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1. Tunabio: biological traits of tropical tuna and bycatch species caught by purse seine fisheries in the Western Indian and Eastern Central Atlantic Oceans

Author

Aurelie Guillou, Nathalie Bodin, Emmanuel Chassot, Antoine Duparc, Théotime Fily, Philippe Sabarros, Mathieu Depetris, Monin Amandè, Juliette Lucas, Emilie Augustin, N’guessan Diaha, Laurent Floch, Julien Barde, Pedro Pascual-Alayón, José Carlos Báez, Pascal Cauquil, Karine Briand, and Julien Lebranchu

Subjects
tropical tunas, bycatch fish, purse seine, length-, Biology (General), QH301-705.5
Abstract

Along with the development of the tropical tuna purse-seine fishery from the 1960s in the Atlantic Ocean and from the 1980s in the Indian Ocean, many projects and studies have been conducted to improve knowledge about the biology, migrations and dynamics of the stocks of target and non-target (i.e. bycatch) species taken in these fisheries. Since the 2000s, the European Union (EU) has been supporting Member States in the collection of biological data on species caught by their purse seine and pole and line fisheries, thus making it possible to have a long-term series of data. Biological data have never been saved by the different tuna commissions, unlike the catches by species and sizes by areas and periods. However, these data are essential to monitor the status of the fisheries and fuel the assessment models used by the tuna Regional Fisheries Management Organisations (tRFMOs) for the sustainable management and conservation of the fish stocks under their mandate.We combined historical (1974-1999) and current (2003-2020) datasets on the biology of tropical tunas and bycatch fish caught by large-scale purse seiners in the Eastern Atlantic Ocean (EAO) and Western Indian Ocean (WIO). The resulting Tunabio database is presented in the present data paper and contains all available morphometric and biological data collected on more than 80,000 fish individuals.

Published
2022
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2. A user-centric metadata model to foster sharing and reuse of multidisciplinary datasets in environmental and life sciences

Author

Julien Barde, Valentina Beretta, Muhammad Arslan, Jean-Christophe Desconnets, Véronique Chaffard, Isabelle Mougenot, UMR 228 Espace-Dev, Espace pour le développement, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Institut des Géosciences de l’Environnement (IGE), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)-Université de Guyane (UG)-Université des Antilles (UA), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )

Subjects
[SPI.OTHER]Engineering Sciences [physics]/Other, Interdisciplinary datasets, Computer science, Data management, 0208 environmental biotechnology, 02 engineering and technology, Reuse, 010502 geochemistry & geophysics, ENVIRONNEMENT, 01 natural sciences, Semantic heterogeneity, OCEANOGRAPHIE BIOLOGIQUE, Computers in Earth Sciences, 0105 earth and related environmental sciences, User-centered design, TRAITEMENT DE DONNEES, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], FAIR principles, INFORMATIQUE SCIENTIFIQUE, business.industry, DONNEES SATELLITE, SEMANTIQUE, Metadata modeling, Data science, MODELISATION, Semantics, 020801 environmental engineering, Metadata, Data sharing, Semantic metadata model, [SDE]Environmental Sciences, business, Lightweight ontology, Information Systems
Abstract

The recent technological advancements and emergence of the open data in environmental and life sciences are opening new research opportunities while creating new challenges around data management. They make available an unprecedented amount of data that can be exploited for studying complex phenomena. However, new challenges related to data management need to be addressed to ensure effective data sharing, discovery and reuse, especially when dealing with interdisciplinary research contexts. These issues are magnified in interdisciplinary context, by the fact that each discipline has its practices, e.g., specific formats and metadata standards. Moreover, the majority of current data management practices do not consider semantic heterogeneity existing among disciplines. For this reason, we introduce a flexible metadata model that describes the datasets of various disciplines using a common paradigm based on the observation concept. It provides a key vision for articulating the user point of view and underlying scientific domains. In this study, we therefore decide to mainly reuse the SOSA lightweight ontology (Sensor, Observation, Sample, and Actuator) to efficiently leverage others existing ontologies to improve datasets discovery and reuse coming from Earth and life observation. The main benefit of the proposed metadata model is that it extends the technical description, usually provided by existing metadata models, with the observation context description enabling the need of a user viewpoint. Moreover, following the FAIR principles, the metadata model specifies the semantics of its elements using ontologies and vocabularies, and reuses as much as possible ontological and terminological existing resources. We show the benefit and applicability of the model through a case study we identified as representative after interviewing researchers in environmental and life sciences.

