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1. UniProt: the universal protein knowledgebase in 2021.

Author

Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan W. Sousa da Silva, Paul Denny 0002, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Leyla Jael García Castro, Penelope Garmiri, George E. Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra 0004, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodríguez-López, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan J. Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard De Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Béatrice A. Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang 0003, Yuqi Wang, Lai-Su Yeh, Jian Zhang 0051, Patrick Ruch, and Douglas Teodoro

Published
2021
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2. The European Nucleotide Archive in 2017.

Author

Nicole Silvester, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Laura Clarke, Iain Cleland, Peter W. Harrison, Suran Jayathilaka, Simon Kay, Thomas M. Keane, Rasko Leinonen, Xin Liu 0006, Josué Martínez-Villacorta, Manuela Menchi, Kethi Reddy, Nima Pakseresht, Jeena Rajan, Marc Rossello, Dmitriy Smirnov 0002, Ana Luisa Toribio, Daniel Vaughan, Vadim Zalunin, and Guy Cochrane

Published
2018
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3. UniProt: the universal protein knowledgebase in 2021

Author

Fábio Madeira, Emmanuel Boutet, Ursula Hinz, Teresa Batista Neto, Parit Bansal, Manuela Pruess, Kristian B. Axelsen, Arnaud Kerhornou, Cecilia N. Arighi, Lai-Su L. Yeh, Shadab Ahmad, John S. Garavelli, Cathy H. Wu, Florence Jungo, Alan Bridge, Leonardo Gonzales, Sandra Orchard, Patrick Masson, Douglas Teodoro, Maria Jesus Martin, Anne Estreicher, Kamal Chikh Echioukh, Hongzhan Huang, Patrick Ruch, Christian J. A. Sigrist, C. R. Vinayaka, Yvonne Lussi, Anne Morgat, Yongxing Chen, Austra Cukura, Emanuele Alpi, Ramona Britto, Alexandr Ignatchenko, Sylvain Poux, Rizwan Ishtiaq, Lionel Breuza, Jun Fan, Edouard de Castro, Petteri Jokinen, Nicole Redaschi, Darren A. Natale, Daniel Rice, Giuseppe Insana, George Georghiou, Nevila Hyka-Nouspikel, Karen E. Ross, Katie Moulang, Vicente Lara, Arnaud Gos, Michael Tognolli, Alok Mishra, Ivo Pedruzzi, Nidhi Tyagi, Leyla Jael Garcia Castro, Edward Turner, Cristina Casals-Casas, Tunca Doğan, Nadine Gruaz-Gumowski, Chantal Hulo, Maria Livia Famiglietti, Andrew Nightingale, Paul Denny, Lucila Aimo, Rossana Zaru, Vishal Joshi, Alistair MacDougall, Andre Stutz, Penelope Garmiri, Carla Susana Oliveira, Hermann Zellner, Marie-Claude Blatter, Emily H Bowler-Barnett, Philippe Le Mercier, Abdulrahman Hussein, Catherine Rivoire, Tony Sawford, Milagros Rodriguez Lopez, Salvo Paesano, Vladimir Volynkin, Manuela Menchi, Hema Bye-A-Jee, Monica Pozzato, Kati Laiho, Delphine Baratin, Qinghua Wang, Leslie Arminski, Preethi Vasudev, Sangya Pundir, Jian Zhang, Emma Hatton-Ellis, Kate Warner, Lucille Pourcel, Elisabeth Gasteiger, Marc Feuermann, Thierry Lombardot, Jerven Bolleman, Mahdi Mahmoudy, Shyamala Sundaram, Alex Bateman, Xavier Watkins, Rahat Agivetova, Guoying Qi, Peter B. McGarvey, Xavier D. Martin, Chuming Chen, Jie Luo, Ray Coetzee, K Sonesson, Alan Wilter Sousa da Silva, ThankGod Ebenezer, Elena Speretta, Rodrigo Lopez, Elisabeth Coudert, Aurelien Luciani, Vivienne Baillie Gerritsen, Yuqi Wang, M Doche, Michele Magrane, Antonia Lock, Dolnide Dornevil, Sandrine Pilbout, Borisas Bursteinas, Andrea H. Auchincloss, Béatrice A. Cuche, Dushyanth Jyothi, Rabie Saidi, Joseph Sampson, Laure Verbregue, Sebastien Gehant, Guillaume Keller, Shriya Raj, Damien Lieberherr, Ghislaine Argoud-Puy, and Teodoro, Douglas

