1
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Venables H, Meredith MP, Hendry KR, Ten Hoopen P, Peat H, Chapman A, Beaumont J, Piper R, Miller AJ, Mann P, Rossetti H, Massey A, Souster T, Reeves S, Fenton M, Heiser S, Pountney S, Reed S, Waring Z, Clark M, Bolton E, Mathews R, London H, Clement A, Stuart E, Reichardt A, Brandon M, Leng M, Arrowsmith C, Annett A, Henley SF, Clarke A. Sustained year-round oceanographic measurements from Rothera Research Station, Antarctica, 1997-2017. Sci Data 2023; 10:265. [PMID: 37164979 PMCID: PMC10172177 DOI: 10.1038/s41597-023-02172-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/21/2023] [Indexed: 05/12/2023] Open
Abstract
Oceanographic changes adjacent to Antarctica have global climatic and ecological impacts. However, this is the most challenging place in the world to obtain marine data due to its remoteness and inhospitable nature, especially in winter. Here, we present more than 2000 Conductivity-Temperature-Depth (CTD) profiles and associated water sample data collected with (almost uniquely) full year-round coverage from the British Antarctic Survey Rothera Research Station at the west Antarctic Peninsula. Sampling is conducted from a small boat or a sled, depending on the sea ice conditions. When conditions allow, sampling is twice weekly in summer and weekly in winter, with profiling to nominally 500 m and with discrete water samples taken at 15 m water depth. Daily observations are made of the sea ice conditions in the area. This paper presents the first 20 years of data collection, 1997-2017. This time series represents a unique and valuable resource for investigations of the high-latitude ocean's role in climate change, ocean/ice interactions, and marine biogeochemistry and carbon drawdown.
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Affiliation(s)
- Hugh Venables
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Michael P Meredith
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Katharine R Hendry
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - Petra Ten Hoopen
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Helen Peat
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Alice Chapman
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Jennifer Beaumont
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand
| | - Rayner Piper
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Fathom Ecology, 39 Maisemore Gardens, Emsworth, Hampshire, England, PO10 7JX, UK
| | - Andrew J Miller
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- National Institute of Water and Atmospheric Research (NIWA), Christchurch, New Zealand
| | - Paul Mann
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Geography and Environmental Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne, NE1 8ST, UK
| | - Helen Rossetti
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Ali Massey
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Terri Souster
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- The Norwegian College of Fishery Science, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Simon Reeves
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mairi Fenton
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- The Lyell Centre, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Sabrina Heiser
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
| | - Sam Pountney
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Sarah Reed
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Ocean Ecology Limited - Scottish Office, European Marine Science Park, Malin House, Dunbeg, Oban, PA37 1SZ, UK
| | - Zoë Waring
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Marlon Clark
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Basecamp Research, Unit 510 Clerkenwell Workshops, 27 Clerkenwell Close, London, EC1R 0AT, UK
| | - Emma Bolton
- Previously affiliated with: British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Basecamp Research, Unit 510 Clerkenwell Workshops, 27 Clerkenwell Close, London, EC1R 0AT, UK
| | - Ryan Mathews
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Hollie London
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Alice Clement
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Emma Stuart
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Aurelia Reichardt
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mark Brandon
- School of Environment, Earth and Ecosystem Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
| | - Melanie Leng
- Centre for Environmental Geochemistry, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
- British Geological Survey, Environmental Science Centre, Nicker Hill, Keyworth, Nottingham, NG12 5GG, UK
| | - Carol Arrowsmith
- British Geological Survey, Environmental Science Centre, Nicker Hill, Keyworth, Nottingham, NG12 5GG, UK
| | - Amber Annett
- School of Ocean and Earth Science, University of Southampton, European Way, Southampton, SO14 3ZH, UK
| | - Sian F Henley
- School of GeoSciences, James Hutton Road, The University of Edinburgh, Edinburgh, EH9 3FE, UK
| | - Andrew Clarke
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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2
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Ten Hoopen P, Finn RD, Bongo LA, Corre E, Fosso B, Meyer F, Mitchell A, Pelletier E, Pesole G, Santamaria M, Willassen NP, Cochrane G. The metagenomic data life-cycle: standards and best practices. Gigascience 2018. [PMID: 28637310 PMCID: PMC5737865 DOI: 10.1093/gigascience/gix047] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community, but greater awareness and adoption is still needed. We emphasize the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.
