The 24th annualNucleic Acids Researchdatabase issue: a look back and upcoming changes

Abstract

This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR. As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein–protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as ‘breakthrough’ contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the ‘golden set’ of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/.

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

“…There are currently many open sources of chemistry and biology data serving a broad range of scientific disciplines and needs [ 1 ]. While early internet chemistry databases delivered limited data for hundreds to thousands of chemical structures, advances in modern Internet technologies had enabled an explosion of freely available online chemistry data over the past decade.…”

Analysis of impact metrics for the Protein Data Bank

“…From the 1,737 resources in the Online Molecular Biology Database Collection, the leading 108 databases used most intensively across the scientific community have been identified by NAR as the “golden set” of successful resources 41 . Our review revealed that 52 of these elite databases incorporate PDB data, demonstrating the importance of the PDB archive in resources widely used in the biological research community.…”

“…Moreover, keywords associated with structure determination and description were prevalent among citing publications in the early 2000s, but keywords pertinent to drug discovery, then genetics and genomics, and most recently protein structure prediction have come to the fore. Usage across disciplines is unmistakably confirmed by review of PDB usage within the NAR Online Molecular Biology Database Collection 41 .…”

Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption

“…Further, we queried cis-meQTLs in the platform of Functional Mapping and Annotation of Genome-Wide Association Studies (FUMA GWAS) 40 . Using this platform, we examined the overlap between cis-meQTLs with signals in the NHGRI-EBI Catalog of published GWAS 41 . As epigenetic signatures are tissue dependent, and our analysis was limited in blood samples, we used the GTEx expression database -which provides an insight into differential expression of relevant genes across different human tissues.…”