Subjects
Proteomics, COVID-19 / virology, Computational Biology / methods, Molecular Sequence Annotation / methods, Proteome, AcademicSubjects/SCI00010, Knowledge Bases, Computational biology, Proteomics / methods, Biology, ddc:616.0757, SARS-CoV-2 / physiology, COVID-19 / epidemiology, User-Computer Interface, Viral Proteins, 03 medical and health sciences, 0302 clinical medicine, SARS-CoV-2 / genetics, Data Curation / methods, Genetics, Redundancy (engineering), Viral Proteins / genetics, Humans, Database Issue, SARS-CoV-2 / metabolism, Databases, Protein, Pandemics, Data Curation, Proteome / metabolism, 030304 developmental biology, Proteome / genetics, Internet, 0303 health sciences, SARS-CoV-2, COVID-19 / prevention & control, COVID-19, Computational Biology, Molecular Sequence Annotation, Viral Proteins / metabolism, UniProt Knowledgebase, UniProt, 030217 neurology & neurosurgery
Abstract

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

Published
2020

4. UniProt: a worldwide hub of protein knowledge

Author

Fábio Madeira, Alexandr Ignatchenko, George Georghiou, Martin Dichgans, Dushyanth Jyothi, Parit Bansal, Alexandre Renaux, Ivo Pedruzzi, Arnaud Kerhornou, Maurizio De Giorgi, Emanuele Alpi, Manuela Menchi, Rossana Zaru, Edward Turner, Sandra Orchard, Alex Bateman, Peter McGarvey, Emma Hatton-Ellis, Michele Magrane, Alan Bridge, Jie Luo, Benoit Bely, Leyla Jael Castro, Shriya Raj, Rodrigo López, Maria-Jesus Martin, and Gianluca Busiello

Subjects
0301 basic medicine, Proteome, 030102 biochemistry & molecular biology, Knowledge Bases, Molecular Sequence Annotation, Computational biology, Biology, 03 medical and health sciences, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Sequence Analysis, Protein, Genetics, Database Issue, UniProt, Databases, Protein, Data Curation
Abstract

The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of these proteins. These annotations are supplemented by annotations provided by rule based automated systems, and those imported from other resources. In this article we describe significant updates that we have made over the last 2 years to the resource. We have greatly expanded the number of Reference Proteomes that we provide and in particular we have focussed on improving the number of viral Reference Proteomes. The UniProt website has been augmented with new data visualizations for the subcellular localization of proteins as well as their structure and interactions. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.

Published
2018
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5. The European Nucleotide Archive in 2017

Author

Jeena Rajan, Rasko Leinonen, Josué Martínez-Villacorta, Ana Luisa Toribio, Nicole Silvester, Peter W. Harrison, Guy Cochrane, Blaise T. F. Alako, Clara Amid, Vadim Zalunin, Xin Liu, Iain Cleland, Simon Kay, Nima Pakseresht, Thomas M. Keane, Dmitriy Smirnov, Kethi Reddy, Manuela Menchi, Daniel Vaughan, Suran Jayathilaka, Marc Rossello, Ana Cerdeño-Tárraga, and Laura Clarke

Subjects
0301 basic medicine, European Nucleotide Archive, Internet, Sequencing data, Computational Biology, High-Throughput Nucleotide Sequencing, Information Storage and Retrieval, Molecular Sequence Annotation, Biology, World Wide Web, Europe, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Genetics, Database Issue, Humans, Databases, Nucleic Acid, 030217 neurology & neurosurgery
Abstract

For 35 years the European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) has been responsible for making the world’s public sequencing data available to the scientific community. Advances in sequencing technology have driven exponential growth in the volume of data to be processed and stored and a substantial broadening of the user community. Here, we outline ENA services and content in 2017 and provide insight into a selection of current key areas of development in ENA driven by challenges arising from the above growth.

Published
2017
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