The 27th annual Nucleic Acids Research database issue and molecular biology database collection

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/.

Diagnostic model of combined ceRNA and DNA methylation related genes in esophageal carcinoma

“…The selected differential mRNA, lncRNA, and differential miRNA were paired in the miRcode database. Target gene prediction was performed on the selected differential miRNAs using the starBase (Han et al, 2020) online software (http://starbase.sysu.edu.cn/), and the target genes were predicted by miRDB (Rigden & Fernández, 2020), miRTarBase (Liu, Huang &Luo, 2020), andTargetScan (Dong et al, 2020) databases, thereby obtaining ceRNA regulation of lncRNA-miRNA-mRNA network, using Cytoscape v3.5.1 software (Qi et al, 2019) for mapping.…”

Identifying protein subcellular localisation in scientific literature using bidirectional deep recurrent neural network

“…In 2020, NAR reported 125 discontinued databases, with the number of obsolete databases increasing five times over the last five years. In contrast, 65 new database resources were published in the same database issue, with the number remaining steady over the same five year period 32 . While the study here focuses on protein subcellular information, the pipeline developed provides a framework for capturing key functional properties of proteins from published studies and assisting in biocuration efforts.…”

Integrating Network Pharmacology and Experimental Validation to Investigate the Mechanisms of Huazhuojiedu Decoction to Treat Chronic Atrophic Gastritis

“…All chemical structures and corresponding canonical simplified molecular-input line-entry systems (SMILES) were retrieved from PubChem ( https://pubchem.ncbi.nlm.nih.gov/ ), an organic small molecule bioactivity database, which is a database of chemical modules [ 14 ]. The protein names were standardized through the UniProt database ( http://www.uniprot.org/ ), an informative and resource-rich protein database [ 15 ], and the objects were selected as “homo sapiens,” which was the potential target species of the main active components of the drug.…”