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1. Sustained year-round oceanographic measurements from Rothera Research Station, Antarctica, 1997–2017

Author

Hugh Venables, Michael P. Meredith, Katharine R. Hendry, Petra ten Hoopen, Helen Peat, Alice Chapman, Jennifer Beaumont, Rayner Piper, Andrew J. Miller, Paul Mann, Helen Rossetti, Ali Massey, Terri Souster, Simon Reeves, Mairi Fenton, Sabrina Heiser, Sam Pountney, Sarah Reed, Zoë Waring, Marlon Clark, Emma Bolton, Ryan Mathews, Hollie London, Alice Clement, Emma Stuart, Aurelia Reichardt, Mark Brandon, Melanie Leng, Carol Arrowsmith, Amber Annett, Sian F. Henley, and Andrew Clarke

Subjects
Science
Abstract

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.

Published
2023
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5. European Nucleotide Archive in 2016.

Author

Ana Luisa Toribio, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu 0006, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rossello, Nicole Silvester, Dimitriy Smirnov, Daniel Vaughan, Vadim Zalunin, and Guy Cochrane

Published
2017
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6. Interannual variability in biogeochemical cycling around the island of South Georgia: insights from a new database of macronutrients from productive regions of the Southern Ocean

Author

Katharine R Hendry, Sally Thorpe, Emma F Young, Petra ten Hoopen, Geraint A Tarling, and Michael J Whitehouse

Abstract

A key challenge in understanding carbon cycling in the Southern Ocean is disentangling long-term responses from significant spatial and temporal variability in physical and biogeochemical parameters. As such, there is a critical need for regional long-term observations for the model validation and testing needed for a better mechanistic understanding of primary production drivers. We present a new macronutrient data product for the South Atlantic sector of the Southern Ocean, including depth profiles and underway surface measurements of nitrate, nitrite, ammonium, phosphate, silicic acid, temperature and salinity, collected from 1980 to 2009 and covering most months of the year (https://doi.org/10/h3qr). Using this data product, we explore the differences in shallow and deep-water nutrients around the island of South Georgia that are observed between years. We discuss both the biological and physical driving mechanisms behind this variability, which are interconnected with climate feedbacks. The new data product provides an unprecedented view of biogeochemical cycling in biologically productive regions of the Southern Ocean across a critical period in recent climate history, and illustrates the importance of building these scientifically valuable and FAIR (findability, accessibility, interoperability, and reusability) observational datasets.

Published
2023
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7. Biocuration of functional annotation at the European nucleotide archive.

Author

Richard Gibson, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu 0006, Swapna Pallreddy, Nima Pakseresht, Jeena Rajan, Marc Rossello, Nicole Silvester, Dimitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, and Guy Cochrane

Published
2016
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9. A database of marine macronutrient, temperature and salinity measurements made around the highly productive island of South Georgia, the Scotia Sea and the Antarctic Peninsula between 1980 and 2009

Author

Michael J. Whitehouse, Katharine R. Hendry, Geraint A. Tarling, Sally E. Thorpe, and Petra ten Hoopen

Subjects
General Earth and Planetary Sciences
Abstract

We present a database from substantial collections of macronutrient data made on 20 oceanographic cruises, primarily from around the island of South Georgia and the Scotia Sea. This sector of the Southern Ocean was studied comprehensively during the Discovery Investigations between ∼1920 and 1950 and resulted in the hugely influential Discovery Reports. Following this pioneering research period, there was a lull of several decades prior to the British Antarctic Survey (BAS) initiation of an offshore biological programme to study the ecology of the South Atlantic sector of the Southern Ocean. These studies began in the late 1970s and have continued until the present day. Between 1980 and 2009, the programme included macronutrient measurements as part of an integrated ecosystem analysis. In addition to South Georgia and the Scotia Sea, measurements were also made in the Bellingshausen Sea and the waters to the west of the Antarctic Peninsula. Data were collected during all months of the year with the exceptions of May and June and compiled into a database. Vertical profile samples were taken from water bottles, while data along transects were collected by monitoring the ship's non-toxic seawater supply. Nutrients measured were silicate (Si(OH)4–Si), phosphate (PO4–P), nitrate (NO3–N), ammonium (NH4–N), and nitrite (NO2–N). Our database includes nutrient data along with contemporaneous temperature and salinity data where available. Further background and supporting information is included for context. The profile and underway sample data have been deposited at the UK Polar Data Centre and are publicly available in NetCDF and CSV formats from https://doi.org/10.5285/4014370F-8EB2-492B-A5F3-6DC68BF12C1E (Whitehouse et al., 2022).

Published
2023

10. Content discovery and retrieval services at the European Nucleotide Archive.

Author

Nicole Silvester, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Simon Kay, Rasko Leinonen, Weizhong Li 0001, Xin Liu 0006, Rodrigo Lopez, Nima Pakseresht, Swapna Pallreddy, Sheila Plaister, Rajesh Radhakrishnan, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, and Guy Cochrane

Published
2015
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12. Assembly information services in the European Nucleotide Archive.