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Affiliation(s)
- Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | | | - Erwan Corre
- CNRS-UPMC, FR 2424, Station Biologique, Roscoff 29680, France
| | - Bruno Fosso
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari 70126, Italy
| | - Folker Meyer
- Argonne National Laboratory, Argonne IL 60439, USA
| | - Alex Mitchell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Eric Pelletier
- Genoscope, CEA, Évry 91000, France.,CNRS/UMR-8030, Évry 91000, France.,Université Évry val d'Essonne, Évry 91000, France
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari 70126, Italy.,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "A. Moro," Bari 70126, Italy
| | - Monica Santamaria
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari 70126, Italy
| | | | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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3
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Gelová Z, Ten Hoopen P, Novák O, Motyka V, Pernisová M, Dabravolski S, Didi V, Tillack I, Okleštková J, Strnad M, Hause B, Haruštiaková D, Conrad U, Janda L, Hejátko J. Antibody-mediated modulation of cytokinins in tobacco: organ-specific changes in cytokinin homeostasis. J Exp Bot 2018; 69:441-454. [PMID: 29294075 DOI: 10.1093/jxb/erx426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 11/06/2017] [Indexed: 05/20/2023]
Abstract
Cytokinins comprise a group of phytohormones with an organ-specific mode of action. Although the mechanisms controlling the complex networks of cytokinin metabolism are partially known, the role of individual cytokinin types in the maintenance of cytokinin homeostasis remains unclear. Utilizing the overproduction of single-chain Fv antibodies selected for their ability to bind trans-zeatin riboside and targeted to the endoplasmic reticulum, we post-synthetically modulated cytokinin ribosides, the proposed transport forms of cytokinins. We observed asymmetric activity of cytokinin biosynthetic genes and cytokinin distribution in wild-type tobacco seedlings with higher cytokinin abundance in the root than in the shoot. Antibody-mediated modulation of cytokinin ribosides further enhanced the relative cytokinin abundance in the roots and induced cytokinin-related phenotypes in an organ-specific manner. The activity of cytokinin oxidase/dehydrogenase in the roots was strongly up-regulated in response to antibody-mediated formation of the cytokinin pool in the endoplasmic reticulum. However, we only detected a slight decrease in the root cytokinin levels. In contrast, a significant decrease of cytokinins occurred in the shoot. We suggest the roots as the main site of cytokinin biosynthesis in tobacco seedlings. Conversely, cytokinin levels in the shoot seem to depend largely on long-range transport of cytokinin ribosides from the root and their subsequent metabolic activation.
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Affiliation(s)
- Zuzana Gelová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ondrej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR & Palacký University, Olomouc, Czech Republic
| | - Václav Motyka
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic
| | - Markéta Pernisová
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Siarhei Dabravolski
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vojtech Didi
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Isolde Tillack
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Stadt Seeland, Germany
| | - Jana Okleštková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR & Palacký University, Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR & Palacký University, Olomouc, Czech Republic
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Danka Haruštiaková
- Institute of Biostatistics and Analyses, Faculty of Medicine and Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Udo Conrad
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Stadt Seeland, Germany
| | - Lubomír Janda
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jan Hejátko
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
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4
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Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Pesant S, Karsenti E, Wincker P. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data 2017; 4:170093. [PMID: 28763055 PMCID: PMC5538240 DOI: 10.1038/sdata.2017.93] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/05/2017] [Indexed: 02/01/2023] Open
Abstract
A unique collection of oceanic samples was gathered by the Tara Oceans
expeditions (2009–2013), targeting plankton organisms ranging from viruses to
metazoans, and providing rich environmental context measurements. Thanks to recent advances in
the field of genomics, extensive sequencing has been performed for a deep genomic analysis of
this huge collection of samples. A strategy based on different approaches, such as
metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for
analysis of size-fractionated plankton communities. Here, we provide detailed procedures
applied for genomic data generation, from nucleic acids extraction to sequence production, and
we describe registries of genomics datasets available at the European Nucleotide Archive (ENA,
www.ebi.ac.uk/ena). The association of these metadata to the experimental
procedures applied for their generation will help the scientific community to access these data
and facilitate their analysis. This paper complements other efforts to provide a full
description of experiments and open science resources generated from the Tara
Oceans project, further extending their value for the study of the world’s planktonic
ecosystems.
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Affiliation(s)
- Adriana Alberti
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Poulain
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Stefan Engelen
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Karine Labadie
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Guillaume Albini
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Caroline Belser
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Alexis Bertrand
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Da Silva
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Carole Dossat
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Frédérick Gavory
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Shahinaz Gas
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Guy
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Maud Haquelle
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - E'krame Jacoby
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Olivier Jaillon
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Arnaud Lemainque
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Eric Pelletier
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Gaëlle Samson
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Mark Wessner
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | | | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Francisco M Cornejo-Castillo
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Beatriz Fernández-Gómez
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain.,FONDAP Center for Genome Regulation, Moneda 1375, Santiago 8320000, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Libano Macul, Santiago 5524, Chile
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Colomban De Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Elodie Desgranges
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Stefanie Kandels-Lewis
- Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA
| | - Michael E Sieracki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA.,National Science Foundation, Arlington, Virginia 22230, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona 85719, USA
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, Bremen 28359, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Leobener Str. 8, Bremen 28359, Germany
| | - Eric Karsenti
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France.,Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, 181 Chemin du Lazaret, Villefranche-sur-mer F-06230, France
| | - Patrick Wincker
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
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5
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Hoopen PT, Walls RL, Cannon EK, Cochrane G, Cole J, Johnston A, Karsch-Mizrachi I, Yilmaz P. Plant specimen contextual data consensus. Gigascience 2016; 5:1-4. [PMID: 28369359 PMCID: PMC5572840 DOI: 10.1093/gigascience/giw002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/04/2016] [Indexed: 11/12/2022] Open
Abstract
The Compliance and Interoperability Working Group of the Genomic Standards Consortium facilitates the establishment of a community of experts and the development of recommendations to describe genomic data and associated information. Here we present our ongoing conation to harmonise the reporting of contextual plant specimen data associated with genomics and functional genomics. This commentary summarises the current state of our plant sample contextual data harmonisation efforts to engage a broad plant science community.
