Article
Biochemical Research Methods
Miguel Roncoroni, Bert Droesbeke, Ignacio Eguinoa, Kim De Ruyck, Flora D'Anna, Dilmurat Yusuf, Bjoern Gruening, Rolf Backofen, Frederik Coppens
Summary: This work introduces a tool for submitting raw sequencing reads of SARS-CoV-2 to the European Nucleotide Archive, featuring a user-friendly interface, streamlined submission process, and the ability to remove human reads before submission. Additionally, a Galaxy wrap of the tool enables bulk sequencing read submissions for users with limited bioinformatics knowledge. The tool is also packaged in a Docker container for easier deployment.
Article
Biochemistry & Molecular Biology
David Yuan, Alisha Ahamed, Josephine Burgin, Carla Cummins, Rajkumar Devraj, Khadim Gueye, Dipayan Gupta, Vikas Gupta, Muhammad Haseeb, Maira Ihsan, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Ankur Lathi, Rasko Leinonen, Jasmine McKinnon, Lili Meszaros, Colman O'Cathail, Dennis Ouma, Joana Pauperio, Stephane Pesant, Nadim Rahman, Gabriele Rinck, Sandeep Selvakumar, Swati Suman, Yanisa Sunthornyotin, Marianna Ventouratou, Senthilnathan Vijayaraja, Zahra Waheed, Peter Woollard, Ahmad Zyoud, Tony Burdett, Guy Cochrane
Summary: The European Nucleotide Archive (ENA) is a database maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) that provides services for the submission, processing, archiving, and dissemination of sequence data. Recent progress and improvements to ENA services include enhancing the FAIRness of data, focusing on pandemic preparedness and foundational technology, and supporting genomic surveillance efforts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Josephine Burgin, Alisha Ahamed, Carla Cummins, Rajkumar Devraj, Khadim Gueye, Dipayan Gupta, Vikas Gupta, Muhammad Haseeb, Maira Ihsan, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Ankur Lathi, Rasko Leinonen, Milena Mansurova, Jasmine McKinnon, Colman O'Cathail, Joana Pauperio, Stephane Pesant, Nadim Rahman, Gabriele Rinck, Sandeep Selvakumar, Swati Suman, Senthilnathan Vijayaraja, Zahra Waheed, Peter Woollard, David Yuan, Ahmad Zyoud, Tony Burdett, Guy Cochrane
Summary: The European Nucleotide Archive (ENA) is an open and supported platform for data management, archiving, publication, and dissemination. It provides comprehensive data sets and tools for data discovery and retrieval. Recent updates have focused on improving connectivity, reusability, and interoperability of ENA data and metadata.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Carla Cummins, Alisha Ahamed, Raheela Aslam, Josephine Burgin, Rajkumar Devraj, Ossama Edbali, Dipayan Gupta, Peter W. Harrison, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Kadhirvelu, Simon Kay, Manish Kumar, Ankur Lathi, Rasko Leinonen, Fabio Madeira, Nandana Madhusoodanan, Milena Mansurova, Colman O'Cathail, Matt Pearce, Stephane Pesant, Nadim Rahman, Jeena Rajan, Gabriele Rinck, Sandeep Selvakumar, Alexey Sokolov, Swati Suman, Ross Thorne, Prabhat Totoo, Senthilnathan Vijayaraja, Zahra Waheed, Ahmad Zyoud, Rodrigo Lopez, Tony Burdett, Guy Cochrane
Summary: The European Nucleotide Archive, maintained at EMBL-EBI, offers free services for deposition and access to open nucleotide sequencing data, playing a crucial role in advancing scientific research.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Peter W. Harrison, Alisha Ahamed, Raheela Aslam, Blaise T. F. Alako, Josephine Burgin, Nicola Buso, Melanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Rodrigo Lopez, Simon Kay, Rasko Leinonen, Xin Liu, Colman O'Cathail, Amir Pakseresht, Youngmi Park, Stephane Pesant, Nadim Rahman, Jeena Rajan, Alexey Sokolov, Senthilnathan Vijayaraja, Zahra Waheed, Ahmad Zyoud, Tony Burdett, Guy Cochrane