Author

Nima Pakseresht, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Tamer Gur, Mikyung Jang, Simon Kay, Rasko Leinonen, Weizhong Li 0001, Xin Liu 0006, Rodrigo Lopez, Hamish McWilliam, Arnaud Oisel, Swapna Pallreddy, Sheila Plaister, Rajesh Radhakrishnan, Stéphane Rivière, Marc Rossello, Alexander Senf, Nicole Silvester, Dimitriy Smirnov, Silvano Squizzato, Petra ten Hoopen, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, and Guy Cochrane

Published
2014
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13. Facing growth in the European Nucleotide Archive.

Author

Guy Cochrane, Blaise T. F. Alako, Clara Amid, Lawrence Bower, Ana Cerdeño-Tárraga, Iain Cleland, Richard Gibson, Neil Goodgame, Mikyung Jang, Simon Kay, Rasko Leinonen, Xiu Lin, Rodrigo Lopez, Hamish McWilliam, Arnaud Oisel, Nima Pakseresht, Swapna Pallreddy, Young Mi Park, Sheila Plaister, Rajesh Radhakrishnan, Stéphane Rivière, Marc Rossello, Alexander Senf, Nicole Silvester, Dimitriy Smirnov, Petra ten Hoopen, Ana Luisa Toribio, Daniel Vaughan, and Vadim Zalunin

Published
2013
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14. A database of marine macronutrient, temperature and salinity measurements made around the highly productive island of South Georgia, the Scotia Sea and the Antarctic Peninsula between 1980–2009

Author

Michael J. Whitehouse, Katharine R. Hendry, Geraint A. Tarling, Sally E. Thorpe, and Petra ten Hoopen

Abstract

We present a database from substantial collections of macronutrient data made on 20 oceanographic cruises, primarily from around the island of South Georgia and the Scotia Sea. This sector of the Southern Ocean was studied comprehensively during the Discovery Investigations between ~1920 and 1950 and resulted in the hugely influential Discovery Reports. Following this pioneering research period, there was a lull of several decades prior to the British Antarctic Survey’s (BAS) initiation of an offshore biological programme to study the ecology of the South Atlantic sector of the Southern Ocean. These studies began in the late 1970s and have continued until the present day. Between 1980–2009, the programme included macronutrient measurements as part of an integrated ecosystem analysis. In addition to South Georgia and the Scotia Sea, measurements were also made in the Bellingshausen Sea and the waters to the west of the Antarctic Peninsula. Data were collected during all months of the year with the exceptions of May and June and compiled into a database. Vertical profile samples were taken from water bottles while data along transects were collected through monitoring the ship’s non-toxic seawater supply. Nutrients measured were silicate, Si(OH)4-Si; phosphate, PO4-P; nitrate, NO3-N; ammonium NH4-N; and nitrite, NO2-N. Our database includes nutrient data along with contemporaneous temperature and salinity data where available. Further background and supporting information are included for context.

Published
2022

15. Major submissions tool developments at the European nucleotide archive.

Author

Clara Amid, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Richard Gibson, Neil Goodgame, Christopher I. Hunter, Mikyung Jang, Rasko Leinonen, Xin Liu 0006, Arnaud Oisel, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Stéphane Rivière, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Petra ten Hoopen, Daniel Vaughan, Robert Vaughan 0001, Vadim Zalunin, and Guy Cochrane

Published
2012
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16. The European Nucleotide Archive.

Author

Rasko Leinonen, Ruth Akhtar, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Mikyung Jang, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Siamak Sobhany, Petra ten Hoopen, Robert Vaughan 0001, Vadim Zalunin, and Guy Cochrane

Published
2011
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17. Improvements to services at the European Nucleotide Archive.

Author

Rasko Leinonen, Ruth Akhtar, Ewan Birney, James K. Bonfield, Lawrence Bower, Matthew Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher I. Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra ten Hoopen, Franck Valentin, Robert Vaughan 0001, Vadim Zalunin, Daniel R. Zerbino, and Guy Cochrane

Published
2010
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18. Petabyte-scale innovations at the European Nucleotide Archive.

Author

Guy Cochrane, Ruth Akhtar, James K. Bonfield, Lawrence Bower, Fehmi Demiralp, Nadeem Faruque, Richard Gibson, Gemma Hoad, Tim J. P. Hubbard, Christopher I. Hunter, Mikyung Jang, Szilveszter Juhos, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Sheila Plaister, Rajesh Radhakrishnan, Stephen Robinson, Siamak Sobhany, Petra ten Hoopen, Robert Vaughan 0001, Vadim Zalunin, and Ewan Birney

Published
2009
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19. Value, but high costs in post-deposition data curation.