Published
2021

3. Fish aggregating devices drift like oceanographic drifters in the near-surface currents of the Atlantic and Indian Oceans

Author

Christophe Lett, Jean-François Ternon, T. Imzilen, A. Maufroy, Hervé Demarcq, Emmanuel Chassot, Julien Barde, L. Roa-Pascuali, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Fishing, satellite, Fisheries, FOS: Physical sciences, Aquatic Science, Oceanography, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, pacific, Lagrangian transport, wind, 14. Life underwater, driven, science, 0105 earth and related environmental sciences, search, Surface currents, business.industry, 010604 marine biology & hydrobiology, Ocean current, Geology, Fish aggregating device, tuna purse seiners, Current (stream), Drifter, Physics - Atmospheric and Oceanic Physics, Fishing industry, Atmospheric and Oceanic Physics (physics.ao-ph), Environmental science, circulation, Satellite, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Tuna, business
Abstract

Knowledge of ocean surface dynamics is crucial for oceanographic and climate research. The satellite-tracked movements of hundreds of drifters deployed by research and voluntary observing vessels provide high-frequency and high-resolution information on near-surface currents around the globe. Consequently, they constitute a major component of the Global Ocean Observing System (GOOS). However, maintaining this array is costly and in some oceanic regions such as the tropics, spatio-temporal coverage is limited. Here, we demonstrate that the GPS-buoy equipped fish aggregating devices (FADs) used in tropical tuna fisheries to increase fish catchability are also capable of providing comparable near-surface current information. We analyzed millions of position data collected between 2008 and 2014 from more than 15,000 FADs and 2,000 drifters, and combined this information with remotely-sensed near-surface current data to demonstrate that the surface velocity components of FADs and drifters are highly correlated in the Atlantic and Indian Oceans. While it was noted that the subsurface structures of FADs (typically made of recycled fishing nets) did slow them down relative to the drifters, particularly in the Atlantic Ocean, this bias was measurable and could be accounted for in future studies. Our findings show that the physical meteorological and oceanographic data collected by fishermen could provide an invaluable source of information to the GOOS. Furthermore, by forging closer collaborations with the fishing industry and ensuring their contributions to global ocean databases are properly acknowledged, there is significant scope to capture this data more effectively.

Published
2019

4. Ecological data for western Indian Ocean tuna

Author

Nathalie Bodin, Hilario Murua, Zahirah Dhurmeea, Iker Zudaire, Emmanuel Chassot, Julien Barde, Maitane Grande, Fany Sardenne, Seychelles Fishing Authority (SFA) (SFA), Université des Seychelles, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), AZTI-Tecnalia, Marine Research Division, University of Mauritius, and Azti Tecnalia, Centro Tecnológico del Mar y los Alimentos (Marine Resarch Unit) (Azti)

Subjects
0106 biological sciences, [SDE.MCG]Environmental Sciences/Global Changes, Fishing, stable isotopes, Biology, 010603 evolutionary biology, 01 natural sciences, tropical marine ecosystems, fatty acids, lipids, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Marine ecosystem, 14. Life underwater, multi-tissues, Ecology, Evolution, Behavior and Systematics, Apex predator, Trophic level, trophic ecology, energetics, morphometrics, Albacore, Ecology, 010604 marine biology & hydrobiology, tuna fisheries, Pelagic zone, biology.organism_classification, proteins, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Tuna, Thunnus
Abstract

