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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The 2011 <italic>Nucleic Acids Research</italic> Database Issue and the online Molecular Biology Database Collection</title><author><name sortKey="Galperin, Michael Y" sort="Galperin, Michael Y" uniqKey="Galperin M" first="Michael Y." last="Galperin">Michael Y. Galperin</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA</nlm:aff></affiliation></author><author><name sortKey="Cochrane, Guy R" sort="Cochrane, Guy R" uniqKey="Cochrane G" first="Guy R." last="Cochrane">Guy R. Cochrane</name><affiliation><nlm:aff id="AFF1">EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21177655</idno><idno type="pmc">3013748</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013748</idno><idno type="RBID">PMC:3013748</idno><idno type="doi">10.1093/nar/gkq1243</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000585</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The 2011 <italic>Nucleic Acids Research</italic> Database Issue and the online Molecular Biology Database Collection</title><author><name sortKey="Galperin, Michael Y" sort="Galperin, Michael Y" uniqKey="Galperin M" first="Michael Y." last="Galperin">Michael Y. Galperin</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA</nlm:aff></affiliation></author><author><name sortKey="Cochrane, Guy R" sort="Cochrane, Guy R" uniqKey="Cochrane G" first="Guy R." last="Cochrane">Guy R. Cochrane</name><affiliation><nlm:aff id="AFF1">EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</nlm:aff></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The current 18th Database Issue of <italic>Nucleic Acids Research</italic> features descriptions of 96 new and 83 updated online databases covering various areas of molecular biology. It includes two editorials, one that discusses COMBREX, a new exciting project aimed at figuring out the functions of the ‘conserved hypothetical’ proteins, and one concerning BioDBcore, a proposed description of the ‘minimal information about a biological database’. Papers from the members of the International Nucleotide Sequence Database collaboration (INSDC) describe each of the participating databases, DDBJ, ENA and GenBank, principles of data exchange within the collaboration, and the recently established Sequence Read Archive. A testament to the longevity of databases, this issue includes updates on the RNA modification database, Definition of Secondary Structure of Proteins (DSSP) and Homology-derived Secondary Structure of Proteins (HSSP) databases, which have not been featured here in >12 years. There is also a block of papers describing recent progress in protein structure databases, such as Protein DataBank (PDB), PDB in Europe (PDBe), CATH, SUPERFAMILY and others, as well as databases on protein structure modeling, protein–protein interactions and the organization of inter-protein contact sites. Other highlights include updates of the popular gene expression databases, GEO and ArrayExpress, several cancer gene databases and a detailed description of the UK PubMed Central project. The <italic>Nucleic Acids Research</italic> online Database Collection, available at: <ext-link ext-link-type="uri" xlink:href="http://www.oxfordjournals.org/nar/database/a/">http://www.oxfordjournals.org/nar/database/a/</ext-link>, now lists 1330 carefully selected molecular biology databases. The full content of the Database Issue is freely available online at the <italic>Nucleic Acids Research</italic> web site (<ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/">http://nar.oxfordjournals.org/</ext-link>).</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Gaudet, P" uniqKey="Gaudet P">P. Gaudet</name></author><author><name sortKey="Bairoch, A" uniqKey="Bairoch A">A. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21177655</article-id><article-id pub-id-type="pmc">3013748</article-id><article-id pub-id-type="doi">10.1093/nar/gkq1243</article-id><article-id pub-id-type="publisher-id">gkq1243</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>The 2011 <italic>Nucleic Acids Research</italic> Database Issue and the online Molecular Biology Database Collection</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Galperin</surname><given-names>Michael Y.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Cochrane</surname><given-names>Guy R.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and<sup>2</sup>EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed. Tel: <phone>+1 301 435 5910</phone>; Fax: <fax>+1 301 435 7793</fax>; Email: <email>galperin@ncbi.nlm.nih.gov</email></corresp></author-notes><pmc-comment>For NAR both ppub and collection dates generated for PMC processing 1/27/05 beck</pmc-comment>