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Affiliation(s)
- Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | | | - Ethalinda Ks Cannon
- Department of Computer Science, Iowa State University, Ames, Iowa, USA
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics, Ames, Iowa, USA
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - James Cole
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA
| | - Anjanette Johnston
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
| | - Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Celsius str. 1, Bremen 28359, Germany
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6
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Toribio AL, Alako B, Amid C, Cerdeño-Tarrága A, Clarke L, Cleland I, Fairley S, Gibson R, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Martínez-Villacorta J, Pakseresht N, Rajan J, Reddy K, Rosello M, Silvester N, Smirnov D, Vaughan D, Zalunin V, Cochrane G. European Nucleotide Archive in 2016. Nucleic Acids Res 2016; 45:D32-D36. [PMID: 27899630 PMCID: PMC5210577 DOI: 10.1093/nar/gkw1106] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 10/25/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA.
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Affiliation(s)
- Ana Luisa Toribio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Blaise Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ana Cerdeño-Tarrága
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Iain Cleland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Richard Gibson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Neil Goodgame
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Josué Martínez-Villacorta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kethi Reddy
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Rosello
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dmitriy Smirnov
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Vaughan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vadim Zalunin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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7
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Gibson R, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Goodgame N, Ten Hoopen P, Jayathilaka S, Kay S, Leinonen R, Liu X, Pallreddy S, Pakseresht N, Rajan J, Rosselló M, Silvester N, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Biocuration of functional annotation at the European nucleotide archive. Nucleic Acids Res 2016; 44:D58-66. [PMID: 26615190 PMCID: PMC4702917 DOI: 10.1093/nar/gkv1311] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 01/03/2023] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achievements. This is followed by a focus on sustainable biocuration of functional annotation, an area which has particularly felt the pressure of sequencing growth. The importance of functional annotation, how it can be submitted and the shifting role of the biocurator in the context of increasing volumes of data are all discussed.
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Affiliation(s)
- Richard Gibson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Blaise Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ana Cerdeño-Tárraga
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Iain Cleland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Neil Goodgame
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Swapna Pallreddy
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Rosselló
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dmitriy Smirnov
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ana Luisa Toribio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Daniel Vaughan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Vadim Zalunin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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8
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Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid EH, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L'Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JAH, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PAF, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N, Field D, Glöckner FO. The ocean sampling day consortium. Gigascience 2015; 4:27. [PMID: 26097697 PMCID: PMC4473829 DOI: 10.1186/s13742-015-0066-5] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/06/2015] [Indexed: 11/26/2022] Open
Abstract
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
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Affiliation(s)
- Anna Kopf
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Mesude Bicak
- University of Oxford, 7 Keble Road, OX1 3QG Oxford, Oxfordshire UK
| | - Renzo Kottmann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Julia Schnetzer
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Ivaylo Kostadinov
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Katja Lehmann
- Centre for Ecology & Hydrology, MacLean Building, Benson Lane, Crowmarsh Gifford, OX10 8BB Wallingford, Oxfordshire UK
| | - Antonio Fernandez-Guerra
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; University of Oxford, 7 Keble Road, OX1 3QG Oxford, Oxfordshire UK
| | - Christian Jeanthon
- CNRS & Sorbonne Universités, UPMC Univ Paris 06, Station Biologique, Place Georges Teissier, F-29680 Roscoff, France