Author

Petra ten Hoopen, Clara Amid, Pier Luigi Buttigieg, Evangelos Pafilis, Panos Bravakos, Ana Cerdeño-Tárraga, Richard Gibson, Tim Kahlke, Aglaia Legaki, Kada Narayana Murthy, Gabriella Papastefanou, Emiliano Pereira, Marc Rossello, Ana Luisa Toribio, and Guy Cochrane

Published
2016
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20. Antibody-mediated modulation of cytokinins in tobacco: organ-specific changes in cytokinin homeostasis

Author

Miroslav Strnad, Markéta Pernisová, Lubomír Janda, Václav Motyka, Siarhei A. Dabravolski, Zuzana Gelová, Udo Conrad, Isolde Tillack, Ondřej Novák, Jan Hejátko, Vojtěch Didi, Bettina Hause, Jana Oklešťková, Petra ten Hoopen, and Danka Haruštiaková

Subjects
0106 biological sciences, 0301 basic medicine, Cytokinins, Physiology, Plant Science, 01 natural sciences, Plantibodies, Isopentenyladenosine, 03 medical and health sciences, chemistry.chemical_compound, Plant Growth Regulators, Biosynthesis, Tobacco, Homeostasis, heterocyclic compounds, Mode of action, chemistry.chemical_classification, Endoplasmic reticulum, fungi, food and beverages, Metabolism, Riboside, Cell biology, Phenotype, 030104 developmental biology, Enzyme, chemistry, Seedlings, Shoot, Cytokinin, 010606 plant biology & botany
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.

Published
2017
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21. DNA and RNA backups v1

Author

Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker

Subjects
chemistry.chemical_compound, Biochemistry, chemistry, RNA, DNA
Abstract

This protocol is part of Nucleic acids preparationsforViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition.

Published
2018
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22. Sequencing and data quality control v1

Author

Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker

Subjects
Computer science, Data quality, Control (management), Data mining, computer.software_genre, computer
Abstract

This protocol describes the sequencing and data quality control for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 3:Overview of experimental pipeline from nucleic acids to sequences. (Red crosses highlight QC steps where experiments can be stopped.)

Published
2018
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23. Sequencing library preparation v1

Author

Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker

Subjects
Computer science, Library preparation, Operating system, computer.software_genre, computer, Protocol (object-oriented programming)
Abstract

This protocol describes the sequencing library preparation for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.

Published
2018
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24. Handling of genomics samples v1

Author

Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker

Subjects
Genomics, Computational biology, Biology
Abstract

This protocol describes the handling of genomics samples for the Tara Oceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.

Published
2018
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25. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition v1

Author

Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker

Abstract

The protocols in this collection are from the Alberti A., et al manuscript (Alberti A. 2017, Scientific Data). These protocols 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). This collection complements other efforts to provide a full description of experiments and open science resources generated from theTaraOceans project, further extending their value for the study of the world’s planktonic ecosystems.' From the Methods section: 'The generation of information-rich data from marine plankton samples presents unique challenges that are inherent to the particular sampling conditions at sea and the wide spectrum of organisms included in that environment. All processing steps, including biomass collection, sample preservation, nucleic acids extractions and sequencing library preparation, are critical and require specific protocols and robust methods in order to ensure comparability of results and limit potential biases. Our methods were either developed specifically forTaraOceans samples or carefully selected among existing ones in order to meet the requirements of our sequencing strategy and to produce optimized datasets for downstream bioinformatics analyses, as for example the production of overlapping reads from metagenomics libraries to facilitate assembly. They are presented in five sub-sections, starting with a brief description of how samples were handled between the research vessel and the processing laboratories (protocol 1). Protocol 2reports on DNA and RNA extractions procedures for -omics analyses, including the generation of amplified genomic DNA from uncultured isolated unicellular eukaryotes. The generation of 18S and 16S rRNA amplicons from DNA of specific size-fractions is described in protocol 3 and Illumina libraries preparation in protocol 4. Sequencing procedures and post-sequencing data processing are described in protocol 5. For details on the onboard sampling protocols, see Pesantet al.'

Published
2018
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26. Nucleic acids preparations v1

Author

Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker

Subjects
Biochemistry, Nucleic acid
Abstract

This protocol describes thenucleic acids preparations for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.

Published
2018
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27. 18S and 16S rRNA genes amplicon generation for eukaryotic and prokaryotic metabarcoding v1

Author

Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, and Patrick Wincker

Subjects
Genetics, Amplicon, Biology, 16S ribosomal RNA, Gene
Abstract

This protocol describes the 18S and 16S rRNA genes amplicon generation for eukaryotic and prokaryotic metabarcoding for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.

Published
2018
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28. The metagenomic data life-cycle: standards and best practices

Author

Alex L. Mitchell, Graziano Pesole, Petra ten Hoopen, Robert D. Finn, Bruno Fosso, Lars Ailo Bongo, Eric Pelletier, Nils Peder Willassen, Guy Cochrane, Monica Santamaria, Folker Meyer, Erwan Corre, Wellcome Trust Genome Campus, The Arctic University of Norway [Tromsø, Norway] (UiT), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), CNR - Bari, Argonne National Lab., Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université d'Évry-Val-d'Essonne (UEVE), Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), The Arctic University of Norway, University of Bari Aldo Moro (UNIBA), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay

Subjects
0301 basic medicine, sampling, [SDV]Life Sciences [q-bio], Best practice, best practice, data analysis, Health Informatics, Review, Biology, VDP::Matematikk og Naturvitenskap: 400::Informasjons- og kommunikasjonsvitenskap: 420, Workflow, 03 medical and health sciences, Marine research, VDP::Mathematics and natural science: 400::Information and communication science: 420, 0302 clinical medicine, Databases, Genetic, Data Mining, Repurposing, metadata, Computational Biology, Sampling (statistics), standard, sequencing, Data life cycle, Data science, Computer Science Applications, Metadata, 030104 developmental biology, Metagenomics, Metagenome, Sequence Analysis, 030217 neurology & neurosurgery
Abstract

Source at https://doi.org/10.1093/gigascience/gix047. Accepted manuscript version, licensed CC BY-NC-ND 4.0. 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.