International audience; Tuna are marine apex predators that inhabit the tropical and subtropical waters of the Indian Ocean where they support socially and economically important fisheries. Key component of pela-gic communities, tuna are bioindicator species of anthropogenic and climate-induced changes through modifications of the structure and related energy-flow of food webs and ecosystems. The IndianEcoTuna dataset provides a panel of ecological tracers measured in four soft tissues (white muscle, red muscle, liver, gonads) from 1,364 individuals of four species, i.e., the albacore (ALB, Thunnus alalunga), the bigeye (BET, T. obesus), the skipjack (SKJ, Katsuwomus pelamis), and the yellowfin (YFT, T. albacares), collected throughout the western Indian Ocean from 2009 to 2015. Sampling was carried out during routine monitoring programs, at sea by observers onboard professional vessels or at landing. For each record, the type of fishing gear, the conservation mode, as well as the fishing date and catch location are provided. Individuals were sampled to span a wide range of body sizes: 565 ALB with fork length from 58 to 118 cm, 155 BET from 29.5 to 173 cm, 304 SKJ from 30 to 74 cm, and 340 YFT from 29 to 171.5 cm. The IndianEcoTuna dataset combines: (1) 9,512 records of carbon and nitrogen stable isotopes (percent element weights, d 13 C and d 15 N values) in 1,185 fish, (2) 887 concentrations of total proteins in 242 fish, (3) 8,356 concentrations of total lipids and three lipid classes (triacylglycerols TAG; phospholipids PL; sterols ST) in 695 fish, and (4) 1,150 and 1,033 profiles of neutral and polar fatty acids in 397 and 342 fish, respectively. Information on sex and weights of the whole fish, gonads, liver and stomach is provided. Because of the essential trophic role and wide-ranging of tuna in marine systems, and the large panel of tropho-energetic tracers and derived-key quantitative parameters provided (e.g., niche width, trophic position, condition indices), the IndianEcoTuna dataset should be of high interest for global and regional research on marine trophic ecology and food web analysis, as well as on the impacts of anthropogenic changes on Indian Ocean marine ecosystems. There are no copyright restrictions for research and/or teaching purposes. Usage of the dataset must include citation of this Data Paper.

Published
2018

5. Reply to Feeley and Machovina: Trophic ecology complements estimates of land use change due to food production

Author

Laurent Dubroca, Emmanuel Chassot, Sylvain Bonhommeau, Carlos Manacorda, Anne-Elise Nieblas, Olivier Le Pape, David M. Kaplan, Julien Barde, UMR 212 EME 'écosystèmes marins exploités' (EME), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM), Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria (INTA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Bonhommeau, Sylvain, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
2. Zero hunger, Multidisciplinary, Food Chain, Meat, business.industry, Ecology, Ecology (disciplines), Population size, [SDV]Life Sciences [q-bio], 15. Life on land, Biology, Models, Biological, Food chain, Food Preferences, Food processing, Animals, Humans, Land use, land-use change and forestry, Ecosystem, Letters, business, Inefficiency, Trophic level
Abstract

Feeley and Machovina assert that even though humans occupy a low trophic level, we have larger ecosystem impacts than any other species because of the sheer volume of food consumed (linked to population size) and the inefficiency of its production (1). The authors argue that large differences in the impact on resource use exist between dietary preferences (e.g., differing proportions of beef, pork, or poultry in a diet), even if human diets are represented by the same trophic level. We are in complete agreement that humans have among the largest ecological impact of any species and that the human trophic level (HTL) (2) does not capture … [↵][1]1To whom correspondence should be addressed. E-mail: sylvain.bonhommeau{at}ifremer.fr. [1]: #xref-corresp-1-1

Published
2014

6. Un service de métadonnées pour gérer les ressources spatiales des zones côtières

Author

Julien Barde, Nabila Mazouni, Thérèse Libourel, Lionel Loubersac, Pierre Maurel, Jean-Christophe Desconnets, Carvalho De Matos, Christine, Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de Recherche pour le Développement (IRD), Centre d'étude pour la promotion des activités lagunaires et maritimes [Montpellier] (CEPRALMAR), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Models And Reuse Engineering, Languages (MAREL), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Expertise et spatialisation des connaissances en environnement (ESPACE), Université de la Polynésie Française (UPF), and Laboratoire Laboratoire Environnement Ressources Morbihan Pays de Loire (LER/MPL)

Subjects
0106 biological sciences, Service (systems architecture), Standards, Computer science, Metadata Internet mapping, Integrated coastal zone management, Interoperability, Scalable Vector Graphics, 02 engineering and technology, [INFO] Computer Science [cs], 01 natural sciences, World Wide Web, Resource (project management), 0202 electrical engineering, electronic engineering, information engineering, [INFO]Computer Science [cs], 14. Life underwater, ComputingMilieux_MISCELLANEOUS, 010604 marine biology & hydrobiology, Network mapping, 020207 software engineering, computer.file_format, Metadata, Thematic map, [SDE]Environmental Sciences, computer
Abstract

International audience; Within the framework of the SYSCOLAG pluridisciplinary research programme on ICZM in the Languedoc-Roussillon region of France, we propose an ISO-19115-compliant metadata service to share informational resources. Each resource is described using a metadata form. Each form consists of textually and spatially controlled terms which are stored in a single DBMS (Postgres and Postgis). The graphical user-interfaces contain the expert knowledge (thematic and spatial ontologies) and include a mapping service (SVG and OGC-compliant WMS-WFS) that allows spatial and thematic queries to be addressed to the metadata service.