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel- Shikmona, POB 8030, 31080 Haifa, Israel
| | - Matthias Ullrich
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Antje Wichels
- Alfred Wegener Institute, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Gunnar Gerdts
- Alfred Wegener Institute, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Paraskevi Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Gournes Pediados, 71500 Heraklion, Crete Greece
| | - Giorgos Kotoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Gournes Pediados, 71500 Heraklion, Crete Greece
| | - Rania Siam
- Biology Department and YJ-Science and Technology Research Center, American University in Cairo, New Cairo, 11835 Cairo Governorate Egypt
| | - Rehab Z Abdallah
- Biology Department and YJ-Science and Technology Research Center, American University in Cairo, New Cairo, 11835 Cairo Governorate Egypt
| | - Eva C Sonnenschein
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet 301, 2800 Kgs., Lyngby, Denmark
| | - Thierry Cariou
- CNRS & Sorbonne Universités, UPMC Univ Paris 06, Station Biologique, Place Georges Teissier, F-29680 Roscoff, France
| | - Fergal O'Gara
- National University of Ireland-University College Cork, Cork, Ireland ; Curtin University, Biomedical Sciences, Perth, Western Australia Australia
| | - Stephen Jackson
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet 301, 2800 Kgs., Lyngby, Denmark
| | - Sandi Orlic
- Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Michael Steinke
- School of Biological Sciences, University of Essex, CO4 3SQ Colchester, Essex UK
| | - Julia Busch
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26383 Wilhemshaven, Germany
| | - Bernardo Duarte
- Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon, Campo Grande 1749-016, Lisbon, Portugal
| | - Isabel Caçador
- Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon, Campo Grande 1749-016, Lisbon, Portugal
| | - João Canning-Clode
- Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon, Campo Grande 1749-016, Lisbon, Portugal ; Smithsonian Environmental Research Center, 21037 Edgewater, Maryland USA
| | - Oleksandra Bobrova
- Department of Microbiology, Virology and Biotechnology, Odessa National II Mechnikov University, Dvoryanskaya str.2, 65082 Odessa, Ukraine
| | | | | | - Clara Magalhães Loureiro
- InBio/CIBIO, Departamento de Biologia da Universidade dos Açores, 9501-801 Ponta Delgada, Portugal
| | - Gian Marco Luna
- National Research Council, Institute of Marine Sciences (CNR-ISMAR), Castello 2737/f, Arsenale Tesa 104, 30122 Venezia, Italy
| | - Grazia Marina Quero
- National Research Council, Institute of Marine Sciences (CNR-ISMAR), Castello 2737/f, Arsenale Tesa 104, 30122 Venezia, Italy
| | - Carolin R Löscher
- Institute of Microbiology/ GEOMAR, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Anke Kremp
- Marine Research Centre, Finnish Environment Institute, Erik Palmenin aukio 1, 00560 Helsinki, Finland
| | - Marie E DeLorenzo
- NOAA/National Ocean Service/NCCOS/Center for Coastal Environmental Health & Biomolecular Research Charleston, 29412 South Carolina, USA
| | - Lise Øvreås
- Department of Biology, University of Bergen, Thormøhlensgate 53B, 5020 Bergen, Norway
| | - Jennifer Tolman
- LaRoche Research Group, Department of Biology, Dalhousie University, B3H 4R2 Halifax, Nova Scotia Canada
| | - Julie LaRoche
- LaRoche Research Group, Department of Biology, Dalhousie University, B3H 4R2 Halifax, Nova Scotia Canada
| | - Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy
| | - Marc Frischer
- University of Georgia's Skidaway Institute of Oceanography, 10 Ocean Science Circle, 31411 Savannah, Georgia USA
| | - Timothy Davis
- NOAA-Great Lakes Environmental Research Laboratory, 4840 S State Road, 48108 Ann Arbor, Michigan USA
| | - Barker Katherine
- National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, 20013 Washington, DC USA
| | - Christopher P Meyer
- National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, 20013 Washington, DC USA
| | - Sandra Ramos
- CIIMAR, Interdisciplinary Center of Environmental and Marine Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Catarina Magalhães
- CIIMAR, Interdisciplinary Center of Environmental and Marine Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Florence Jude-Lemeilleur
- Station Marine d'Arcachon, CNRS & Univ Bordeaux, 2 rue Professeur Jolyet, F-33120 Arcachon, France
| | - Ma Leopoldina Aguirre-Macedo
- Centro de Investigación y de Estudios Avanzados (CINVESTAV), Unidad Mérida, Carretera Antigua a Progreso Km 6 Cordemex, C.P., 97310 Yucatan, Mexico
| | - Shiao Wang
- Department of Biological Sciences, University of Southern Mississippi, 39406 Hattiesburg, Mississippi USA
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, 04544 East Boothbay, Maine USA
| | - Scott Jones
- Smithsonian Marine Station, 701 Seaway Drive, 34949 Fort Pierce, Florida USA
| | - Rachel Collin
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
| | - Jed A Fuhrman
- Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California, 90089-0371 Los Angeles, California USA
| | - Pascal Conan
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66651 Banyuls sur Mer, France
| | - Cecilia Alonso
- Microbial Ecology of Aquatic Transitional Systems Research Group, Centro Universitario de la Región Este, Universidad de la República, Ruta 15, km 28.500, Rocha, Uruguay