Published
2017
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29. Plant specimen contextual data consensus

Author

Petra ten Hoopen, Ilene Karsch-Mizrachi, Pelin Yilmaz, Ethalinda K. S. Cannon, Anjanette Johnston, Guy Cochrane, James R. Cole, and Ramona Walls

Subjects
Societies, Scientific, 0301 basic medicine, Knowledge management, Interoperability, Health Informatics, Genomics, Sample (statistics), Article, World Wide Web, 03 medical and health sciences, Contextual design, Political science, Specimen, Metadata, business.industry, Conation, Plant specimen, Plant, Plants, Checklist, Computer Science Applications, Contextual data, 030104 developmental biology, business, Functional genomics, Genome, Plant
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.

Published
2016
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30. Major submissions tool developments at the European nucleotide archive

Author

Sheila Plaister, Marc Rossello, Dimitriy Smirnov, Petra ten Hoopen, Neil Goodgame, Daniel Vaughan, Stéphane Rivière, Nima Pakseresht, Rajesh Radhakrishnan, Rasko Leinonen, Clara Amid, Iain Cleland, Nadeem Faruque, Kethi Reddy, Robert Vaughan, Lawrence Bower, Alexander Senf, Xin Liu, Richard Gibson, Christopher I. Hunter, Guy Cochrane, Vadim Zalunin, Ana Cerdeño-Tárraga, Mikyung Jang, Arnaud Oisel, Ying Cheng, and Ewan Birney

Subjects
European Nucleotide Archive, 0206 medical engineering, Genomics, 02 engineering and technology, Biology, World Wide Web, 03 medical and health sciences, User-Computer Interface, Genetics, Base sequence, Sequence Read Archive, 030304 developmental biology, 0303 health sciences, Internet, business.industry, Sequence Analysis, RNA, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Articles, Sequence Analysis, DNA, The Internet, Raw data, business, Databases, Nucleic Acid, 020602 bioinformatics, Software
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.

Published
2011

31. Improvements to services at the European Nucleotide Archive

Author

Rajesh Radhakrishnan, Daniel R. Zerbino, Rasko Leinonen, Matthew Corbett, Richard Gibson, Christopher I. Hunter, Robert Vaughan, Siamak Sobhany, Vadim Zalunin, Franck Valentin, Neil Goodgame, Sheila Plaister, Petra ten Hoopen, Hamish McWilliam, Gemma Hoad, Ewan Birney, Lawrence Bower, Michael Maguire, Quan Lin, Mikyung Jang, Ruth Akhtar, Rodrigo Lopez, Steven Leonard, Guy Slater, Ying Cheng, Guy Cochrane, Nadeem Faruque, Fehmi Demiralp, and James K. Bonfield

Subjects
European Nucleotide Archive, Information Storage and Retrieval, Biology, Bioinformatics, World Wide Web, Access to Information, 03 medical and health sciences, Databases, Genetic, Genetics, Animals, Humans, Sequence Read Archive, 030304 developmental biology, 0303 health sciences, Internet, business.industry, 030302 biochemistry & molecular biology, Computational Biology, Articles, DNA, Metadata, Europe, Data access, Data exchange, GenBank, Table (database), The Internet, business, Databases, Nucleic Acid, Algorithms, Software
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.

Published
2009

32. Immunomodulation of jasmonate to manipulate the wound response

Author

Axel Müller, Bettina Hause, Petra ten Hoopen, Udo Conrad, Sabine Rosahl, Astrid Hunger, Claus Wasternack, and Robert Kramell

Subjects
Methyl jasmonate, biology, Physiology, Endoplasmic reticulum, Transgene, Nicotiana tabacum, Jasmonic acid, fungi, food and beverages, Germination, Cyclopentanes, Plant Science, Endoplasmic Reticulum, Plants, Genetically Modified, biology.organism_classification, Antibodies, Cytosol, chemistry.chemical_compound, chemistry, Biochemistry, Tobacco, Gene expression, Oxylipins, Jasmonate
Abstract

Jasmonates are signals in plant stress responses and development. The exact mode of their action is still controversial. To modulate jasmonate levels intracellularly as well as compartment-specifically, transgenic Nicotiana tabacum plants expressing single-chain antibodies selected against the naturally occurring (3R,7R)-enantiomer of jasmonic acid (JA) were created in the cytosol and the endoplasmic reticulum. Consequently, the expression of anti-JA antibodies in planta caused JA-deficient phenotypes such as insensitivity of germinating transgenic seedlings towards methyl jasmonate and the loss of wound-induced gene expression. Results presented here suggest an essential role for cytosolic JA in the wound response of tobacco plants. The findings support the view that substrate availability takes part in regulating JA biosynthesis upon wounding. Moreover, high JA levels observed in immunomodulated plants in response to wounding suggest that tobacco plants are able to perceive a reduced level of physiologically active JA and attempt to compensate for this by increased JA accumulation.

