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/.

[1]  Vackar Afzal,et al.  The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics , 2017, Nucleic Acids Res..

[2]  Sachi Kato,et al.  SCPortalen: human and mouse single-cell centric database , 2017, Nucleic Acids Res..

[3]  Zhenglu Yang,et al.  dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation , 2017, Nucleic Acids Res..

[4]  Yi Jiang,et al.  VarCards: an integrated genetic and clinical database for coding variants in the human genome , 2017, Nucleic Acids Res..

[5]  Edith D. Wong,et al.  Saccharomyces genome database informs human biology , 2017, Nucleic Acids Res..

[6]  Nga Thi Thuy Nguyen,et al.  Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing , 2017, Nucleic Acids Res..

[7]  Yang Zhang,et al.  Database Resources of the BIG Data Center in 2018 , 2017, Nucleic Acids Res..

[8]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[9]  Karsten M. Borgwardt,et al.  The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog , 2017, Nucleic Acids Res..

[10]  Bo Wang,et al.  Gramene 2018: unifying comparative genomics and pathway resources for plant research , 2017, Nucleic Acids Res..

[11]  Marcin Feder,et al.  MODOMICS: a database of RNA modification pathways , 2005, Nucleic Acids Res..

[12]  G. Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[13]  David S. Wishart,et al.  HMDB 4.0: the human metabolome database for 2018 , 2017, Nucleic Acids Res..

[14]  Wen J. Li,et al.  RefSeq: an update on prokaryotic genome annotation and curation , 2017, Nucleic Acids Res..

[15]  Erik Kristiansson,et al.  ECOdrug: a database connecting drugs and conservation of their targets across species , 2017, Nucleic Acids Res..

[16]  Daniel V. Oliveira,et al.  StemMapper: a curated gene expression database for stem cell lineage analysis , 2017, Nucleic Acids Res..

[17]  Brandi L. Cantarel,et al.  The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..

[18]  Alasdair J. G. Gray,et al.  The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY , 2017, Nucleic Acids Res..

[19]  David S. Wishart,et al.  PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database , 2017, Nucleic Acids Res..

[20]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[21]  Elliot J. Lefkowitz,et al.  Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV) , 2017, Nucleic Acids Res..

[22]  Jörg Stülke,et al.  SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis , 2017, Nucleic Acids Res..

[23]  Lei Shi,et al.  Updates to the RNA mapping database (RMDB), version 2 , 2018, Nucleic Acids Res..

[24]  Johanna R. McEntyre,et al.  The BioStudies database—one stop shop for all data supporting a life sciences study , 2017, Nucleic Acids Res..

[25]  Robert D. Finn,et al.  Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species , 2017, Nucleic Acids Res..

[26]  Toby J. Gibson,et al.  The eukaryotic linear motif resource – 2018 update , 2017, Nucleic Acids Res..

[27]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[28]  Yue Zhao,et al.  MNDR v2.0: an updated resource of ncRNA–disease associations in mammals , 2017, Nucleic Acids Res..

[29]  Yaoqi Zhou,et al.  EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments , 2017, Nucleic Acids Res..

[30]  Robert D. Finn,et al.  Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families , 2017, Nucleic Acids Res..

[31]  Jun Yu,et al.  LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs , 2014, Nucleic Acids Res..

[32]  Igor Jurisica,et al.  mirDIP 4.1—integrative database of human microRNA target predictions , 2017, Nucleic Acids Res..

[33]  Benoît Ballester,et al.  ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments , 2017, Nucleic Acids Res..

[34]  Yan Zhang,et al.  MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases , 2017, Nucleic Acids Res..

[35]  David J. Arenillas,et al.  JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework , 2017, Nucleic acids research.

[36]  David Haussler,et al.  The UCSC Genome Browser database: 2018 update , 2017, Nucleic Acids Res..

[37]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[38]  Abhik Mukhopadhyay,et al.  PDBe: towards reusable data delivery infrastructure at protein data bank in Europe , 2017, Nucleic Acids Res..