<pub-date pub-type="collection"><month>1</month><year>2011</year></pub-date><pub-date pub-type="ppub"><month>1</month><year>2011</year></pub-date><pub-date pub-type="epub"><day>16</day><month>12</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>16</day><month>12</month><year>2010</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>39</volume><issue>Database issue</issue><issue-title>Database issue</issue-title><fpage>D1</fpage><lpage>D6</lpage><history><date date-type="received"><day>12</day><month>11</month><year>2010</year></date><date date-type="accepted"><day>15</day><month>11</month><year>2010</year></date></history><permissions><copyright-statement>Published by Oxford University Press 2010.</copyright-statement><copyright-year>2010</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.5"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5">http://creativecommons.org/licenses/by-nc/2.5</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>The current 18th Database Issue of <italic>Nucleic Acids Research</italic> features descriptions of 96 new and 83 updated online databases covering various areas of molecular biology. It includes two editorials, one that discusses COMBREX, a new exciting project aimed at figuring out the functions of the ‘conserved hypothetical’ proteins, and one concerning BioDBcore, a proposed description of the ‘minimal information about a biological database’. Papers from the members of the International Nucleotide Sequence Database collaboration (INSDC) describe each of the participating databases, DDBJ, ENA and GenBank, principles of data exchange within the collaboration, and the recently established Sequence Read Archive. A testament to the longevity of databases, this issue includes updates on the RNA modification database, Definition of Secondary Structure of Proteins (DSSP) and Homology-derived Secondary Structure of Proteins (HSSP) databases, which have not been featured here in >12 years. There is also a block of papers describing recent progress in protein structure databases, such as Protein DataBank (PDB), PDB in Europe (PDBe), CATH, SUPERFAMILY and others, as well as databases on protein structure modeling, protein–protein interactions and the organization of inter-protein contact sites. Other highlights include updates of the popular gene expression databases, GEO and ArrayExpress, several cancer gene databases and a detailed description of the UK PubMed Central project. The <italic>Nucleic Acids Research</italic> online Database Collection, available at: <ext-link ext-link-type="uri" xlink:href="http://www.oxfordjournals.org/nar/database/a/">http://www.oxfordjournals.org/nar/database/a/</ext-link>, now lists 1330 carefully selected molecular biology databases. The full content of the Database Issue is freely available online at the <italic>Nucleic Acids Research</italic> web site (<ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/">http://nar.oxfordjournals.org/</ext-link>).</p></abstract></article-meta></front><body><sec><title>COMMENTARY</title><p>This current, 18th annual Database Issue of <italic>Nucleic Acids Research</italic> (NAR) features descriptions of 96 new (<xref ref-type="table" rid="T1">Table 1</xref>) online databases covering a variety of molecular biology data and 83 data resources that have previously been published in NAR or other journals. The accompanying NAR online Molecular Biology Database Collection (<ext-link ext-link-type="uri" xlink:href="http://www.oxfordjournals.org/nar/database/a/">http://www.oxfordjournals.org/nar/database/a/</ext-link>) now includes 1330 data sources.
<table-wrap id="T1" position="float"><label>Table 1.