Summary: The European Nucleotide Archive (ENA) has been dedicated to freely archiving and presenting global public sequencing data for nearly 40 years, benefiting the entire scientific community and accelerating global research efforts. In 2020, major developments to ENA services and content included the release of an updated ENA browser, modernization of the release process, and collaborations with specific research communities for data coordination.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Mallory Ann Freeberg, Lauren A. Fromont, Teresa D'Altri, Anna Foix Romero, Jorge Izquierdo Ciges, Aina Jene, Giselle Kerry, Mauricio Moldes, Roberto Ariosa, Silvia Bahena, Daniel Barrowdale, Marcos Casado Barbero, Dietmar Fernandez-Orth, Carles Garcia-Linares, Emilio Garcia-Rios, Frederic Haziza, Bela Juhasz, Oscar Martinez Llobet, Gemma Milla, Anand Mohan, Manuel Rueda, Aravind Sankar, Dona Shaju, Ashutosh Shimpi, Babita Singh, Coline Thomas, Sabela de la Torre, Umuthan Uyan, Claudia Vasallo, Paul Flicek, Roderic Guigo, Arcadi Navarro, Helen Parkinson, Thomas Keane, Jordi Rambla
Summary: The European Genome-phenome Archive (EGA) is a resource for secure archiving of genetic, phenotypic, and clinical data, promoting data reuse, reproducibility, and accelerating biomedical research. EGA operates a distributed data access model, providing strong data protection control.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Geochemistry & Geophysics
Peter Danecek, Stefano Pintore, Salvatore Mazza, Alfonso Mandiello, Massimo Fares, Ivano Carluccio, Emiliano Della Bina, Diego Franceschi, Milena Moretti, Valentino Lauciani, Matteo Quintiliani, Alberto Michelini
Summary: The Istituto Nazionale di Geofisica e Vulcanologia is a founding partner of the EIDA federation, managing the EIDA data distribution node in Italy. Their data archive currently contains 90 TBytes of waveform data available for download, originating from various networks and stations mainly in Italy and the Mediterranean region, with an annual growth rate of 11 TB.
SEISMOLOGICAL RESEARCH LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Timothe Cezard, Fiona Cunningham, Sarah E. Hunt, Baron Koylass, Nitin Kumar, Gary Saunders, April Shen, Andres F. Silva, Kirill Tsukanov, Sundararaman Venkataraman, Paul Flicek, Helen Parkinson, Thomas M. Keane
Summary: The European Variation Archive (EVA) is a resource for sharing genetic variation data for all species, hosting over 3 billion records. EVA and dbSNP have established a global system to assign unique identifiers to all submitted genetic variants. EVA is active within GA4GH, maintaining and implementing standards such as VCF, Refget, and VRS.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Dietmar Fernandez-Orth, Manuel Rueda, Babita Singh, Mauricio Moldes, Aina Jene, Marta Ferri, Claudia Vasallo, Lauren A. Fromont, Arcadi Navarro, Jordi Rambla
Summary: The European Genome-Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data since 2008. To increase the reusability of data, EGA has developed a new File QC Portal that allows users to assess the quality of data before accessing it.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Geochemistry & Geophysics
Angelo Strollo, Didem Cambaz, John Clinton, Peter Danecek, Christos P. Evangelidis, Alexandru Marmureanu, Lars Ottemoller, Helle Pedersen, Reinoud Sleeman, Klaus Stammler, Daniel Armbruster, Jarek Bienkowski, Kostas Boukouras, Peter L. Evans, Massimo Fares, Cristian Neagoe, Stefan Heimers, Andres Heinloo, Matthias Hoffmann, Philippe Kaestli, Valentino Lauciani, Jan Michalek, Erich Odon Muhire, Mehmet Ozer, Lucian Palangeanu, Constanza Pardo, Javier Quinteros, Matteo Quintiliani, Jose Antonio Jara-Salvador, Jonathan Schaeffer, Antje Schloemer, Nikolaos Triantafyllis
Summary: The European Integrated Data Archive (EIDA) is an infrastructure that provides access to seismic-waveform archives collected by European agencies. It currently offers seamless access to seismic data from 12 data archives with a growing user base and data holdings. EIDA is actively developing new approaches to data management for emerging technologies and challenges to meet evolving demands.
SEISMOLOGICAL RESEARCH LETTERS
(2021)
Article
Clinical Neurology
Claudio L. A. Bassetti
Summary: Founded in 2014, the European Academy of Neurology (EAN) aims to reduce the burden of neurological disorders. Over the past three years, the EAN has focused on education, science, membership, and advocacy. The outbreak of COVID-19 in 2020 brought significant changes to the EAN, including the implementation of new digital technologies. The virtual congress in 2020 saw record levels of attendance, and various initiatives and programs were launched to improve neurological care and advance scientific research.
