Abstract
The 2019 Nucleic Acids Research (NAR) Database Issue contains 168 papers spanning molecular biology. Among them, 64 are new and another 92 are updates describing resources that appeared in the Issue previously. The remaining 12 are updates on databases most recently published elsewhere. This Issue contains two Breakthrough articles, on the Virtual Metabolic Human (VMH) database which links human and gut microbiota metabolism with diet and disease, and Vibrism DB, a database of mouse brain anatomy and gene (co-)expression with sophisticated visualization and session sharing. Major returning nucleic acid databases include RNAcentral, miRBase and LncRNA2Target. Protein sequence databases include UniProtKB, InterPro and Pfam, while wwPDB and RCSB cover protein structure. STRING and KEGG update in the section on metabolism and pathways. Microbial genomes are covered by IMG/M and resources for human and model organism genomics include Ensembl, UCSC Genome Browser, GENCODE and Flybase. Genomic variation and disease are well-covered by GWAS Catalog, PopHumanScan, OMIM and COSMIC, CADD being another major newcomer. Major new proteomics resources reporting here include iProX and jPOSTdb. The entire database issue is freely available online on the NAR website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 506 entries, adding 66 new resources and eliminating 147 discontinued URLs, bringing the current total to 1613 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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