The 27th annual Nucleic Acids Research database issue and molecular biology database collection
Reads0
Chats0
TLDR
This issue contains three breakthrough articles: AntiBodies Chemically Defined curates antibody sequences and their cognate antigens; SCOP returns with a new schema and breaks away from a purely hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools.Abstract:
The 2020 Nucleic Acids Research Database Issue contains 148 papers spanning molecular biology. They include 59 papers reporting on new databases and 79 covering recent changes to resources previously published in the issue. A further ten papers are updates on databases most recently published elsewhere. This issue contains three breakthrough articles: AntiBodies Chemically Defined (ABCD) curates antibody sequences and their cognate antigens; SCOP returns with a new schema and breaks away from a purely hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools. Major returning nucleic acid databases include miRDB and miRTarBase. Databases for protein sequence analysis include CDD, DisProt and ELM, alongside no fewer than four newcomers covering proteins involved in liquid-liquid phase separation. In metabolism and signaling, Pathway Commons, Reactome and Metabolights all contribute papers. PATRIC and MicroScope update in microbial genomes while human and model organism genomics resources include Ensembl, Ensembl genomes and UCSC Genome Browser. Immune-related proteins are covered by updates from IPD-IMGT/HLA and AFND, as well as newcomers VDJbase and OGRDB. Drug design is catered for by updates from the IUPHAR/BPS Guide to Pharmacology and the Therapeutic Target Database. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been revised, updating 305 entries, adding 65 new resources and eliminating 125 discontinued URLs; so bringing the current total to 1637 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.read more
Citations
More filters
Journal ArticleDOI
ResFinder 4.0 for predictions of phenotypes from genotypes.
Valeria Bortolaia,Rolf Sommer Kaas,Etienne Ruppé,Marilyn C. Roberts,Stefan Schwarz,Vincent Cattoir,Alain Philippon,Rosa Lundbye Allesøe,Rosa Lundbye Allesøe,Ana-Rita Rebelo,Alfred Ferrer Florensa,Linda Fagelhauer,Trinad Chakraborty,Bernd Neumann,Guido Werner,Jennifer K. Bender,Kerstin Stingl,Minh Ngoc Nguyen,Jasmine Coppens,Basil Britto Xavier,Surbhi Malhotra-Kumar,Henrik Westh,Henrik Westh,Mette Pinholt,Muna F. Anjum,Nicholas A. Duggett,Isabelle Kempf,Suvi Nykäsenoja,Satu Olkkola,Kinga Wieczorek,Ana Amaro,Lurdes Clemente,Joël Mossong,Serge Losch,Catherine Ragimbeau,Ole Lund,Frank Møller Aarestrup +36 more
TL;DR: WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
Journal ArticleDOI
MetaboLights: a resource evolving in response to the needs of its scientific community
Kenneth Haug,Keeva Cochrane,Venkata Chandrasekhar Nainala,Mark Williams,Jiakang Chang,Kalai Vanii Jayaseelan,Claire O'Donovan +6 more
TL;DR: The submission process was completely overhauled to enable MetaboLights to deliver a far more user-friendly submission process and to facilitate the growing demand for reproducibility and integration with other ‘omics.
Journal ArticleDOI
Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools.
Faviel F. Gonzalez-Galarza,Antony McCabe,Eduardo José Melo dos Santos,James T. A. Jones,Louise Y. Takeshita,Nestor D. Ortega-Rivera,Glenda M. Del Cid-Pavon,Kerry A Ramsbottom,Gurpreet S. Ghattaoraya,Ana Alfirevic,Derek Middleton,Andrew R. Jones +11 more
TL;DR: AFND has become more popular in terms of clinical and scientific usage, with a recent increase in genotyping data as a necessary component of Short Population Report article submissions to another scientific journal, and a user-friendly desktop application for HLA and KIR genotype/population data submissions.
Journal ArticleDOI
Formation of biological condensates via phase separation: Characteristics, analytical methods, and physiological implications.