EUROPEAN JOURNAL OF NEUROLOGY
(2022)
Article
Infectious Diseases
Mark Muscat, Belete Gebrie, Androulla Efstratiou, Siddhartha S. Datta, Danni Daniels
Summary: Diphtheria is rare in the WHO European Region, but sporadic cases continue to be reported. The high DTP3 coverage in the Region may explain the relatively low number of diphtheria cases. However, suboptimal surveillance systems and inadequate laboratory diagnostic capacity may contribute to the problem. Achieving high DTP3 coverage in all districts and implementing booster doses are necessary to control diphtheria and prevent outbreaks.
Article
Geography, Physical
Michael Matiu, Alice Crespi, Giacomo Bertoldi, Carlo Maria Carmagnola, Christoph Marty, Samuel Morin, Wolfgang Schoener, Daniele Cat Berro, Gabriele Chiogna, Ludovica De Gregorio, Sven Kotlarski, Bruno Majone, Gernot Resch, Silvia Terzago, Mauro Valt, Walter Beozzo, Paola Cianfarra, Isabelle Gouttevin, Giorgia Marcolini, Claudia Notarnicola, Marcello Petitta, Simon C. Scherrer, Ulrich Strasser, Michael Winkler, Marc Zebisch, Andrea Cicogna, Roberto Cremonini, Andrea Debernardi, Mattia Faletto, Mauro Gaddo, Lorenzo Giovannini, Luca Mercalli, Jean-Michel Soubeyroux, Andrea Susnik, Alberto Trenti, Stefano Urbani, Viktor Weilguni
Summary: This study presents an Alpine-wide analysis of snow depth in the European Alps, incorporating data from over 2000 stations in six countries. The analysis reveals decreasing trends in snow depth for most stations from November to May over the past few decades. Different regions within the Alps show varying trends, challenging the generalization of results across the entire mountain range.
Article
Infectious Diseases
Scarlett Sett, Carolina dos Santos Ribeiro, Christine Prat, George Haringhuizen, Amber Hartman Scholz
Summary: Biobanking infrastructures are crucial for early response to new viral outbreaks. The European Virus Archive played a key role in the global response to the COVID-19 pandemic, distributing viral resources for free and implementing benefit-sharing policies.
Article
Geochemistry & Geophysics
Klaus Stammler, Monika Bischoff, Andrea Bruestle, Lars Ceranna, Stefanie Donner, Kasper Fischer, Peter Gaebler, Wolfgang Friederich, Sigward Funke, Gernot Hartmann, Benjamin Homuth, Brigitte Knapmeyer-Endrun, Michael Korn, Tobias Megies, Christoph Pilger, Thomas Plenefisch, Ina Pustal, Ivo Rappsilber, Bernd Schmidt, Lutz Sonnabend, Stefan Stange, Joachim Wassermann, Ulrich Wegler
Summary: Germany has a long history in seismic instrumentation, establishing state services, scientific research institutions, and nationwide networks. These entities provide high-level data products to support government authorities, inform the public on seismology-related topics, and exchange information with international organizations.
SEISMOLOGICAL RESEARCH LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Fergal J. Martin, M. Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R. Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fiorretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Gurpreet S. Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, Jose Carlos Marugan, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N. Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Pilizota, Irina Prosovetskaia, Jose G. Perez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyosti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gomez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Elizabeth Wass, Natalie Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R. Ilsley, Jane E. Loveland, Benjamin Moore, Jonathan M. Mudge, John Tate, David Thybert, Stephen J. Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E. Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D. Finn, Kevin L. Howe, Peter W. Harrison, Andrew D. Yates, Paul Flicek
Summary: Ensembl has been providing high-quality genomic resources for vertebrates and model organisms for over 20 years. With the increase in high-quality reference genomes and the development of pangenome representations, Ensembl aims to support downstream research by creating high-quality annotations, tools, and services for species across the tree of life. This report highlights Ensembl's resources for popular reference genomes, the growing annotations, updates to the Variant Effect Predictor, protein structure predictions, and the beta release of their new website.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Noah Fahlgren, Muskan Kapoor, Galabina Yordanova, Irene Papatheodorou, Jamie Waese, Benjamin Cole, Peter Harrison, Doreen Ware, Timothy Tickle, Benedict Paten, Tony Burdett, Christine G. Elsik, Christopher K. Tuggle, Nicholas J. Provart
Summary: Building a data infrastructure for the Plant Cell Atlas using existing infrastructure and platforms will allow biologists and data scientists to gain new insights into plant biology. The development of the Human Cell Atlas and the Single Cell Expression Atlas by the European Bioinformatics Institute has laid the foundation for constructing the data infrastructure for the Plant Cell Atlas. The utilization of appropriate ontologies is crucial for describing plant single cell experiments.