</label><caption><p>New molecular biology databases featured in the 2011 NAR Database Issue</p></caption><table frame="hsides" rules="groups"><thead align="left"><tr><th rowspan="1" colspan="1">Database name</th><th rowspan="1" colspan="1">URL</th><th rowspan="1" colspan="1">Brief description</th></tr></thead><tbody align="left"><tr><td rowspan="1" colspan="1">Allele Frequency Net</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.allelefrequencies.net">http://www.allelefrequencies.net</ext-link></td><td rowspan="1" colspan="1">Immunogenetic gene frequencies in worldwide populations</td></tr><tr><td rowspan="1" colspan="1">AmoebaDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://amoebadb.org/amoeba/">http://amoebadb.org/amoeba/</ext-link></td><td rowspan="1" colspan="1">Functional genomics resource for Amoebazoa</td></tr><tr><td rowspan="1" colspan="1">ArachnoServer<xref ref-type="table-fn" rid="TF1"><sup>a</sup></xref></td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://archnoserver.org">http://archnoserver.org</ext-link></td><td rowspan="1" colspan="1">Sequence, structure and activity of protein toxins from spider venom</td></tr><tr><td rowspan="1" colspan="1">AREsite</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://rna.tbi.univie.ac.at/AREsite">http://rna.tbi.univie.ac.at/AREsite</ext-link></td><td rowspan="1" colspan="1">AU-Rich Elements in vertebrate mRNA UTR sequences</td></tr><tr><td rowspan="1" colspan="1">ASD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://mdl.shsmu.edu.cn/ASD/">http://mdl.shsmu.edu.cn/ASD/</ext-link></td><td rowspan="1" colspan="1">Allosteric Site Database</td></tr><tr><td rowspan="1" colspan="1">ASPicDB<xref ref-type="table-fn" rid="TF1"><sup>a</sup></xref></td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.caspur.it/ASPicDB/">http://www.caspur.it/ASPicDB/</ext-link></td><td rowspan="1" colspan="1">Alternative Splicing Prediction DataBase</td></tr><tr><td rowspan="1" colspan="1">Autophagy Database</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://tp-apg.genes.nig.ac.jp/autophagy/">http://tp-apg.genes.nig.ac.jp/autophagy/</ext-link></td><td rowspan="1" colspan="1">Proteins involved in autophagy (self-digestion of eukaryotic cells)</td></tr><tr><td rowspan="1" colspan="1">BISC</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bisc.soe.ucsc.edu">http://bisc.soe.ucsc.edu</ext-link></td><td rowspan="1" colspan="1">BInary SubComplexes in Proteins</td></tr><tr><td rowspan="1" colspan="1">Bovine Genome</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://BovineGenome.org">http://BovineGenome.org</ext-link></td><td rowspan="1" colspan="1">Bovine Genome database</td></tr><tr><td rowspan="1" colspan="1">BriX</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://brix.switchlab.org/">http://brix.switchlab.org/</ext-link></td><td rowspan="1" colspan="1">Protein building blocks for structural analysis</td></tr><tr><td rowspan="1" colspan="1">BSDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ifpan.edu.pl/BSDB">http://www.ifpan.edu.pl/BSDB</ext-link></td><td rowspan="1" colspan="1">Biomolecule Stretching Database</td></tr><tr><td rowspan="1" colspan="1">BRENDA-BTO</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.brenda-enzymes.org/BTO">http://www.brenda-enzymes.org/BTO</ext-link></td><td rowspan="1" colspan="1">BRENDA Tissue Ontology database</td></tr><tr><td rowspan="1" colspan="1">CADgene</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.bioguo.org/CADgene/">http://www.bioguo.org/CADgene/</ext-link></td><td rowspan="1" colspan="1">Coronary artery disease gene database</td></tr><tr><td rowspan="1" colspan="1">CAMERA<xref ref-type="table-fn" rid="TF1"><sup>a</sup></xref></td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://camera.calit2.net/">http://camera.calit2.net/</ext-link></td><td rowspan="1" colspan="1">Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis</td></tr><tr><td rowspan="1" colspan="1">CancerResource</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinformatics.charite.de/cancerresource/">http://bioinformatics.charite.de/cancerresource/</ext-link></td><td rowspan="1" colspan="1">Cancer-related proteins and compounds</td></tr><tr><td rowspan="1" colspan="1">CaSNP</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://cistrome.dfci.harvard.edu/snparray/">http://cistrome.dfci.harvard.edu/snparray/</ext-link></td><td rowspan="1" colspan="1">Copy number alterations in cancer genomes</td></tr><tr><td rowspan="1" colspan="1">cBARBEL</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.catfishgenome.org/">http://www.catfishgenome.org/</ext-link></td><td rowspan="1" colspan="1">Catfish genome database</td></tr><tr><td rowspan="1" colspan="1">CCDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://crdd.osdd.net/raghava/ccdb/">http://crdd.osdd.net/raghava/ccdb/</ext-link></td><td rowspan="1" colspan="1">Cervical cancer gene database</td></tr><tr><td rowspan="1" colspan="1">CDDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.cdyn.org/">http://www.cdyn.org/</ext-link></td><td rowspan="1" colspan="1">Conformational Dynamics Data Bank of proteins and protein assemblies</td></tr><tr><td