The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources

The current issue of Nucleic Acids Research includes descriptions of 58 new and 73 updated data resources. The accompanying online Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, now lists 1230 carefully selected databases covering various aspects of molecular and cell biology. While most data resource descriptions remain very brief, the issue includes several longer papers that highlight recent significant developments in such databases as Pfam, MetaCyc, UniProt, ELM and PDBe. The databases described in the Database Issue and Database Collection, however, are far more than a distinct set of resources; they form a network of connected data, concepts and shared technology. The full content of the Database Issue is available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

[1]  María Martín,et al.  The Universal Protein Resource (UniProt) in 2010 , 2010 .

[2]  I-Min A. Chen,et al.  The integrated microbial genomes system: an expanding comparative analysis resource , 2009, Nucleic Acids Res..

[3]  K. Sjölander,et al.  Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). , 2006, Omics : a journal of integrative biology.

[4]  Scott Cain,et al.  ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data , 2006, Nucleic Acids Res..

[5]  Alessandro Sette,et al.  The Immune Epitope Database 2.0 , 2009, Nucleic Acids Res..

[6]  Doina Caragea,et al.  BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum , 2009, Nucleic Acids Res..

[7]  Michael Y. Galperin,et al.  Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009 , 2008, Nucleic Acids Res..

[8]  Jakub Pas,et al.  ELM: the status of the 2010 eukaryotic linear motif resource , 2009, Nucleic Acids Res..

[9]  Lu Huang,et al.  Update of TTD: Therapeutic Target Database , 2009, Nucleic Acids Res..

[10]  Gautier Koscielny,et al.  Ensembl Genomes: Extending Ensembl across the taxonomic space , 2009, Nucleic Acids Res..

[11]  David Osumi-Sutherland,et al.  FlyBase: enhancing Drosophila Gene Ontology annotations , 2008, Nucleic Acids Res..

[12]  Hugh D. Spence,et al.  Minimum information requested in the annotation of biochemical models (MIRIAM) , 2005, Nature Biotechnology.

[13]  Giorgio Valle,et al.  The Gene Ontology in 2010: extensions and refinements , 2009, Nucleic Acids Res..

[14]  Ibrahim Emam,et al.  Gene Expression Atlas at the European Bioinformatics Institute , 2009, Nucleic Acids Res..

[15]  Sven Griep,et al.  PDBselect 1992–2009 and PDBfilter-select , 2009, Nucleic Acids Res..

[16]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[17]  Xiaowei Wang,et al.  PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification , 2009, Nucleic Acids Res..

[18]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[19]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[20]  Sameer Velankar,et al.  PDBe: Protein Data Bank in Europe , 2009, Nucleic Acids Res..

[21]  Don G. Gilbert,et al.  wFleaBase: the Daphnia genome database , 2005, BMC Bioinformatics.

[22]  Erin Beck,et al.  The comprehensive microbial resource , 2000, Nucleic Acids Res..

[23]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[24]  Lennart Martens,et al.  The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.

[25]  Taro Nakamura,et al.  NBRP databases: databases of biological resources in Japan , 2009, Nucleic Acids Res..

[26]  Chris Mungall,et al.  A Chado case study: an ontology-based modular schema for representing genome-associated biological information , 2007, ISMB/ECCB.

[27]  Inna Dubchak,et al.  MicrobesOnline: an integrated portal for comparative and functional genomics , 2009, Nucleic Acids Res..

[28]  Lubos Klucar,et al.  phiSITE: database of gene regulation in bacteriophages , 2009, Nucleic Acids Res..