The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Abstract

The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

COVID-19 Infection and Transmission Includes Complex Sequence Diversity

“…Our observations of biallelic variant positions are consistent with those from other studies describing subconsensus SNPs or iSNVs [30][31][32][33][34][35][36][37][38]. To determine how often biallelic variations were included in SARS-CoV-2 sequences submitted to international repositories, we randomly selected and analyzed 110 additional COVID-19 infections (Supplemental Table 4) reported from 18 different laboratories or consortia with raw sequence data available in the sequence read archive (SRA) [39]; the same ³80% coverage, ³100X read-depth inclusion threshold was applied. Results summarized in Supplemental Fig.…”

COVID-19 Times: Impact on Information Generation and Data Sharing

“…Due to their significance, each year, since 1999, the Nucleic Acids Research journal reviews new biological databases, eliminates discontinued URLs, and updates an existing compilation of them. This resource can be freely consulted at https://www.oxfordjournals.org/nar/database/c/, rendering a current total of 1637 databases for the early 2021 issue [9] and 1645 for the following one [10],…”

“…A clear example of this was illustrated by the emergence of biological databases, such as LitCovid, which reached more than 85,000 publications on the subject by December the 31 st , 2020 [14]. In the latest Nucleic Acids Research review issue [10], seven new databases inspired by the COVID-19 pandemic were added:…”

Construction and contextualization approaches for protein-protein interaction networks

“…Hence, caution must be exercised when using gene expression as a proxy for protein expression. Background on various experimental techniques, an overview of how PPI databases are built, and a recent list of PPI databases can be found here [3] , [32] . Some examples of PPI databases are shown in Table 2 .…”

“…The emergence and growth of network medicine in the last decade has been facilitated by the growth of publicly-accessible molecular datasets [1] . Various kinds of interactions such as protein-protein interactions (PPIs), transcription factor-gene regulatory interactions, perturbation effects of drugs and small molecules on gene expression, etc., have been systematically documented [2] , [3] , [4] . These interactions can be represented as networks or graphs, which are composed of a set of nodes, also called vertices, representing the discrete interacting entities (whose nature depends on the type of data under study), and a set of links, also called edges, representing physical or functional interactions between nodes.…”