| | - Noga Stambler
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel ; Interuniversity Institute for Marine Sciences in Eilat, 88103 Eilat, Israel
| | - Kelly Goodwin
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, 4301 Rickenbacker Causeway, 33149 Miami, Florida USA
| | - Michael M Yakimov
- Institute for Coastal Marine Environment, IAMC-CNR, Spianata S Raineri, 86 - 98122, Messina, Sicily Italy
| | - Federico Baltar
- Department of Marine Science, University of Otago, PO Box 56, 9054 Dunedin, New Zealand
| | - Levente Bodrossy
- CSIRO Oceans and Atmosphere Flagship, 7000 Hobart, Tasmania Australia
| | - Jodie Van De Kamp
- CSIRO Oceans and Atmosphere Flagship, 7000 Hobart, Tasmania Australia
| | - Dion Mf Frampton
- CSIRO Oceans and Atmosphere Flagship, 7000 Hobart, Tasmania Australia
| | - Martin Ostrowski
- Department of Chemistry and Biomolecular Science, Macquarie University, 2109 Sydney, Australia
| | - Paul Van Ruth
- South Australian Research and Development Institute (SARDI) - Aquatic Sciences, PO Box 120, 5022 Henley Beach, South Australia Australia
| | - Paul Malthouse
- South Australian Research and Development Institute (SARDI) - Aquatic Sciences, PO Box 120, 5022 Henley Beach, South Australia Australia
| | - Simon Claus
- Flanders Marine Institute, InnovOcean site, Wandelaarkaai 7, 8400 Oostende, Belgium
| | - Klaas Deneudt
- Flanders Marine Institute, InnovOcean site, Wandelaarkaai 7, 8400 Oostende, Belgium
| | - Jonas Mortelmans
- Flanders Marine Institute, InnovOcean site, Wandelaarkaai 7, 8400 Oostende, Belgium
| | - Sophie Pitois
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Pakefield Road, NR33 0HT Lowestoft, Suffolk UK
| | - David Wallom
- University of Oxford, 7 Keble Road, OX1 3QG Oxford, Oxfordshire UK
| | - Ian Salter
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66651 Banyuls sur Mer, France ; Alfred-Wegener-Institut-Helmholtz-Zentrum für Polar-und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, Algarve University, Gambelas Campus, Building 7, Room 2.77, 8005-139 Faro, Portugal
| | - Declan C Schroeder
- Marine Biological Association of the UK, Citadel Hill, PL1 2PB Plymouth, Devon UK
| | - Mahrous M Kandil
- Soil and Water Science Department, Faculty of Agriculture, Alexandria University, El-Shatbi, 21545 Alexandria, Egypt
| | - Valentina Amaral
- Microbial Ecology of Aquatic Transitional Systems Research Group, Centro Universitario de la Región Este, Universidad de la República, Ruta 15, km 28.500, Rocha, Uruguay
| | - Florencia Biancalana
- Marine Biogeochemistry - Argentine Institute of Oceanography, Camino La Carrindanga Km 7,5, 8000 Florida, Bahia Blanca Argentina
| | - Rafael Santana
- Microbial Ecology of Aquatic Transitional Systems Research Group, Centro Universitario de la Región Este, Universidad de la República, Ruta 15, km 28.500, Rocha, Uruguay
| | - Maria Luiza Pedrotti
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7093, LOV, Observatoire océanologique, F-Villefranche-sur-Mer, Paris, France
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, 606-8502 Sakyo-ku, Kyoto Japan
| | - Hiroyuki Ogata
- Graduate School of Agriculture, Kyoto University, 606-8502 Sakyo-ku, Kyoto Japan
| | - Tim Ingleton
- Waters, Wetlands and Coasts, New South Wales Office of Environment and Heritage, Sydney South 1232, 59-61 Goulburn Street, 2001 PO Box A290, Sydney, New South Wales Australia ; Antarctic and Southern Ocean Studies, University of Tasmania, 7004 Hobart, Tasmania Australia
| | - Kate Munnik
- Lwandle Technologies, Black River Park, Fir Road, 7925 Observatory, Cape Town South Africa
| | | | | | - Patricia Wecker
- CRIOBE, USR3278 CNRS-EPHE-UPVD, LabEx Corail, BP 1013-98729 Papetoai Moorea, French Polynesia
| | - Ibon Cancio
- University of the Basque Country, PO Box 644, E-48080 Bilbao, Basque Country Spain
| | - Daniel Vaulot
- CNRS & Sorbonne Universités, UPMC Univ Paris 06, Station Biologique, Place Georges Teissier, F-29680 Roscoff, France
| | - Christina Bienhold
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; Alfred-Wegener-Institut-Helmholtz-Zentrum für Polar-und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Hassan Ghazal
- Polydisciplinary Faculty of Nador, University Mohammed Premier, Selouane, Nador Morocco ; Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco
| | - Bouchra Chaouni
- Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco ; Faculty of Sciences of Rabat, University Mohammed Fifth Rabat, Rabat, Morocco
| | - Soumya Essayeh
- Polydisciplinary Faculty of Nador, University Mohammed Premier, Selouane, Nador Morocco
| | - Sara Ettamimi
- Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco ; Polydisciplinary Faculty of Taza, University Sidi Mohammed Ben Abdallah, Fes, Morocco
| | - El Houcine Zaid
- Faculty of Sciences of Rabat, University Mohammed Fifth Rabat, Rabat, Morocco
| | - Noureddine Boukhatem
- Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco
| | - Abderrahim Bouali
- Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco
| | - Rajaa Chahboune
- Polydisciplinary Faculty of Nador, University Mohammed Premier, Selouane, Nador Morocco ; Faculté des Sciences et Techniques de Tanger, Université Abdelmalek Essaâdi, Tanger, Morocco
| | - Said Barrijal
- Faculté des Sciences et Techniques de Tanger, Université Abdelmalek Essaâdi, Tanger, Morocco
| | - Mohammed Timinouni