TL;DR: In this article, the authors summarize commonly used methods to investigate various forms of liquid-liquid phase separation occurring both in 3D aqueous solution and on 2D membrane bilayers, such as LLPS condensates arising from intrinsically disordered proteins or structured modular protein domains.
Journal ArticleDOI
MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems.
TL;DR: The updated MiST database provides a comprehensive classification of microbial signal transduction systems, and a novel MiST feature is the integration of unique profile HMMs to link complex chemosensory systems with corresponding chemoreceptors in bacterial and archaeal genomes.
References
More filters
Journal ArticleDOI
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences.
TL;DR: The BioImage Archive is described, a deposition database for raw images derived from primary research that will supply data for future knowledgebases that will add value through curation of primary image data.
Journal ArticleDOI
Transcriptome visualization and data availability at the Saccharomyces Genome Database.
Patrick Ng,Edith D. Wong,Kevin A. MacPherson,Suzi Aleksander,Joanna Argasinska,Barbara Dunn,Robert S. Nash,Marek S. Skrzypek,Felix Gondwe,Sagar Jha,Kalpana Karra,Shuai Weng,Stuart R. Miyasato,Matt Simison,Stacia R. Engel,J. Michael Cherry +15 more
TL;DR: This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. Cerevisiae by integrating manually curated experimental data.
Journal ArticleDOI
CancerTracer: a curated database for intrapatient tumor heterogeneity.
Chen Wang,Jian Yang,Hong Luo,Kun Wang,Yu Wang,Zhi-Xiong Xiao,Xiang Tao,Hao Jiang,Haoyang Cai +8 more
TL;DR: A manually curated database designed to track and characterize the evolutionary trajectories of tumor growth in individual patients, it is hoped that CancerTracer will significantly improve the understanding of the evolutionary histories of tumors, and may facilitate the identification of predictive biomarkers for personalized cancer therapies.
Journal ArticleDOI
FoldamerDB: a database of peptidic foldamers.
Bilal Nizami,Dorottya Bereczki-Szakál,Nikolett Varró,Kamal El Battioui,Vignesh U Nagaraj,Imola Cs. Szigyártó,István M. Mándity,Tamás Beke-Somfai +7 more
TL;DR: FoldamerDB is hoped to bridge the gap in the freely available web-based resources on foldamers and will be of interest to diverse groups of scientists from chemists to biologists.
Journal ArticleDOI
Genus for biomolecules.
Pawel Rubach,Pawel Rubach,Sebastian Zajac,Borys Jastrzebski,Joanna I. Sulkowska,Piotr Sułkowski,Piotr Sułkowski +6 more
TL;DR: This database collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given chain and its subchains, as well as a genus matrix diagram for each biomolecule.
Related Papers (5)
The FAIR Guiding Principles for scientific data management and stewardship
Mark Wilkinson,Michel Dumontier,IJsbrand Jan Aalbersberg,Gabrielle Appleton,Myles Axton,Arie Baak,Niklas Blomberg,Jan-Willem Boiten,Luiz Olavo Bonino da Silva Santos,Philip E. Bourne,Jildau Bouwman,Anthony J. Brookes,Timothy Clark,Mercè Crosas,Ingrid Dillo,Olivier G. Dumon,Scott C. Edmunds,Chris T. Evelo,Richard Finkers,Alejandra Gonzalez-Beltran,Alasdair J. G. Gray,Paul Groth,Carole Goble,Jeffrey S. Grethe,Jaap Heringa,Peter A C 't Hoen,Rob Hooft,Tobias Kuhn,Ruben Kok,Joost N. Kok,Scott J. Lusher,Maryann E. Martone,Albert Mons,Abel L. Packer,Bengt Persson,Philippe Rocca-Serra,Marco Roos,Rene van Schaik,Susanna-Assunta Sansone,Erik Anthony Schultes,Thierry Sengstag,Ted Slater,George Strawn,Morris A. Swertz,Mark Thompson,Johan van der Lei,Erik M. van Mulligen,Jan Velterop,Andra Waagmeester,Peter Wittenburg,Katherine Wolstencroft,Jun Zhao,Barend Mons,Barend Mons +53 more