rowspan="1" colspan="1">ChemProt</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.cbs.dtu.dk/services/ChemProt/">http://www.cbs.dtu.dk/services/ChemProt/</ext-link></td><td rowspan="1" colspan="1">Annotated and predicted interactions of chemicals with proteins</td></tr><tr><td rowspan="1" colspan="1">CLIPZ</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.clipz.unibas.ch">http://www.clipz.unibas.ch</ext-link></td><td rowspan="1" colspan="1">Experimentally-determined binding sites of RNA-binding proteins</td></tr><tr><td rowspan="1" colspan="1">COMBREX</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.combrex.org/">http://www.combrex.org/</ext-link></td><td rowspan="1" colspan="1">COMputational BRidges to EXperiments</td></tr><tr><td rowspan="1" colspan="1">CPLA</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://cpla.biocuckoo.org/">http://cpla.biocuckoo.org/</ext-link></td><td rowspan="1" colspan="1">Compendium of protein lysine acetylation</td></tr><tr><td rowspan="1" colspan="1">DAnCER</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://wodaklab.org/dancer/">http://wodaklab.org/dancer/</ext-link></td><td rowspan="1" colspan="1">Disease Annotated Chromatin Epigenetic Resource</td></tr><tr><td rowspan="1" colspan="1">DBASS5/3</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.dbass.org.uk">http://www.dbass.org.uk</ext-link></td><td rowspan="1" colspan="1">Database of Aberrant Splice Sites: 5′ and 3′ splice sites</td></tr><tr><td rowspan="1" colspan="1">dbCRID</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://dbcrid.biolead.org">http://dbcrid.biolead.org</ext-link></td><td rowspan="1" colspan="1">Database of Chromosomal Rearrangements In Diseases</td></tr><tr><td rowspan="1" colspan="1">dbDNV</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://140.109.42.20/DNVs">http://140.109.42.20/DNVs</ext-link></td><td rowspan="1" colspan="1">Database of Duplicated-gene Nucleotide Variants</td></tr><tr><td rowspan="1" colspan="1">dbSNP-Q</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://cgsmd.isi.edu/dbsnpq">http://cgsmd.isi.edu/dbsnpq</ext-link></td><td rowspan="1" colspan="1">GWAS prioritization tool</td></tr><tr><td rowspan="1" colspan="1">DDPC</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://apps.sanbi.ac.za/ddpc/">http://apps.sanbi.ac.za/ddpc/</ext-link></td><td rowspan="1" colspan="1">Database of Genes Associated with Prostate Cancer</td></tr><tr><td rowspan="1" colspan="1">EDULISS</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://eduliss.bch.ed.ac.uk/">http://eduliss.bch.ed.ac.uk/</ext-link></td><td rowspan="1" colspan="1">EDinburgh University Ligand Selection System</td></tr><tr><td rowspan="1" colspan="1">Effective</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.effectors.org">http://www.effectors.org</ext-link></td><td rowspan="1" colspan="1">Predicted secreted bacterial proteins</td></tr><tr><td rowspan="1" colspan="1">EMDataBank</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://emdatabank.org">http://emdatabank.org</ext-link></td><td rowspan="1" colspan="1">3D cryo-electron microscopy maps, models and metadata</td></tr><tr><td rowspan="1" colspan="1">FlyFactorSurvey</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://pgfe.umassmed.edu/TFDBS/">http://pgfe.umassmed.edu/TFDBS/</ext-link></td><td rowspan="1" colspan="1">Drosophila transcription factor and their binding specificities</td></tr><tr><td rowspan="1" colspan="1">FragmentStore</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinformatics.charite.de/fragment_store">http://bioinformatics.charite.de/fragment_store</ext-link></td><td rowspan="1" colspan="1">Compound fragment library for fragment-based drug design</td></tr><tr><td rowspan="1" colspan="1">FusariumDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.fusariumdb.org/">http://www.fusariumdb.org/</ext-link></td><td rowspan="1" colspan="1">Comparative genomics of Fusarium strains</td></tr><tr><td rowspan="1" colspan="1">GET-Evidence</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://get-evidence.org">http://get-evidence.org</ext-link></td><td rowspan="1" colspan="1">A system for analyzing non-synonymous SNPs in human genes</td></tr><tr><td rowspan="1" colspan="1">GlycomeDB<xref ref-type="table-fn" rid="TF1"><sup>a</sup></xref></td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.glycome-db.org">http://www.glycome-db.org</ext-link></td><td rowspan="1" colspan="1">Carbohydrate structures</td></tr><tr><td rowspan="1" colspan="1">Herb Ingredient Targets</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://lifecenter.sgst.cn/hit">http://lifecenter.sgst.cn/hit</ext-link></td><td