- Pasteur Institute of Morocco, 1 Place Louis Pasteur, 20100 Casablanca, Morocco
| | - Fatima El Otmani
- Microbiology, Health and Environment Team, Department of Biology, Faculty of Sciences, Chouaib Doukkali University, Rte Ben Maachou, BP 20 Avenue des Facultés, El Jadida, Morocco
| | - Mohamed Bennani
- Pasteur Institute of Morocco, 1 Place Louis Pasteur, 20100 Casablanca, Morocco
| | - Marianna Mea
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Nadezhda Todorova
- Institute of Biodiversity and Ecosystem Research (IBER), Bulgarian Academy of Sciences, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | - Ventzislav Karamfilov
- Institute of Biodiversity and Ecosystem Research (IBER), Bulgarian Academy of Sciences, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, Cambridgeshire UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, Cambridgeshire UK
| | - Stephane L'Haridon
- Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Kemal Can Bizsel
- Dokuz Eylul University (DEU), Institute of Marine Sciences and Technology (IMST), Baku Bulvard, No: 100, Inciralti, 35340 Izmir, Balcova Turkey
| | - Alessandro Vezzi
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Federico M Lauro
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, SBS 01N-27, 637551 Singapore, Singapore
| | - Patrick Martin
- Earth Observatory of Singapore, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore, Singapore
| | - Rachelle M Jensen
- Indigo V Expeditions, ONE°15 Marina, #01-01, 11 Cove Drive, Sentosa Cove, 098497 Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, SBS 01N-27, 637551 Singapore, Singapore
| | - Susan Gebbels
- School of Marine Science and Technology, Newcastle University, Dove Marine Laboratory, Cullercoats, NE30 4PZ Tyne and Wear UK
| | - Riccardo Rosselli
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Fabio De Pascale
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Riccardo Schiavon
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Antonina Dos Santos
- IPMA, Department of Sea and Marine Resources, Avenida de Brasília, s/n, 1449-006 Lisboa, Portugal
| | - Emilie Villar
- Aix Marseille Université, CNRS, IGS UMR 7256, 163 Avenue de Luminy, 13288 Marseille, France
| | - Stéphane Pesant
- PANGAEA - Data Publisher for Earth & Environmental Science, MARUM Center for Marine Environmental Sciences, University Bremen, Hochschulring 18, 28359 Bremen, Germany
| | - Bruno Cataletto
- OGS, National Institute of Oceanography and Experimental Geophysics, Via Auguste Piccard, 54, 34151, Santa Croce, Trieste, Italy
| | - Francesca Malfatti
- OGS, National Institute of Oceanography and Experimental Geophysics, Via Auguste Piccard, 54, 34151, Santa Croce, Trieste, Italy
| | - Ranjith Edirisinghe
- Department of Physical Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka, Mihintale, Sri Lanka
| | - Jorge A Herrera Silveira
- Department of Biological Sciences, University of Southern Mississippi, 39406 Hattiesburg, Mississippi USA
| | - Michele Barbier
- Mediterranean Science Commission, 16 Bd de Suisse, 98 000 Monaco, Monaco
| | - Valentina Turk
- Marine Biology Station, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia
| | - Wayne J Fuller
- Near East University, TRNC Mersin 10, 99138 Nicosia, Northern Cyprus
| | - Ilkay Salihoglu
- Near East University, TRNC Mersin 10, 99138 Nicosia, Northern Cyprus
| | - Nedime Serakinci
- Near East University, TRNC Mersin 10, 99138 Nicosia, Northern Cyprus
| | | | - Eileen Bresnan
- Phytoplankton Ecology, Marine Scotland Marine Laboratory, 375 Victoria Road, AB11 9DB Aberdeen, Aberdeenshire UK
| | - Juan Iriberri
- University of the Basque Country, PO Box 644, E-48080 Bilbao, Basque Country Spain
| | | | - Edvardsen Bente
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, PO Box 1066, 0316 Blindern, Oslo Norway
| | - Hans Erik Karlsen
- Drøbak Field Station, Marine Biology Research station, Biologiveien 2, 1440 Drøbak, Norway
| | - Peter N Golyshin
- School of Biological Sciences, College of Natural Sciences, Bangor University, LL57 2UW Gwynedd, Bangor UK
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Pg Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya Spain
| | - Snejana Moncheva
- Fridtjof Nansen Institute of Oceanology, First May Street 40, 9000 Varna, Bulgaria
| | - Nina Dzhembekova
- Fridtjof Nansen Institute of Oceanology, First May Street 40, 9000 Varna, Bulgaria
| | - Zackary Johnson
- Nicholas School of the Environment and Biology Department, Duke University, 135 Marine Lab Road, 28516 Beaufort, North Carolina USA
| | - Christopher David Sinigalliano
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, 4301 Rickenbacker Causeway, 33149 Miami, Florida USA
| | - Maribeth Louise Gidley
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, 4301 Rickenbacker Causeway, 33149 Miami, Florida USA ; Cooperative Institute of Marine and Atmospheric Sciences, Rosenstiel School of Marine & Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, 33149 Miami, Florida USA
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy ; Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, 2 Seferi Street, 301 00 Agrinio, Greece
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, CB3 0ET Cambridge, Cambridgeshire UK
| | - Ana Cristina Costa
- InBio/CIBIO, Departamento de Biologia da Universidade dos Açores, 9501-801 Ponta Delgada, Portugal
| | - Monia El Bour
