The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

Abstract

The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest. In the area of metabolism, HMDB and Reactome both report new features while PULDB appears in NAR for the first time. This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE. Update papers from the IUPHAR/BPS Guide to Pharmacology and DrugBank are highlights of the drug and drug target section while a number of proteomics databases including proteomicsDB are also covered. 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 updated, reviewing 138 entries, adding 88 new resources and eliminating 47 discontinued URLs, bringing the current total to 1737 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.

Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

“…To retain high confidence snoRNAs, we excluded snoRNAs that have low reads (<5 reads), residing on exons and repeats. Ensembl (version-79) has 312 annotated snoRNAs 53 and 270 of them are supported by at least 5 reads in developmental stages we analyzed. Out of 270 snoRNAs from Ensembl, we predicted 264 snoRNAs and annotated 176 novel snoRNAs.…”

Biotechnology, Big Data and Artificial Intelligence

“…This exponential growth raises significant challenges to the organizations that have the mission of storing and organizing such data but provides a bounty for biotechnology researchers who have the ability to explore and exploit the ever‐increasing information stored in servers, worldwide. The (nonexhaustive) list of databases in the online molecular biology database collection kept by the Nucleic Acids Research journal includes more than 1700 operating databases . These databases include information about nonvertebrate genomics (280 of them), protein sequence (214), human genes and diseases (176), molecule and protein structure (172), metabolic and signaling pathways (168), DNA nucleotide sequence (157), plants (131), vertebrate genomes (116), RNA sequence (104), microarray and gene expression (60), immunology (31), proteomics (28), organelles (20), cell biology (8), and other molecular biology information (92).…”

Integrative Systems Biology Resources and Approaches in Disease Analytics

“…Databases form the basis for most applications in bioinformatics. The number of biological databases available now is enormous, the journal of Nucleic Acids Research (NAR) catalogues a total of 1737 molecular biology databases (2018 edition) [54]. The 2018 edition contains an enormous set of 181 papers that describe the adding of 82…”