rowspan="1" colspan="1">Protein targets for active compounds from Chinese herbs</td></tr><tr><td rowspan="1" colspan="1">HitPredict</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://hintdb.hgc.jp/htp/">http://hintdb.hgc.jp/htp/</ext-link></td><td rowspan="1" colspan="1">High-confidence protein–protein interactions</td></tr><tr><td rowspan="1" colspan="1">Hymenoptera Genome</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://HymenopteraGenome.org">http://HymenopteraGenome.org</ext-link></td><td rowspan="1" colspan="1">Genome sequences for honey bee and the wasp <italic>Nasonia vitripennis</italic></td></tr><tr><td rowspan="1" colspan="1">IGDD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://115.248.74.248/igdd/home.aspx">http://115.248.74.248/igdd/home.aspx</ext-link></td><td rowspan="1" colspan="1">Indian Genetic Disease Database</td></tr><tr><td rowspan="1" colspan="1">IGRhCellID</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://igrcid.ibms.sinica.edu.tw">http://igrcid.ibms.sinica.edu.tw</ext-link></td><td rowspan="1" colspan="1">Integrated Genomic Resources of Human Cell Lines for Identification</td></tr><tr><td rowspan="1" colspan="1">IKMC</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.knockoutmouse.org">http://www.knockoutmouse.org</ext-link></td><td rowspan="1" colspan="1">The International Knockout Mouse Consortium database</td></tr><tr><td rowspan="1" colspan="1">Isobase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://isobase.csail.mit.edu">http://isobase.csail.mit.edu</ext-link></td><td rowspan="1" colspan="1">IsoRank PPI Network Alignment Based Ortholog Database</td></tr><tr><td rowspan="1" colspan="1">KaPPA-View</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://kpv.kazusa.or.jp/kpv4">http://kpv.kazusa.or.jp/kpv4</ext-link></td><td rowspan="1" colspan="1">Kazusa Plant Pathway Viewer</td></tr><tr><td rowspan="1" colspan="1">KUPS</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ittc.ku.edu/chenlab/">http://www.ittc.ku.edu/chenlab/</ext-link></td><td rowspan="1" colspan="1">University of Kansas Proteomics Service: protein–protein interaction</td></tr><tr><td rowspan="1" colspan="1">Laminin Database</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.lm.lncc.br">http://www.lm.lncc.br</ext-link></td><td rowspan="1" colspan="1">Laminin Database</td></tr><tr><td rowspan="1" colspan="1">lncRNAdb</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.lncrnadb.com">http://www.lncrnadb.com</ext-link></td><td rowspan="1" colspan="1">Long Non-Coding RNA Database</td></tr><tr><td rowspan="1" colspan="1">LocDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.rostlab.org/services/locDB">http://www.rostlab.org/services/locDB</ext-link></td><td rowspan="1" colspan="1">Protein localization data for human and Arabidopsis</td></tr><tr><td rowspan="1" colspan="1">LSD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.eplantsenescence.org">http://www.eplantsenescence.org</ext-link></td><td rowspan="1" colspan="1">Leaf Senescence Database</td></tr><tr><td rowspan="1" colspan="1">MatrixDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://matrixdb.ibcp.fr">http://matrixdb.ibcp.fr</ext-link></td><td rowspan="1" colspan="1">Extracellular matrix proteins and their interactions</td></tr><tr><td rowspan="1" colspan="1">mESAdb</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://konulab.fen.bilikent.edu.tr/mirna">http://konulab.fen.bilikent.edu.tr/mirna</ext-link></td><td rowspan="1" colspan="1">microRNA Expression and Sequence Analysis Database</td></tr><tr><td rowspan="1" colspan="1">MicrosporidiaDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://microsporidiadb.org">http://microsporidiadb.org</ext-link></td><td rowspan="1" colspan="1">Functional genomics resource for Microsporidia</td></tr><tr><td rowspan="1" colspan="1">miRTarBase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://mirtarbase.mbc.nctu.edu.tw">http://mirtarbase.mbc.nctu.edu.tw</ext-link></td><td rowspan="1" colspan="1">Experimentally validated interactions of microRNA with their targets</td></tr><tr><td rowspan="1" colspan="1">MitoGenesisDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.dsimb.inserm.fr/dsimb_tools/mitgene">http://www.dsimb.inserm.fr/dsimb_tools/mitgene</ext-link></td><td rowspan="1" colspan="1">Gene expression in mitochondrial biogenesis</td></tr><tr><td rowspan="1" colspan="1">NCBI Epigenomics</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/epigenomics/">http://www.ncbi.nlm.nih.gov/epigenomics/</ext-link></td><td