Published
2007
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33. Value, but high costs in post-deposition data Curation

Author

Evangelos Pafilis, Emiliano Pereira, Aglaia Legaki, Pier Luigi Buttigieg, Richard Gibson, Tim Kahlke, Kada Narayana Murthy, Ana Luisa Toribio, Marc Rossello, Ana Cerdeño-Tárraga, Clara Amid, Gabriella Papastefanou, Panos Bravakos, Guy Cochrane, and Petra ten Hoopen

Subjects
0106 biological sciences, 0301 basic medicine, European Nucleotide Archive, Computer science, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Environmental data, 03 medical and health sciences, Annotation, Humans, Ecosystem, Information retrieval, Data collection, Data curation, Geography, business.industry, Data Collection, Microbiota, Computational Biology, Usability, Molecular Sequence Annotation, Data science, Discoverability, Semantics, Europe, 030104 developmental biology, Original Article, Metagenomics, General Agricultural and Biological Sciences, business, Databases, Nucleic Acid, Sequence Analysis, Information Systems
Abstract

© The Author(s) 2016. Published by Oxford University Press. Discoverability of sequence data in primary data archives is proportional to the richness of contextual information associated with the data. Here, we describe an exercise in the improvement of contextual information surrounding sample records associated with metagenomics sequence reads available in the European Nucleotide Archive. We outline the annotation process and summarize findings of this effort aimed at increasing usability of publicly available environmental data. Furthermore, we emphasize the benefits of such an exercise and detail its costs. We conclude that such a third party annotation approach is expensive and has value as an element of curation, but should form only part of a more sustainable submitter-driven approach.

Published
2015

34. Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards

Author

Mesude Bicak, Catherine Borremans, S. Dekeyzer, Simon Claus, Stephane Pesant, Renzo Kottmann, Anna Kopf, Guy Cochrane, Dick Ma Schaap, Chris Bowler, Klaas Deneudt, Frank Oliver Glöckner, Petra ten Hoopen, and Peter Thijsse

Subjects
Service (systems architecture), Marine, Bioinformatics, business.industry, Interoperability, Biodiversity, Molecular, Sample (statistics), Biology, Biotechnology, Data Standard, Data standard, Microbial, Contextual design, Reporting, Metagenomics, Commentary, Genetics, 14. Life underwater, Data reporting, business
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

Published
2015
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35. The barley two-pore K+-channel HvKCO1 interacts with 14-3-3 proteins in an isoform specific manner

Author

Jos Mol, Petra ten Hoopen, Mark P. Sinnige, Peter J. Schoonheim, Albertus H. de Boer, Paul W.J. van den Wijngaard, and Ilja Roobeek

Subjects
Gene isoform, biology, Plant Science, General Medicine, biology.organism_classification, Cell biology, Electrophysiology, Membrane, Biochemistry, Arabidopsis, Genetics, Hordeum vulgare, Patch clamp, Surface plasmon resonance, Agronomy and Crop Science, Gene
Abstract

Members of the highly conserved family of 14-3-3 proteins play an important role in various cellular processes. Recent studies, using electrophysiological techniques, show that the 14-3-3 proteins also regulate plasma membrane and vacuolar K+ conducting channels. The molecular mechanism behind the regulatory effect of 14-3-3 proteins on K+ channels remains to be shown. One vacuolar channel down-regulated by 14-3-3 proteins is the slow-activating vacuolar (SV) channel. In Arabidopsis, the protein coded by the KCO1 gene was recently shown to be present in the vacuolar membrane and identified as a component of the SV channel. These two observations raised the question whether the KCO1 protein does interact with 14-3-3 proteins. Therefore, we isolated the barley HvKCO1 gene and the encoded protein indeed contains a canonical 14-3-3 interaction motif, which is conserved in all other KCO1 orthologues from other plant species. Using surface plasmon resonance (SPR) we determined in real-time the affinity between the phospho-peptide derived from the putative KCO1 14-3-3 interaction motif and three barley 14-3-3 proteins. The 14-3-3A protein showed the highest affinity, whereas the binding of all three isoforms was dependent on the presence of either Ca2+ or Mg2+. Interestingly, the barley SV current was strongly reduced by 14-3-3B and C protein, but not by 14-3-3A. This difference between the SPR and patch-clamp data will be discussed, along with the role for Ca2+ in activation of the SV channel by direct interaction and inactivation of the channel by facilitating the binding of 14-3-3 to the channel.

