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Literature DB >> 34850158

The European Nucleotide Archive in 2021.

Carla Cummins¹, Alisha Ahamed¹, Raheela Aslam¹, Josephine Burgin¹, Rajkumar Devraj¹, Ossama Edbali¹, Dipayan Gupta¹, Peter W Harrison¹, Muhammad Haseeb¹, Sam Holt¹, Talal Ibrahim¹, Eugene Ivanov¹, Suran Jayathilaka¹, Vishnukumar Kadhirvelu¹, Simon Kay¹, Manish Kumar¹, Ankur Lathi¹, Rasko Leinonen¹, Fabio Madeira¹, Nandana Madhusoodanan¹, Milena Mansurova¹, Colman O'Cathail¹, Matt Pearce¹, Stéphane Pesant¹, Nadim Rahman¹, Jeena Rajan¹, Gabriele Rinck¹, Sandeep Selvakumar¹, Alexey Sokolov¹, Swati Suman¹, Ross Thorne¹, Prabhat Totoo¹, Senthilnathan Vijayaraja¹, Zahra Waheed¹, Ahmad Zyoud¹, Rodrigo Lopez¹, Tony Burdett¹, Guy Cochrane¹.

Abstract

The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to the scientific community and contribute daily to the acceleration of scientific advance. Here, we outline the major updates to ENA's services and infrastructure that have been delivered over the past year.

Entities: Chemical

Mesh：

Substances：
Nucleotides

Year: 2022 PMID： 34850158 PMCID： PMC8728206 DOI： 10.1093/nar/gkab1051

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

6 in total

1. Identifying ELIXIR Core Data Resources.

Authors: Christine Durinx; Jo McEntyre; Ron Appel; Rolf Apweiler; Mary Barlow; Niklas Blomberg; Chuck Cook; Elisabeth Gasteiger; Jee-Hyub Kim; Rodrigo Lopez; Nicole Redaschi; Heinz Stockinger; Daniel Teixeira; Alfonso Valencia
Journal: F1000Res Date: 2016-09-30

2. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Authors: Robert M Bowers; Nikos C Kyrpides; Ramunas Stepanauskas; Miranda Harmon-Smith; Devin Doud; T B K Reddy; Frederik Schulz; Jessica Jarett; Adam R Rivers; Emiley A Eloe-Fadrosh; Susannah G Tringe; Natalia N Ivanova; Alex Copeland; Alicia Clum; Eric D Becraft; Rex R Malmstrom; Bruce Birren; Mircea Podar; Peer Bork; George M Weinstock; George M Garrity; Jeremy A Dodsworth; Shibu Yooseph; Granger Sutton; Frank O Glöckner; Jack A Gilbert; William C Nelson; Steven J Hallam; Sean P Jungbluth; Thijs J G Ettema; Scott Tighe; Konstantinos T Konstantinidis; Wen-Tso Liu; Brett J Baker; Thomas Rattei; Jonathan A Eisen; Brian Hedlund; Katherine D McMahon; Noah Fierer; Rob Knight; Rob Finn; Guy Cochrane; Ilene Karsch-Mizrachi; Gene W Tyson; Christian Rinke; Alla Lapidus; Folker Meyer; Pelin Yilmaz; Donovan H Parks; A M Eren; Lynn Schriml; Jillian F Banfield; Philip Hugenholtz; Tanja Woyke
Journal: Nat Biotechnol Date: 2017-08-08 Impact factor: 54.908

3. Minimum Information about an Uncultivated Virus Genome (MIUViG).

Authors: Simon Roux; Evelien M Adriaenssens; Bas E Dutilh; Eugene V Koonin; Andrew M Kropinski; Mart Krupovic; Jens H Kuhn; Rob Lavigne; J Rodney Brister; Arvind Varsani; Clara Amid; Ramy K Aziz; Seth R Bordenstein; Peer Bork; Mya Breitbart; Guy R Cochrane; Rebecca A Daly; Christelle Desnues; Melissa B Duhaime; Joanne B Emerson; François Enault; Jed A Fuhrman; Pascal Hingamp; Philip Hugenholtz; Bonnie L Hurwitz; Natalia N Ivanova; Jessica M Labonté; Kyung-Bum Lee; Rex R Malmstrom; Manuel Martinez-Garcia; Ilene Karsch Mizrachi; Hiroyuki Ogata; David Páez-Espino; Marie-Agnès Petit; Catherine Putonti; Thomas Rattei; Alejandro Reyes; Francisco Rodriguez-Valera; Karyna Rosario; Lynn Schriml; Frederik Schulz; Grieg F Steward; Matthew B Sullivan; Shinichi Sunagawa; Curtis A Suttle; Ben Temperton; Susannah G Tringe; Rebecca Vega Thurber; Nicole S Webster; Katrine L Whiteson; Steven W Wilhelm; K Eric Wommack; Tanja Woyke; Kelly C Wrighton; Pelin Yilmaz; Takashi Yoshida; Mark J Young; Natalya Yutin; Lisa Zeigler Allen; Nikos C Kyrpides; Emiley A Eloe-Fadrosh
Journal: Nat Biotechnol Date: 2018-12-17 Impact factor: 54.908

4. The international nucleotide sequence database collaboration.

Authors: Masanori Arita; Ilene Karsch-Mizrachi; Guy Cochrane
Journal: Nucleic Acids Res Date: 2020-11-09 Impact factor: 16.971

5. GenBank.

Authors: Eric W Sayers; Mark Cavanaugh; Karen Clark; Kim D Pruitt; Conrad L Schoch; Stephen T Sherry; Ilene Karsch-Mizrachi
Journal: Nucleic Acids Res Date: 2021-01-08 Impact factor: 16.971

6. DDBJ update: streamlining submission and access of human data.

Authors: Asami Fukuda; Yuichi Kodama; Jun Mashima; Takatomo Fujisawa; Osamu Ogasawara
Journal: Nucleic Acids Res Date: 2021-01-08 Impact factor: 16.971

6 in total

5 in total

5. Highly Similar Sequences of Mature IgA1 Proteases from Neisseria meningitidis, Neisseria gonorrhoeae and Haemophilus influenzae.

Authors: David Karlinsky; Yuri Prokopenko; Alexei Zinchenko; Larisa Zhigis; Olga Kotelnikova; Lev Rumsh; Ivan Smirnov
Journal: Pathogens Date: 2022-06-28

5 in total

The European Nucleotide Archive in 2021.

1. Identifying ELIXIR Core Data Resources.

2. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

3. Minimum Information about an Uncultivated Virus Genome (MIUViG).

4. The international nucleotide sequence database collaboration.

5. GenBank.

6. DDBJ update: streamlining submission and access of human data.

1. dbEssLnc: A manually curated database of human and mouse essential lncRNA genes.

Review 2. Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.

3. Search and sequence analysis tools services from EMBL-EBI in 2022.

4. Faster SARS-CoV-2 sequence validation and annotation for GenBank using VADR.

5. Highly Similar Sequences of Mature IgA1 Proteases from Neisseria meningitidis, Neisseria gonorrhoeae and Haemophilus influenzae.