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/.
Highlights
The Nucleic Acids Research (NAR) Database Issue reaches its 26th annual issue in 2019
An interesting facility reported by the BIG Data Center paper (4) is their BIG Search which scans across the Center’s many resources but accesses indexes from non-Center partner databases on topics as diverse as lncRNAs, plant transcription factors and autophagy-related proteins
Mutations from Adaptive Laboratory Evolution experiments Allosteric signaling and mutations in proteins Ancient mitochondrial DNA Reconstructed ancestral genomes Impact of SNPs on post-translational modifications Sequences, transcriptomes and phenotypes of clinical isolates of Pseudomonas auruginosa Catalog of all germline microsatellites Cancer single-cell state atlas Splicing quantitative trait loci in cancer Cell markers in human and mouse Human cancer cell models qPCR oligonucleotide primers for chromatin immunoprecipitation (ChIP) Collective molecular activities of useful plants Pairwise nucleotide coevolution Validated CRISPR/Cas[9] sgRNAs for model organism lncRNAs Genomics of the Cucurbitaceae family Antimicrobial peptide sequences, structures and properties Database of somatic mutations in normal cells Editome disease knowledgebase Encyclopedia of membrane proteins analyzed by structure and symmetry
Summary
The Nucleic Acids Research (NAR) Database Issue reaches its 26th annual issue in 2019. The EBI paper (3) reports on the new databases Single Cell Expression Atlas and PDBeKnowledgebase The latter encompasses FunPDBe, an initiative to better harness structural bioinformatics methods and international collaborators to annotate the protein structural data in PDBe. An interesting facility reported by the BIG Data Center paper (4) is their BIG Search which scans across the Center’s many resources but accesses indexes from non-Center partner databases on topics as diverse as lncRNAs, plant transcription factors and autophagy-related proteins. Victors VMH YeastRGB http://www.phidias.us/victors http://vmh.life http://www.yeastRGB.org aFor full references to the databases featured in this issue, please see the Table of Contents
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