Published
2005
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36. The Ocean Sampling Day Consortium

Author

Oleksandra Bobrova, Petra ten Hoopen, Rodrigo Costa, Rania Siam, Rehab Z. Abdallah, Jorge A. Herrera Silveira, Catarina Magalhães, Nedime Serakinci, Marie E. DeLorenzo, Riccardo Rosselli, Paul Malthouse, Lise Øvreås, Eyjólfur Reynisson, Susan Gebbels, Francesca Malfatti, Frank Oliver Glöckner, Federico M. Lauro, Hans Erik Karlsen, David Wallom, Christian Jeanthon, Mark J. Costello, Fergal O'Gara, Nadezhda Todorova, Ana C. Costa, Monia El Bour, Paul D. van Ruth, Ivaylo Kostadinov, Martin Ostrowski, Jed A. Fuhrman, Viggo Marteinsson, Thierry Cariou, Hiroyuki Ogata, Maria Luiza Pedrotti, Emilie Villar, Federico Baltar, Sandi Orlić, Valentina Turk, Katja Lehmann, Dawn Field, Renzo Kottmann, Florence Jude-Lemeilleur, Daniel Vaulot, Alessandro Vezzi, Neil M Davies, Mahrous M. Kandil, Véronique Berteaux-Lecellier, Christopher D. Sinigalliano, Timothy W. Davis, Peter N. Golyshin, Stéphane L'Haridon, Jonathan A. Martinez, Sandra Ramos, Pascal Conan, Ma. Leopoldina Aguirre-Macedo, Antonio Fernandez-Guerra, Soumya Essayeh, Clara Loureiro, Edvardsen Bente, Noureddine Boukhatem, Rachelle M. Jensen, Sophie Pitois, Bouchra Chaouni, Kate Munnik, Anke Kremp, Stephane Pesant, Roberto Danovaro, Cecilia Alonso, Said Barrijal, Jodie van de Kamp, Michail M. Yakimov, Nicole J. Poulton, Zackary I. Johnson, Adriana Zingone, Bernardo Duarte, Ilkay Salihoglu, Paraskevi N. Polymenakou, Jack A. Gilbert, Melody S. Clark, Ian Salter, Hassan Ghazal, Julie LaRoche, J. Mortelmans, Ranjith Edirisinghe, Grazia Marina Quero, Dion Matthew Frederick Frampton, Isabel Caçador, Georgios Tsiamis, Declan C. Schroeder, Jamie Hinks, Ana Martins, Noga Stambler, Rachel Collin, João Canning-Clode, Tinkara Tinta, Mesude Bicak, Scott Jones, Valentina Amaral, Matthias S. Ullrich, Gunnar Gerdts, Klaas Deneudt, Michael Steinke, Mohamed Bennani, Rafael Santana, Fabio De Pascale, Jennifer Tolman, Juan Iriberri, Levente Bodrossy, Abderrahim Bouali, Antonella Penna, Bruno Cataletto, Josep M. Gasol, Florencia Biancalana, Maribeth L. Gidley, Stephen A. Jackson, Mahmut Cerkez Ergoren, Carolin R. Löscher, Antje Wichels, Ventzislav Karamfilov, R. Eric Collins, Sara Ettamimi, Riccardo Schiavon, Mohammed Timinouni, Christina Bienhold, Julia Schnetzer, Marc E. Frischer, Wayne J. Fuller, Simon Claus, Ibon Cancio, Guy Cochrane, Patrick Martin, Gian Marco Luna, Snejana Moncheva, Linda A. Amaral-Zettler, Eva C. Sonnenschein, Paul Anders Fronth Nyhus, Shiao Y. Wang, Antonina Dos Santos, Eyal Rahav, Eileen Bresnan, Anna Kopf, Barker Katherine, Michèle Barbier, Naiara Rodríguez-Ezpeleta, Kemal Can Bizsel, Tim Ingleton, Patricia Wecker, Julia A. Busch, Kelly D. Goodwin, El Houcine Zaid, Rajaa Chahboune, Takashi Yoshida, Fatima El Otmani, Marianna Mea, Nina Dzhembekova, Anne-Lise Ducluzeau, Christopher P. Meyer, Georgios Kotoulas, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Jacobs University [Bremen], University of Oxford, Centre for Ecology & Hydrology, Oxfordshire UK, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Israel Oceanographic and Limnological Research (IOLR), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Hellenic Centre for Marine Research (HCMR), American University in Cairo, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University College Cork (UCC), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Institut Ruder Boskovic, Institut Ruđer Bošković (IRB), University of Essex, Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Universidade de Lisboa = University of Lisbon (ULISBOA), Smithonian Environmental Research Center, Research Center, Odessa National I.I.Mechnikov University, Matis Ltd, Universidade dos Açores, Istituto di Science Marine (ISMAR ), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Finnish Environment Institute (SYKE), National Oceanic and Atmospheric Administration (NOAA), University of Bergen (UiB), Dalhousie University [Halifax], Università di Urbino, Skidaway Institute of Oceanography, Smithsonian Institution, Interdisciplinary Centre of Marine and Environmental Research [Matosinhos, Portugal] (CIIMAR), Universidade do Porto = University of Porto, Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mississippi State University [Mississippi], Bigelow Laboratory for Ocean