Article
Biochemistry & Molecular Biology
Josephine Burgin, Alisha Ahamed, Carla Cummins, Rajkumar Devraj, Khadim Gueye, Dipayan Gupta, Vikas Gupta, Muhammad Haseeb, Maira Ihsan, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Ankur Lathi, Rasko Leinonen, Milena Mansurova, Jasmine McKinnon, Colman O'Cathail, Joana Pauperio, Stephane Pesant, Nadim Rahman, Gabriele Rinck, Sandeep Selvakumar, Swati Suman, Senthilnathan Vijayaraja, Zahra Waheed, Peter Woollard, David Yuan, Ahmad Zyoud, Tony Burdett, Guy Cochrane
Summary: The European Nucleotide Archive (ENA) is an open and supported platform for data management, archiving, publication, and dissemination. It provides comprehensive data sets and tools for data discovery and retrieval. Recent updates have focused on improving connectivity, reusability, and interoperability of ENA data and metadata.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Lorna Richardson, Ben Allen, Germana Baldi, Martin Beracochea, Maxwell L. Bileschi, Tony Burdett, Josephine Burgin, Juan Caballero-Perez, Guy Cochrane, Lucy J. Colwell, Tom Curtis, Alejandra Escobar-Zepeda, Tatiana A. Gurbich, Varsha Kale, Anton Korobeynikov, Shriya Raj, Alexander B. Rogers, Ekaterina Sakharova, Santiago Sanchez, Darren J. Wilkinson, Robert D. Finn
Summary: The MGnify platform is a resource for analyzing and storing microbiome-derived nucleic acid sequences. It offers access to taxonomic assignments and functional annotations for a large number of datasets derived from different environments. The platform has expanded in terms of dataset quantity and analysis capabilities over the past three years, and includes a relational database for understanding the genomic context of proteins. Deep learning-based annotation methods have also been implemented to enhance functional annotations. Additionally, the platform's technology has been upgraded, and a Jupyter Lab environment has been introduced for downstream analysis of the data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Austra Cukura, Paul Denny, Tunca Dogan, ThankGod Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasaamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fabio Madeira, Mahdi Mahmoudy, Alok Mishra, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel L. Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Hermann Zellner, Alan J. Bridge, Lucila Aimo, Ghis-laine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Teresa M. Batista Neto, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Edouard de Castro, Anne Estreicher, Maria L. Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Sebastien Gehant, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Cecilia N. Arighi, Leslie Armin-ski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Jian Zhang, Hema Bye-A-Jee, Rossana Zaru, Shyamala Sundaram, Cathy H. Wu
Summary: The UniProt Knowledgebase aims to provide comprehensive, high-quality, and freely accessible protein sequences annotated with functional information. The database has expanded its data processing pipeline and website to accommodate the increasing information content, with over 227 million sequences and plans to include a reference proteome for each taxonomic group. Detailed annotations are extracted from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations from automated systems. The new website, https://www.uniprot.org/, offers enhanced user experience and easy access to data, including AlphaFold structures and improved protein subcellular localization visualizations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Tatiana A. Gurbich, Alexandre Almeida, Martin Beracochea, Tony Burdett, Josephine Burgin, Guy Cochrane, Shriya Raj, Lorna Richardson, Alexander B. Rogers, Ekaterina Sakharova, Gustavo A. Salazar, Robert D. Finn
Summary: An increasing number of shotgun metagenomic datasets now yield metagenome-assembled genomes (MAGs), but the lack of standardization in their generation, annotation, and storage hinders the discovery and comparison of MAG collections. To address this, MGnify Genomes offers a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes. Users can access visualized species representative sequences and annotations on the MGnify website and download the full catalogue and associated analysis outputs from MGnify servers. Currently, there are seven available biomes with over 300,000 genomes representing 11,048 non-redundant species and including 36 taxonomic classes not represented by cultured genomes. MGnify Genomes is accessible at https://www.ebi.ac.uk/metagenomics/browse/genomes/.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