- Institut National des Sciences et Technologies de la Mer (INSTM), 28 rue du 2 mars 1934, 2025 Salammbô, Tunisia
| | - Ana M Martins
- InBio/CIBIO, Departamento de Biologia da Universidade dos Açores, 9501-801 Ponta Delgada, Portugal ; Department of Oceanography and Fisheries, University of the Azores, PT-9901-862 Horta, Portugal
| | - R Eric Collins
- University of Alaska Fairbanks, Box 757220, 99775 Fairbanks, Alaska USA
| | | | - Jonathan Martinez
- University of Hawaii at Manoa, Kewalo Marine Laboratory, 41 Ahui St., Honolulu, 96813 Hawaii, USA
| | - Mark J Costello
- Institute of Marine Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Linda A Amaral-Zettler
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, 02543 Massachusetts, USA ; Department of Earth, Environmental, and Planetary Sciences, Brown University, 02912 Providence, Rhode Island USA
| | - Jack A Gilbert
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China ; Institute for Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory, 9700 South Cass Avenue, 60439 Argonne, Illinois USA ; University of Chicago, 1101 E 57th Street, 60637 Chicago, Illinois USA ; Marine Biological Laboratory, 7 MBL Street, Woods Hole, 02543 Massachusetts, USA
| | - Neil Davies
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany ; Gump South Pacific Research Station, University of California Berkeley, BP 244 98728 Moorea, French Polynesia
| | - Dawn Field
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany ; University of Oxford, 7 Keble Road, OX1 3QG Oxford, Oxfordshire UK
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
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9
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Ten Hoopen P, Pesant S, Kottmann R, Kopf A, Bicak M, Claus S, Deneudt K, Borremans C, Thijsse P, Dekeyzer S, Schaap DM, Bowler C, Glöckner FO, Cochrane G. Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards. Stand Genomic Sci 2015. [PMID: 26203332 PMCID: PMC4511511 DOI: 10.1186/s40793-015-0001-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for “Reporting” and “Serving” data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7th Framework Programme “Ocean of Tomorrow”, and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.
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Affiliation(s)
- Petra Ten Hoopen
- European Nucleotide Archive, EMBL-EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
| | - Stéphane Pesant
- PANGAEA - Data Publisher for Earth & Environmental Science, MARUM Center for Marine Environmental Sciences, Universität Bremen, Hochschulring 18 (Cognium), Bremen, POP 330 440, 28359, Germany
| | - Renzo Kottmann
- Max Planck Institute for Marine Microbial Ecology, Microbial Genomics and Bioinformatics Group, Celsiusstr. 1, Bremen, 28359, Germany
| | - Anna Kopf
- Max Planck Institute for Marine Microbial Ecology, Microbial Genomics and Bioinformatics Group, Celsiusstr. 1, Bremen, 28359, Germany ; Jacobs University Bremen gGmbH, Campusring 1, Bremen, 28759, Germany
| | - Mesude Bicak
- Oxford e-Research Centre (OeRC), University of Oxford, 7Keble Road, Oxford, UK
| | - Simon Claus
- Vlaams Instituut voor de Zee, InnovOcean site, Wandelaarkaai 7, Oostende, B-8400, Belgium
| | - Klaas Deneudt
- Vlaams Instituut voor de Zee, InnovOcean site, Wandelaarkaai 7, Oostende, B-8400, Belgium
| | - Catherine Borremans
- IFREMER-Centre de BREST, IDM/SISMER, ZI de la Pointe du Diable, Plouzane, CS 10070, 29280, France
| | - Peter Thijsse
- MARIS BV, Koningin Julianalaan 345 A 2273 JJ, Voorburg, The Netherlands
| | - Stefanie Dekeyzer
- Vlaams Instituut voor de Zee, InnovOcean site, Wandelaarkaai 7, Oostende, B-8400, Belgium
| | - Dick Ma Schaap
- MARIS BV, Koningin Julianalaan 345 A 2273 JJ, Voorburg, The Netherlands
| | - Chris Bowler
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197 Inserm U1024, Paris, 75005, France
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbial Ecology, Microbial Genomics and Bioinformatics Group, Celsiusstr. 1, Bremen, 28359, Germany ; Jacobs University Bremen gGmbH, Campusring 1, Bremen, 28759, Germany
| | - Guy Cochrane
- European Nucleotide Archive, EMBL-EBI, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
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10
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Silvester N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Ten Hoopen P, Kay S, Leinonen R, Li W, Liu X, Lopez R, Pakseresht N, Pallreddy S, Plaister S, Radhakrishnan R, Rossello M, Senf A, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Content discovery and retrieval services at the European Nucleotide Archive. Nucleic Acids Res 2014; 43:D23-9. [PMID: 25404130 PMCID: PMC4383942 DOI: 10.1093/nar/gku1129] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary resource for nucleotide sequence information. With the growing volume and diversity of public sequencing data comes the need for increased sophistication in data organisation, presentation and search services so as to maximise its discoverability and usability. In response to this, ENA has been introducing and improving checklists for use during submission and expanding its search facilities to provide targeted search results. Here, we give a brief update on ENA content and some major developments undertaken in data submission services during 2014. We then describe in more detail the services we offer for data discovery and retrieval.