[39]  Janusz M. Bujnicki,et al.  MODOMICS: a database of RNA modification pathways. 2017 update , 2017, Nucleic Acids Res..

[40]  Artemis G. Hatzigeorgiou,et al.  DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions , 2017, Nucleic Acids Res..

[41]  Byungwook Lee,et al.  3DIV: A 3D-genome Interaction Viewer and database , 2017, Nucleic Acids Res..

[42]  Rolf Apweiler,et al.  The European Bioinformatics Institute in 2017: data coordination and integration , 2017, Nucleic Acids Res..

[43]  Jaume Bertranpetit,et al.  PopHuman: the human population genomics browser , 2017, Nucleic Acids Res..

[44]  Neil D. Rawlings,et al.  The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database , 2017, Nucleic Acids Res..

[45]  Janusz M. Bujnicki,et al.  RNArchitecture: a database and a classification system of RNA families, with a focus on structural information , 2017, Nucleic Acids Res..

[46]  Peer Bork,et al.  20 years of the SMART protein domain annotation resource , 2017, Nucleic Acids Res..

[47]  Thomas M. Keane,et al.  The European Nucleotide Archive in 2017 , 2017, Nucleic Acids Res..

[48]  Andrew K. Sewell,et al.  VDJdb: a curated database of T-cell receptor sequences with known antigen specificity , 2017, Nucleic Acids Res..

[49]  Xing-Ming Zhao,et al.  MVP: a microbe–phage interaction database , 2017, Nucleic Acids Res..

[50]  Toshihisa Takagi,et al.  DNA Data Bank of Japan: 30th anniversary , 2017, Nucleic Acids Res..

[51]  Karel Berka,et al.  ChannelsDB: database of biomacromolecular tunnels and pores , 2017, Nucleic Acids Res..

[52]  Charlotte M. Deane,et al.  STCRDab: the structural T-cell receptor database , 2017, Nucleic Acids Res..

[53]  G. Traver Hart,et al.  PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens , 2017, Nucleic Acids Res..

[54]  Janet M. Thornton,et al.  Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites , 2017, Nucleic Acids Res..

[55]  Anushya Muruganujan,et al.  PANTHER version 10: expanded protein families and functions, and analysis tools , 2015, Nucleic Acids Res..

[56]  Alexander S. Hauser,et al.  GPCRdb in 2018: adding GPCR structure models and ligands , 2017, Nucleic Acids Res..

[57]  Chunlei Liu,et al.  ClinVar: improving access to variant interpretations and supporting evidence , 2017, Nucleic Acids Res..

[58]  J. Michael Cherry,et al.  The Encyclopedia of DNA elements (ENCODE): data portal update , 2017, Nucleic Acids Res..

[59]  Vincent Lombard,et al.  PULDB: the expanded database of Polysaccharide Utilization Loci , 2017, Nucleic Acids Res..

[60]  Jingfa Xiao,et al.  Genome Variation Map: a data repository of genome variations in BIG Data Center , 2017, Nucleic Acids Res..

[61]  Conrad Bessant,et al.  PITDB: a database of translated genomic elements , 2017, Nucleic Acids Res..

[62]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[63]  Christina Backes,et al.  miRCarta: a central repository for collecting miRNA candidates , 2017, Nucleic Acids Res..

[64]  Hao Zhou,et al.  TADB 2.0: an updated database of bacterial type II toxin–antitoxin loci , 2017, Nucleic Acids Res..

[65]  Yang Gao,et al.  PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations , 2017, Nucleic Acids Res..

[66]  Robert D. Finn,et al.  The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..

[67]  Ryan Miller,et al.  WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research , 2017, Nucleic Acids Res..

[68]  Yves Van de Peer,et al.  PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics , 2017, Nucleic Acids Res..

[69]  David S. Wishart,et al.  DrugBank 5.0: a major update to the DrugBank database for 2018 , 2017, Nucleic Acids Res..