Published
2005

7. Building Spatial data Infrastructures Based on Spatial Cognition: an Example for Integrated Coastal Zone Management

Author

Pierre Maurel, Thérèse Libourel Rouge, Julien Barde, Carvalho De Matos, Christine, Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Models And Reuse Engineering, Languages (MAREL), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), UMR 228 Espace-Dev, Espace pour le développement, Université des Antilles (UA)-Université de Guyane (UG)-Université de Montpellier (UM)-Université de La Réunion (UR)-Avignon Université (AU)-Université de Perpignan Via Domitia (UPVD)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM)

Subjects
[INFO]Computer Science [cs], [INFO] Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2005

8. Un service de métadonnées pour la gestion des connaissances liées aux zones côtières

Author

Pierre Maurel, Thérèse Libourel, Julien Barde, Models And Reuse Engineering, Languages (MAREL), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Irstea Publications, Migration, Carvalho De Matos, Christine, and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
[SDE] Environmental Sciences, Vocabulary, MEDIATION, Knowledge management, Computer Networks and Communications, Computer science, media_common.quotation_subject, 02 engineering and technology, [INFO] Computer Science [cs], Ontology (information science), COASTAL MANAGEMENT, 0202 electrical engineering, electronic engineering, information engineering, Media Technology, [INFO]Computer Science [cs], 14. Life underwater, Integrated management, ComputingMilieux_MISCELLANEOUS, media_common, KNOWLEDGE SHARING, business.industry, 05 social sciences, Knowledge sharing, Metadata, ONTOLOGY, Hardware and Architecture, [SDE]Environmental Sciences, Ontology, Geospatial metadata, 020201 artificial intelligence & image processing, 0509 other social sciences, 050904 information & library sciences, business, METADATA, Software
Abstract

International audience; The research outlined in this paper is part of a wider research program named SYSCOLAG Coastal and LAGoonal SYStems in Languedoc-Roussillon area, France) dedicated to sustainable coastal management. The main objective of this program is to build up a communication infrastructure to improve the exchange of information and knowledge between the various scientific disciplines involved in the research. In order to ensure the sharing of resources without affecting the autonomy and independance of the partners, we propose a three-level infrastructure (resources, federation and knowledge access) based on a metadata service (using ISO 19115 standard for geographic information metadata) completed by a common vocabulary (ontology).

Published
2005

9. Ontologies and Metadata for Sharing use of Geographical Information

Author

Julien Barde, Thérèse Libourel Rouge, Pierre Maurel, Structures et Systèmes Spatiaux (UMR 3S), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF)-Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF), Models And Reuse Engineering, Languages (MAREL), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), UMR 228 Espace-Dev, Espace pour le développement, Université de Guyane (UG)-Université des Antilles (UA)-Institut de Recherche pour le Développement (IRD)-Université de Perpignan Via Domitia (UPVD)-Avignon Université (AU)-Université de La Réunion (UR)-Université de Montpellier (UM), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), and Université des Antilles (UA)-Université de Guyane (UG)-Université de Montpellier (UM)-Université de La Réunion (UR)-Avignon Université (AU)-Université de Perpignan Via Domitia (UPVD)-Institut de Recherche pour le Développement (IRD)

Subjects
INFORMATION GEOGRAPHIQUE, METADONNEES, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS, ONTOLOGIES
Abstract

International audience

Published
2004

10. A Metadata Service for Integrated Management of Knowledges Related to Coastal Areas.

Author

Julien Barde, Thrse Libourel, and Pierre Maurel

Subjects
INFORMATION resources, VOCABULARY, ONTOLOGY, METADATA, MULTIMEDIA systems
Abstract

Abstract The research outlined in this paper is part of a wider research program named SYSCOLAG (Coastal and LAGoonal SYStems in Languedoc-Roussillon area, France) dedicated to sustainable coastal management. The main objective of this program is to build up a communication infrastructure to improve the exchange of information and knowledge between the various scientific disciplines involved in the research. In order to ensure the sharing of resources without affecting the autonomy and independance of the partners, we propose a three-level infrastructure (resources, federation and knowledge access) based on a metadata service (using ISO 19115 standard for geographic information metadata) completed by a common vocabulary (ontology). [ABSTRACT FROM AUTHOR]

Published
2005

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