Sciences, Smithsonian Marine Station, Smithsonian Tropical Research Institute, University of Southern California (USC), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Universidad de la República [Montevideo] (UDELAR), Bar-Ilan University [Israël], The Interuniversity Institute for marine Science in Eilat, IAMC-CNR, Istituto per l'Ambiente Marino Costiero &ndash, University of Otago [Dunedin, Nouvelle-Zélande], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Macquarie University, South Australian Research and Development Institute (SARDI), South Australian Research and Development Institute, Flanders Marine Institute, VLIZ, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), University of Algarve [Portugal], Marine Biological Association of the UK, Department of Chemistry, Alexandria University [Alexandrie], Argentine Institute of Oceanography, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, University of Tasmania [Hobart, Australia] (UTAS), Waters, wetlands & coasts Sydney, Lwande technologies Cape Town, AZTI (AZTI), AZTI, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Université Mohammed Premier [Oujda], Université Mohammed V de Rabat [Agdal] (UM5), Université Sidi Mohamed Ben Abdellah (USMBA), Université Abdelmalek Essaâdi (UAE), Institut Pasteur du Maroc, Réseau International des Instituts Pasteur (RIIP), Faculty of Sciences, Rabat, Morocco., Bulgarian Academy of Sciences (BAS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Université de Brest (UBO), Dokuz Eylül Üniversitesi = Dokuz Eylül University [Izmir] (DEÜ), Università degli Studi di Padova = University of Padua (Unipd), Singapore centre for environmental life sciences engineering, Nanyang Technological University [Singapour], Indigo V Expeditions, Newcastle University [Newcastle], Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Universität Bremen, Istituto Nazionale di Geofisica e di Oceanografia Sperimentale (OGS), Rajarata University of Sri-Lanka (RUSL), University of Southern Mississippi (USM), Mediterranean Science Commission, National institute of biology Fornace, Near East University, Marine Scotland Marine Laboratory, Kind of Blue Project ABS, University of Oslo (UiO), Marine biology research station, Bangor University, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Fridtjof Nansen Institute of oceanology, Duke University [Durham], Miami University, Miami University [Ohio] (MU), Stazione Zoologica Anton Dohrn (SZN), Polytechnic University of Marche, University of Patras, British Antarctic Survey (BAS), Natural Environment Research Council (NERC), INSTIM, University of Alaska [Fairbanks] (UAF), University of Hawaii, University of Auckland [Auckland], Marine Biological Laboratory (MBL), University of Chicago, Brown University, Zhejiang University, Argonne National Laboratory [Lemont] (ANL), Department of Mathematics [Berkeley], University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Repositório da Universidade de Lisboa, 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, Cacador, I, Canning-Clode, J, Bobrova, O, Marteinsson, V, Reynisson, E, Loureiro, Cm, Luna, Gm, Quero, Gm, Loscher, Cr, Kremp, A, Delorenzo, Me, Ovreas, L, Tolman, J, Laroche, J, Penna, A, Frischer, M, Davis, T, Katherine, B, Meyer, Cp, Ramos, S, Magalhaes, 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, Dmf, 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, E, 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, M, Costa, Ac, El Bour, M, Martins, Am, Collins, Re, Ducluzeau, Al, Martinez, J, Costello, Mj, Amaral-Zettler, La, Gilbert, Ja, Davies, N, Field, D, Glockner, Fo, European Commission, University of Oxford [Oxford], Israel Oceanographic and Limnological Research - IOLR (ISRAEL), Danmarks Tekniske Universitet (DTU), Carl Von Ossietzky Universität Oldenburg, Universidade de Lisboa (ULISBOA), Consiglio Nazionale delle Ricerche (CNR), Universidade do Porto, UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Universidad de la República [Montevideo] (UCUR), Kyoto University [Kyoto], Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), University of Mohammed V, Sidi Mohammed Ben Abdellah University, Universita degli Studi di Padova, Rajarata University of Sri-Lanka, University of Patras [Patras], University of California [Berkeley], and University of California-University of California