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Affiliation(s)
- Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Blaise Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ana Cerdeño-Tárraga
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Iain Cleland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Richard Gibson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Neil Goodgame
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Simon Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Weizhong Li
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rodrigo Lopez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Swapna Pallreddy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sheila Plaister
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rajesh Radhakrishnan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Rossello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alexander Senf
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dmitriy Smirnov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ana Luisa Toribio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel Vaughan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vadim Zalunin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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11
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Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Jang M, Kay S, Leinonen R, Lin X, Lopez R, McWilliam H, Oisel A, Pakseresht N, Pallreddy S, Park Y, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Ten Hoopen P, Toribio A, Vaughan D, Zalunin V. Facing growth in the European Nucleotide Archive. Nucleic Acids Res 2012. [PMID: 23203883 PMCID: PMC3531187 DOI: 10.1093/nar/gks1175] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/) collects, maintains and presents comprehensive nucleic acid sequence and related information as part of the permanent public scientific record. Here, we provide brief updates on ENA content developments and major service enhancements in 2012 and describe in more detail two important areas of development and policy that are driven by ongoing growth in sequencing technologies. First, we describe the ENA data warehouse, a resource for which we provide a programmatic entry point to integrated content across the breadth of ENA. Second, we detail our plans for the deployment of CRAM data compression technology in ENA.
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Affiliation(s)
- Guy Cochrane
- EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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12
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Amid C, Birney E, Bower L, Cerdeño-Tárraga A, Cheng Y, Cleland I, Faruque N, Gibson R, Goodgame N, Hunter C, Jang M, Leinonen R, Liu X, Oisel A, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Rivière S, Rossello M, Senf A, Smirnov D, Ten Hoopen P, Vaughan D, Vaughan R, Zalunin V, Cochrane G. Major submissions tool developments at the European Nucleotide Archive. Nucleic Acids Res 2011; 40:D43-7. [PMID: 22080548 PMCID: PMC3245037 DOI: 10.1093/nar/gkr946] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena), Europe's primary nucleotide sequence resource, captures and presents globally comprehensive nucleic acid sequence and associated information. Covering the spectrum from raw data to assembled and functionally annotated genomes, the ENA has witnessed a dramatic growth resulting from advances in sequencing technology and ever broadening application of the methodology. During 2011, we have continued to operate and extend the broad range of ENA services. In particular, we have released major new functionality in our interactive web submission system, Webin, through developments in template-based submissions for annotated sequences and support for raw next-generation sequence read submissions.
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Affiliation(s)
- Clara Amid
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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13
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Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G. The European Nucleotide Archive. Nucleic Acids Res 2011; 39:D28-31. [PMID: 20972220 PMCID: PMC3013801 DOI: 10.1093/nar/gkq967] [Citation(s) in RCA: 330] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 10/03/2010] [Indexed: 11/14/2022] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. The objective of ENA is to support and promote the use of nucleotide sequencing as an experimental research platform by providing data submission, archive, search and download services. In this article, we outline these services and describe major changes and improvements introduced during 2010. These include extended EMBL-Bank and SRA-data submission services, extended ENA Browser functionality, support for submitting data to the European Genome-phenome Archive (EGA) through SRA, and the launch of a new sequence similarity search service.
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Affiliation(s)
- Rasko Leinonen
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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14
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Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen P, Valentin F, Vaughan R, Zalunin V, Zerbino D, Cochrane G. Improvements to services at the European Nucleotide Archive. Nucleic Acids Res 2009; 38:D39-45. [PMID: 19906712 PMCID: PMC2808951 DOI: 10.1093/nar/gkp998] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe’s primary nucleotide sequence archival resource, safeguarding open nucleotide data access, engaging in worldwide collaborative data exchange and integrating with the scientific publication process. ENA has made significant contributions to the collaborative nucleotide archival arena as an active proponent of extending the traditional collaboration to cover capillary and next-generation sequencing information. We have continued to co-develop data and metadata representation formats with our collaborators for both data exchange and public data dissemination. In addition to the DDBJ/EMBL/GenBank feature table format, we share metadata formats for capillary and next-generation sequencing traces and are using and contributing to the NCBI SRA Toolkit for the long-term storage of the next-generation sequence traces. During the course of 2009, ENA has significantly improved sequence submission, search and access functionalities provided at EMBL–EBI. In this article, we briefly describe the content and scope of our archive and introduce major improvements to our services.
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Affiliation(s)
- Rasko Leinonen
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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15
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Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F, Faruque N, Gibson R, Hoad G, Hubbard T, Hunter C, Jang M, Juhos S, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Plaister S, Radhakrishnan R, Robinson S, Sobhany S, Hoopen PT, Vaughan R, Zalunin V, Birney E. Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res 2008; 37:D19-25. [PMID: 18978013 PMCID: PMC2686451 DOI: 10.1093/nar/gkn765] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Dramatic increases in the throughput of nucleotide sequencing machines, and the promise of ever greater performance, have thrust bioinformatics into the era of petabyte-scale data sets. Sequence repositories, which provide the feed for these data sets into the worldwide computational infrastructure, are challenged by the impact of these data volumes. The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis, interpretation and visualization of petabyte-scale data sets. We present here our new repository for next generation sequence data, a brief summary of contents of the ENA and provide details of major developments to submission pipelines, high-throughput rule-based validation infrastructure and data integration approaches.
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Affiliation(s)
- Guy Cochrane
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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