The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection

The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of ‘moonlighting’ proteins, and two new databases of protein–protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

[1]  Michael Y. Galperin,et al.  Expanded microbial genome coverage and improved protein family annotation in the COG database , 2014, Nucleic Acids Res..

[2]  Richard J. Roberts,et al.  REBASE—a database for DNA restriction and modification: enzymes, genes and genomes , 2009, Nucleic Acids Res..

[3]  Klaus Schughart,et al.  INFRAFRONTIER—providing mutant mouse resources as research tools for the international scientific community , 2014, Nucleic Acids Res..

[4]  Kelly P. Williams,et al.  The tmRNA website , 2014, Nucleic Acids Res..

[5]  Dmitri I. Svergun,et al.  SASBDB, a repository for biological small-angle scattering data , 2014, Nucleic Acids Res..

[6]  Kristen M. Naegle,et al.  ProteomeScout: a repository and analysis resource for post-translational modifications and proteins , 2014, Nucleic Acids Res..

[7]  Enrique Querol,et al.  MultitaskProtDB: a database of multitasking proteins , 2013, Nucleic Acids Res..

[8]  Yangyang Zhao,et al.  BioModels: ten-year anniversary , 2014, Nucleic Acids Res..

[9]  Hsien-Da Huang,et al.  RNAcentral: an international database of ncRNA sequences , 2014, Nucleic Acids Res..

[10]  Yu-Ju Chen,et al.  dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation , 2014, Nucleic Acids Res..

[11]  Mary Goldman,et al.  The UCSC Cancer Genomics Browser: update 2015 , 2014, Nucleic Acids Res..

[12]  Hai Fang,et al.  The SUPERFAMILY 1.75 database in 2014: a doubling of data , 2014, Nucleic Acids Res..

[13]  Marco Punta,et al.  Genome3D: exploiting structure to help users understand their sequences , 2015, Nucleic Acids Res..

[14]  Yutaka Suzuki,et al.  DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites , 2014, Nucleic Acids Res..

[15]  David A. Lee,et al.  CATH: comprehensive structural and functional annotations for genome sequences , 2014, Nucleic Acids Res..

[16]  Erik L. L. Sonnhammer,et al.  InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic , 2014, Nucleic Acids Res..

[17]  Víctor de Lorenzo,et al.  SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities , 2014, Nucleic Acids Res..

[18]  François Schiettecatte,et al.  OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders , 2014, Nucleic Acids Res..

[19]  Daisuke Kihara,et al.  GenoBase: comprehensive resource database of Escherichia coli K-12 , 2014, Nucleic Acids Res..

[20]  Thomas C. Wiegers,et al.  The Comparative Toxicogenomics Database's 10th year anniversary: update 2015 , 2014, Nucleic Acids Res..

[21]  Evgeny M. Zdobnov,et al.  OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software , 2014, Nucleic Acids Res..

[22]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[23]  INFRAFRONTIER Consortium.  INFRAFRONTIER – – providing mutant mouse resources as research tools for the international scientific community , 2015 .

[24]  Radka Svobodová Vareková,et al.  ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank , 2014, Nucleic Acids Res..

[25]  Kenta Nakai,et al.  DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data , 2014, Nucleic Acids Res..

[26]  Alfonso Valencia,et al.  ChiTaRS 2.1—an improved database of the chimeric transcripts and RNA-seq data with novel sense–antisense chimeric RNA transcripts , 2014, Nucleic Acids Res..

[27]  Frank Schwach,et al.  PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites , 2014, Nucleic Acids Res..

[28]  Ni Ai,et al.  arrayMap 2014: an updated cancer genome resource , 2014, Nucleic Acids Res..

[29]  Gaston H. Gonnet,et al.  The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements , 2014, Nucleic Acids Res..

[30]  Janan T. Eppig,et al.  Mouse Tumor Biology (MTB): a database of mouse models for human cancer , 2014, Nucleic Acids Res..

[31]  Joaquín Dopazo,et al.  PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins , 2014, Nucleic Acids Res..

[32]  Robert D. Finn,et al.  Making your database available through Wikipedia: the pros and cons , 2011, Nucleic Acids Res..

[33]  Hirokazu Chiba,et al.  MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data , 2014, Nucleic Acids Res..

[34]  Gert Vriend,et al.  A series of PDB related databases for everyday needs , 2010, Nucleic Acids Res..

[35]  Haipeng Liu,et al.  MoonProt: a database for proteins that are known to moonlight , 2013, Nucleic Acids Res..

[36]  Huaiyu Mi,et al.  The InterPro protein families database: the classification resource after 15 years , 2014, Nucleic Acids Res..

[37]  Jean Thierry-Mieg,et al.  Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR) , 2014, Nucleic Acids Res..

[38]  Kengo Kinoshita,et al.  COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems , 2014, Nucleic Acids Res..

[39]  Peer Bork,et al.  SMART: recent updates, new developments and status in 2015 , 2014, Nucleic Acids Res..

[40]  Adam Godzik,et al.  Cancer3D: understanding cancer mutations through protein structures , 2014, Nucleic Acids Res..

[41]  Hsien-Da Huang,et al.  MethHC: a database of DNA methylation and gene expression in human cancer , 2014, Nucleic Acids Res..

[42]  Narmada Thanki,et al.  CDD: NCBI's conserved domain database , 2014, Nucleic Acids Res..

[43]  Kelly P. Williams,et al.  Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes , 2014, Nucleic Acids Res..

[44]  Yen-Yi Ho,et al.  The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice , 2014, Nucleic Acids Res..

[45]  Patrice Duroux,et al.  IMGT®, the international ImMunoGeneTics information system® 25 years on , 2014, Nucleic Acids Res..

[46]  Mingming Jia,et al.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..

[47]  María Martín,et al.  UniProt: A hub for protein information , 2015 .

[48]  The Uniprot Consortium,et al.  UniProt: a hub for protein information , 2014, Nucleic Acids Res..

[49]  João Pedro de Magalhães,et al.  GeneFriends: a human RNA-seq-based gene and transcript co-expression database , 2014, Nucleic Acids Res..

[50]  Chi-Ching Lee,et al.  CMPD: cancer mutant proteome database , 2014, Nucleic Acids Res..

[51]  David S. Goodsell,et al.  The RCSB Protein Data Bank: views of structural biology for basic and applied research and education , 2014, Nucleic Acids Res..

[52]  Marcel E. Dinger,et al.  lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs , 2014, Nucleic Acids Res..