The 27th annual Nucleic Acids Research database issue and molecular biology database collection
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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
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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.
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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.
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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.
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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
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Alliance of Genome Resources Portal: unified model organism research platform
Julie Agapite,Laurent-Philippe Albou,Suzi Aleksander,Joanna Argasinska,Valerio Arnaboldi,Helen Attrill,Susan M. Bello,Judith A. Blake,Olin Blodgett,Yvonne M. Bradford,Carol J. Bult,Scott Cain,Brian R. Calvi,Seth Carbon,Juancarlos Chan,Wen J. Chen,J. Michael Cherry,Jaehyoung Cho,Karen R. Christie,Madeline A. Crosby,Jeff De Pons,Mary E. Dolan,Gilberto dos Santos,Barbara Dunn,Nathan Dunn,Anne E. Eagle,Dustin Ebert,Stacia R. Engel,David Fashena,Ken Frazer,Sibyl Gao,Felix Gondwe,Josh Goodman,L. Sian Gramates,Christian A. Grove,Todd W. Harris,Marie-Claire Harrison,Douglas G. Howe,Kevin L. Howe,Sagar Jha,James A. Kadin,Thomas C. Kaufman,Patrick Kalita,Kalpana Karra,Ranjana Kishore,Stan Laulederkind,Raymond Lee,Kevin A. MacPherson,Steven J Marygold,Beverley B. Matthews,Gillian Millburn,Stuart R. Miyasato,Sierra A. T. Moxon,Hans-Michael Mueller,Christopher J. Mungall,Anushya Muruganujan,Tremayne Mushayahama,Robert S. Nash,Patrick Ng,Michael Paulini,Norbert Perrimon,Christian Pich,Daniela Raciti,Joel E. Richardson,Matthew Russell,Susan Russo Gelbart,Leyla Ruzicka,Kevin Schaper,Mary Shimoyama,Matt Simison,Cynthia L. Smith,David R. Shaw,Ajay Shrivatsav,Marek S. Skrzypek,Jennifer R. Smith,Paul W. Sternberg,Christopher J. Tabone,Paul Thomas,Jyothi Thota,Sabrina Toro,Monika Tomczuk,Marek Tutaj,Monika Tutaj,Jose-Maria Urbano,Kimberly Van Auken,Ceri E. Van Slyke,Shur-Jen Wang,Shuai Weng,Monte Westerfield,Gary Williams,Edith D. Wong,Adam Wright,Karen Yook +92 more
TL;DR: The Alliance of Genome Resources is a consortium of the major model organism databases and the Gene Ontology that is facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms.
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ProteomicsDB: a multi-omics and multi-organism resource for life science research.
Patroklos Samaras,Tobias Schmidt,Martin Frejno,Siegfried Gessulat,Maria Reinecke,Maria Reinecke,Maria Reinecke,Anna Jarzab,Jana Zecha,Julia Mergner,Piero Giansanti,Hans-Christian Ehrlich,Stephan Aiche,Johannes Rank,Harald Kienegger,Helmut Krcmar,Bernhard Kuster,Mathias Wilhelm +17 more
TL;DR: A new service in ProteomicsDB is introduced which allows users to upload their own expression datasets and analyze them alongside with data stored in ProeomicsDB, and supports the storage and visualization of data collected from other organisms, exemplified by Arabidopsis thaliana.
Journal ArticleDOI
PhaSepDB: a database of liquid–liquid phase separation related proteins
Kaiqiang You,Qi Huang,Chunyu Yu,Boyan Shen,Cristoffer Sevilla,Minglei Shi,Henning Hermjakob,Henning Hermjakob,Yang Chen,Tingting Li +9 more
TL;DR: The developed PhaSepDB provides protein summary, publication reference and sequence features of phase separation associated proteins, which reflect the LLPS behavior, and the online database provides a convenient interface for the research community to easily browse, search and download phase separationassociated proteins.
Journal ArticleDOI
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
Charles J. Norsigian,Neha Pusarla,John Luke McConn,James T. Yurkovich,Andreas Dräger,Bernhard O. Palsson,Bernhard O. Palsson,Zachary A. King +7 more
TL;DR: New content and features in the BiGG Models repository are detail, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites.
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.
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