Subjects
0106 biological sciences, Biodiversity, Marine life, 01 natural sciences, Bacteria, Genomics, Health Index, Marine, Metagenomics, Micro B3, Microorganism, OSD, Ocean sampling day, Standards, 11. Sustainability, Data and Information, Ocean Sampling Day, biodiversity, genomics, health index, bacteria, microorganism, metagenomics, marine, standards, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Ecology, Environmental resource management, Geology, Computer Science Applications, Interdisciplinary Natural Sciences, Microbial biodiversity, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Ocean sampling day, OSD, Biodiversity, Genomics, Health Index, Bacteria, Microorganism, Metagenomics,Marine, Micro B3, Standards, Oceans and Seas, Microorganisms, Marine Biology, Health Informatics, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Ecology and Environment, Metagenomic, 03 medical and health sciences, Health index, Medisinske Fag: 700 [VDP], SDG 14 - Life Below Water, 14. Life underwater, 030304 developmental biology, business.industry, 010604 marine biology & hydrobiology, Ocean sampling, 13. Climate action, Commentary, Genomic, Database Management Systems, Global Ocean, business
Abstract

Kopf, Anna ... et. al.-- 5 pages, 1 figure.-- This manuscript is NOAA-GLERL contribution number 1763, 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, This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589

Published
2015
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38. ENA as an Information Hub

Author

Ruth Akhtar, Petra ten Hoopen, Richard Gibson, Bob Vaughan, Guy Cochrane, and Nadeem Faruque

Subjects
Data flow diagram, Identifier, European Nucleotide Archive, Shotgun sequencing, Computer science, Validator, Nucleic acid sequence, General Materials Science, Data set (IBM mainframe), Computational biology, Genome
Abstract

The European Nucleotide Archive (ENA; "http://www.ebi.ac.uk/ena/":http://www.ebi.ac.uk/ena/) is a comprehensive repository for public nucleotide sequence data from nearly four hundred thousand taxonomic nodes. Together with partners in the International Nucleotide Sequence Database Collaboration (INSDC; EBI, NCBI and DDBJ) we provide a broad spectrum of sequences, from raw reads (Sequence Read Archive data class), assembled contigs (Whole Genome Shotgun data class), assemblies of EST transcripts (Transcriptome Shotgun Assembly data set), to partial or complete assembled nucleic acid molecules with functional annotation derived from direct and third party experimental evidence (Standard and TPA data classes, respectively). Resources beyond ENA, such as RNA and protein databases, genome collections and model organism services, use data stored and presented at ENA as both source and underlying supporting evidence for their records. Integration of the growing wealth of molecular information is a great challenge that brings opportunities for ENA to serve as a bioinformatics data information hub, allowing, through its provision of permanent identifiers for sequence and project records, community-recognized identifiers for navigation across databases.As a comprehensive repository of directly sequenced nucleic acid molecules we have the unique opportunity to obtain exact provenance information directly from the submitting researchers. Our pre-publication biocuration efforts are focused on obtaining rich and accurate information on the sample that has been sequenced and on the methodology surrounding its preparation for sequencing. We present here an insight into data flow in the archive and a straightforward biologist-orientated submission system with a rule-based validator for smaller sets of sequences.

Published
2010
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39. Content discovery and retrieval services at the European Nucleotide Archive

Author

Ana Cerdeño-Tárraga, Rasko Leinonen, Swapna Pallreddy, Richard Gibson, Sheila Plaister, Neil Goodgame, Simon Kay, Dimitriy Smirnov, Nicole Silvester, Alexander Senf, Guy Cochrane, Rodrigo Lopez, Nima Pakseresht, Iain Cleland, Blaise T. F. Alako, Daniel Vaughan, Vadim Zalunin, Marc Rossello, Clara Amid, Weizhong Li, Xin Liu, Ana Luisa Toribio, Rajesh Radhakrishnan, and Petra ten Hoopen

Subjects
European Nucleotide Archive, Base Sequence, business.industry, media_common.quotation_subject, Data discovery, Molecular Sequence Annotation, Usability, Genomics, Content discovery, Biology, Bioinformatics, Discoverability, World Wide Web, Presentation, Resource (project management), Genetics, Database Issue, Databases, Nucleic Acid, business, Sequence Analysis, Sophistication, media_common
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.

40. Assembly information services in the European Nucleotide Archive

Author

Clara Amid, Dimitriy Smirnov, Rajesh Radhakrishnan, Rasko Leinonen, Stéphane Rivière, Petra ten Hoopen, Nicole Silvester, Ana Cerdeño-Tárraga, Richard Gibson, Sheila Plaister, Ana Luisa Toribio, Tamer Gur, Mikyung Jang, Swapna Pallreddy, Alexander Senf, Nima Pakseresht, Simon Kay, Rodrigo Lopez, Blaise T. F. Alako, Vadim Zalunin, Iain Cleland, Weizhong Li, Arnaud Oisel, Xin Liu, Daniel Vaughan, Silvano Squizzato, Guy Cochrane, Marc Rossello, Neil Goodgame, and Hamish McWilliam

Subjects
Internet, European Nucleotide Archive, Service (systems architecture), I. Nucleic acid sequence, structure and regulation, business.industry, Sequence assembly, Genomics, Biology, Public domain, Bioinformatics, Europe, World Wide Web, Functional annotation, Genetics, Information system, Base sequence, The Internet, Databases, Nucleic Acid, business
Abstract

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the world public domain nucleotide sequence data output. ENA content covers a spectrum of data types including raw reads, assembly data and functional annotation. ENA has faced a dramatic growth in genome assembly submission rates, data volumes and complexity of datasets. This has prompted a broad reworking of assembly submission services, for which we now reach the end of a major programme of work and many enhancements have already been made available over the year to components of the submission service. In this article, we briefly review ENA content and growth over 2013, describe our rapidly developing services for genome assembly information and outline further major developments over the last year.

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