniques that rely on both initial conditions and slowly varying boundary conditions (e.g., tropical Pacific SST). An outgrowth of this interest has been the development of an Experimental MJO Prediction Project (EMPP). Th project provides real-time weather and climate information and predictions for a variety of applications, broadly encompassing the subseasonal weather-climate connection. Th focus is on the MJO because it represents a repeatable, low-frequency phenomenon. MJO's importance among the subseasonal phenomena is very similar to that of El Nino-Southern Oscillation(ENSO) among the interannual phenomena. This note describes the history and objectives of EMPP, its status,capabilities, and plans

Figure 3 from: De Pooter D, Appeltans W, Bailly N, Bristol S, Deneudt K, Eliezer M, Fujioka E, Giorgetti A, Goldstein P, Lewis M, Lipizer M, Mackay K, Marin M, Moncoiffé G, Nikolopoulou S, Provoost P, Rauch S, Roubicek A, Torres C, van de Putte A, Vandepitte L, Vanhoorne B, Vinci M, Wambiji N, Watts D, Klein Salas E, Hernandez F (2017) Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences. Biodiversity Data Journal 5: e10989. https://doi.org/10.3897/BDJ.5.e10989

Figure 3 - A practical example of Option 1: Occurrence Core combined with MoF Extension. The temperature measurement is duplicated for both occurrences

Expanding the Ocean Biogeographic Information System (OBIS) beyond species occurrences

The Ocean Biogeographic Information System (OBIS) aims to integrate smaller, isolated datasets into a larger, more comprehensive picture of life in our oceans. Therefore, OBIS provides a gateway to many datasets containing information on where and when marine species have been observed. The datasets within OBIS are contributed by a network of hundreds of institutes, projects and individuals, all with the common goal to gain scientific knowledge and to make these data and knowledge easily available to the public. Until recently, OBIS had solely focused on biogeographic data, in the form of presence of marine species in space and time. Data collected for biological studies however often include more than just presence or abundance. Physical and chemical measurements are often taken concomitantly providing insights into the environmental conditions the species live in. Details on the nature of the sampling methods, equipment used and effort can also be of major importance. Based on requirements from the growing OBIS community for data archiving and scientific applications, OBIS completed the OBIS-ENV-DATA project in 2017 to enhance its data standard by accommodating additional data types (De Pooter et al. 2017). The proposed standard allows for the management of sampling methodology, animal tracking and telemetry data, and environmental measurements such as nutrient concentrations, sediment characteristics and other abiotic parameters measured during sampling. The new OBIS data standard builds on the Darwin Core Archive and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of an Event Core in combination with an Occurrence Extension and an enhanced MeasurementOrFact Extension Fig. 1. This new structure enables the linkage of measurements or facts - quantitative or qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. The OBIS standard also embraces the use of the new Darwin Core term parentEventID, enabling a sampling event hierarchy. During the follow-up project “OBIS-Event Data”, the format will be further fine-tuned during two workshops with two different communities of practice. The first workshop (April 2018) will focus on animal tagging and tracking data, while the second one (October 2018) will tackle macro- and meiobenthos data. The OBIS-Event Data project will also develop the first data products and applications based on the standard and make these tools part of the core OBIS data system output. We believe that the adoption of this new data standard by the international community will be key to improving the effectiveness of the knowledge base and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean