A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses

Type Article
Date 2019-12
Language English
Author(s) Howell Kerry L.1, Davies Jaime S.1, Allcock A. Louise2, Braga-Henriques Andreia3, 21, Buhl-Mortensen Pål4, Carreiro-Silva Marina5, 22, Dominguez-Carrió Carlos5, 22, Durden Jennifer M.8, Foster Nicola L.1, Game Chloe A.6, Hitchin Becky7, Horton Tammy8, Hosking Brett8, Jones Daniel Ob8, Mah Christopher9, Laguionie Marchais Claire2, Menot LenaickORCID10, Morato Telmo5, 22, Pearman Tabitha R. R.8, Piechaud Nils1, Ross Rebecca E.1, 4, Ruhl Henry A.8, 23, Saeedi Hanieh11, 18, 24, Stefanoudis Paris V.12, 25, Taranto Gerald H.5, 22, Thompson Michael B.13, Taylor James R.14, Tyler Paul15, Vad Johanne16, Victorero Lissette17, 26, 29, Vieira Rui P.14, 28, Woodall Lucy C.12, 18, Xavier Joana R.19, 27, Wagner Daniel20
Affiliation(s) 1 : School of Biological and Marine Science, Plymouth University, Drake Circus, Plymouth, United Kingdom
2 : Zoology, School of Natural Sciences, and Ryan Institute, National University of Ireland, Galway, Galway, Ireland
3 : MARE-Marine and Environmental Sciences Centre, Estação de Biologia Marinha do Funchal, Cais do Carvão, Funchal, Madeira Island, Portugal
4 : Institute of Marine Research,Nordnes, Bergen, Norway
5 : Okeanos Research Centre, Universidade dos Açores, Departamento de Oceanografia e Pesca, Horta, Portugal
6 : School of Computing Sciences, University of East Anglia, Norwich, United Kingdom
7 : JNCC, Inverdee House, Aberdeen, United Kingdom
8 : National Oceanography Centre, University of Southampton Waterfront Campus, European Way, Southampton, United Kingdom
9 : Dept. of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington D.C., United States of America
10 : Ifremer, Centre de Bretagne, Plouzané, France
11 : Senckenberg Research Institute and Natural History Museum; Department of Marine Zoology, Frankfurt am Main, Germany
12 : Nekton Foundation, Begbroke Science Park, Begbroke Hill, Begbroke, Oxfordshire, United Kingdom
13 : Gardline Limited, Endeavour House, Great Yarmouth, Norfolk, United Kingdom
14 : Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Martin-Luthur-King-Platz, Hamburg, Germany
15 : School of Ocean and Earth Science National Oceanography Centre, University of Southampton Waterfront Campus, European Way, Southampton, United Kingdom
16 : Grant Institute, School of Geosciences, The University of Edinburgh, The King’s Buildings, Edinburgh, United Kingdom
17 : Institut de Systématique, Évolution, Biodiversité (ISYEB), CNRS, Muséum national d'Histoire naturelle,Sorbonne Université, Ecole Pratique des Hautes Etudes, Paris, France
18 : OBIS Data Manager, Deep-Sea Node, Nekton Foundation, Begbroke Science Park, Begbroke Hill, Begbroke, Oxfordshire, United Kingdom
19 : CIIMAR–Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Matosinhos, Portugal
20 : NOAA Office of Ocean Exploration and Research, Charleston, South Carolina, United States of America
21 : ARDITI-Regional Agency for the Development of Research, Technology and Innovation, Oceanic Observatory of Madeira (OOM), Madeira Tecnopolo, Caminho da Penteada, Funchal, Portugal
22 : IMAR Instituto do Mar, Marine and Environmental Sciences Centre (MARE), Universidade dos Açores, Horta, Portugal
23 : Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States of America
24 : Goethe University Frankfurt, Institute for Ecology, Diversity and Evolution, Frankfurt am Main, Germany
25 : Department of Zoology, University of Oxford, Zoology Research and Administration Building, Oxford, United Kingdom
26 : Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), CNRS, MuseUm national d’Histoire naturelle,Sorbonne Université, Université de Caen Normandie, Université des Antilles, IRD, Paris, France
27 : University of Bergen, Department of Biological Sciences and KG Jebsen Centre for Deep-Sea Research, Bergen, Norway
28 : Centre for Environment, Fisheries & Aquaculture Science, Lowestoft Laboratory, Lowestoft, Suffolk, United Kingdom
29 : Centre d’Ecologie et des Sciences de la Conservation (CESCO), CNRS, Museum national d’Histoire naturelle,Sorbonne Université, Paris, France
Source Plos One (1932-6203) (Public Library of Science (PLoS)), 2019-12 , Vol. 14 , N. 12 , P. e0218904 (25p.)
DOI 10.1371/journal.pone.0218904
WOS© Times Cited 1
Abstract

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.

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Howell Kerry L., Davies Jaime S., Allcock A. Louise, Braga-Henriques Andreia, Buhl-Mortensen Pål, Carreiro-Silva Marina, Dominguez-Carrió Carlos, Durden Jennifer M., Foster Nicola L., Game Chloe A., Hitchin Becky, Horton Tammy, Hosking Brett, Jones Daniel Ob, Mah Christopher, Laguionie Marchais Claire, Menot Lenaick, Morato Telmo, Pearman Tabitha R. R., Piechaud Nils, Ross Rebecca E., Ruhl Henry A., Saeedi Hanieh, Stefanoudis Paris V., Taranto Gerald H., Thompson Michael B., Taylor James R., Tyler Paul, Vad Johanne, Victorero Lissette, Vieira Rui P., Woodall Lucy C., Xavier Joana R., Wagner Daniel (2019). A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses. Plos One, 14(12), e0218904 (25p.). Publisher's official version : https://doi.org/10.1371/journal.pone.0218904 , Open Access version : https://archimer.ifremer.fr/doc/00602/71408/