rowspan="1" colspan="1">Genomic maps of nuclear changes that control gene expression</td></tr><tr><td rowspan="1" colspan="1">NGSmethDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinfo2.ugr.es/meth/NGSmethDB.php">http://bioinfo2.ugr.es/meth/NGSmethDB.php</ext-link></td><td rowspan="1" colspan="1">Next-generation sequencing DNA methylation data</td></tr><tr><td rowspan="1" colspan="1">NIAS GeneBank</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.gene.affrc.go.jp/databases_en.php">http://www.gene.affrc.go.jp/databases_en.php</ext-link></td><td rowspan="1" colspan="1">Plant genetic resources at the National Institute of Agrobiological Sciences in Tsukuba, Japan</td></tr><tr><td rowspan="1" colspan="1">non-B DB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://nonb.abcc.ncifcrf.gov">http://nonb.abcc.ncifcrf.gov</ext-link></td><td rowspan="1" colspan="1">Non-B DNA forming motifs in mammalian genomes</td></tr><tr><td rowspan="1" colspan="1">OMA browser<xref ref-type="table-fn" rid="TF1"><sup>a</sup></xref></td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.omabrowser.org">http://www.omabrowser.org</ext-link></td><td rowspan="1" colspan="1">Orthology Matrix</td></tr><tr><td rowspan="1" colspan="1">OMPdb</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinformatics.biol.uoa.gr/OMPdb">http://bioinformatics.biol.uoa.gr/OMPdb</ext-link></td><td rowspan="1" colspan="1">Outer membrane proteins from Gram-negative bacteria</td></tr><tr><td rowspan="1" colspan="1">P2CS<xref ref-type="table-fn" rid="TF1"><sup>a</sup></xref></td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.p2cs.org">http://www.p2cs.org</ext-link></td><td rowspan="1" colspan="1">Prokaryotic 2-Component Systems database</td></tr><tr><td rowspan="1" colspan="1">PAIR</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.cls.zju.edu.cn/pair/">http://www.cls.zju.edu.cn/pair/</ext-link></td><td rowspan="1" colspan="1">Predicted Arabidopsis Interactome Resource</td></tr><tr><td rowspan="1" colspan="1">Pancreas Expression<xref ref-type="table-fn" rid="TF1"><sup>a</sup></xref></td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.pancreasexpression.org">http://www.pancreasexpression.org</ext-link></td><td rowspan="1" colspan="1">Pancreatic gene Expression database</td></tr><tr><td rowspan="1" colspan="1">Pathway Commons</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.pathwaycommons.org/pc/">http://www.pathwaycommons.org/pc/</ext-link></td><td rowspan="1" colspan="1">Metabolic and signaling pathways from multiple organisms</td></tr><tr><td rowspan="1" colspan="1">PCDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://pcdb.unq.edu.ar/">http://pcdb.unq.edu.ar/</ext-link></td><td rowspan="1" colspan="1">Protein Conformational Diversity database</td></tr><tr><td rowspan="1" colspan="1">PCDDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://pcddb.cryst.bbk.ac.uk">http://pcddb.cryst.bbk.ac.uk</ext-link></td><td rowspan="1" colspan="1">Protein Circular Dichroism Database</td></tr><tr><td rowspan="1" colspan="1">PCRPi-DB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.bioinsilico.org/PCRPIDB">http://www.bioinsilico.org/PCRPIDB</ext-link></td><td rowspan="1" colspan="1">Presaging Critical Residues in Protein interface-DataBase</td></tr><tr><td rowspan="1" colspan="1">PhEVER</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://pbil.univ-lyon1.fr/databases/phever/index.php">http://pbil.univ-lyon1.fr/databases/phever/index.php</ext-link></td><td rowspan="1" colspan="1">Phylogenetic Exploration of Viruses and their Evolutionary Relationships</td></tr><tr><td rowspan="1" colspan="1">PHOSIDA<xref ref-type="table-fn" rid="TF1"><sup>a</sup></xref></td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.phosida.com">http://www.phosida.com</ext-link></td><td rowspan="1" colspan="1">Posttranslational modification sites identified by mass spectrometry</td></tr><tr><td rowspan="1" colspan="1">PmiRKB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bis.zju.edu.cn/pmirkb">http://bis.zju.edu.cn/pmirkb</ext-link></td><td rowspan="1" colspan="1">Plant microRNA knowledge base</td></tr><tr><td rowspan="1" colspan="1">PolyQ</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://pxgrid.med.monash.edu.au/polyq2i/">http://pxgrid.med.monash.edu.au/polyq2i/</ext-link></td><td rowspan="1" colspan="1">Polyglutamine Repeats in Proteins</td></tr><tr><td rowspan="1" colspan="1">PREX</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://csb.wfu.edu/PREX">http://csb.wfu.edu/PREX</ext-link></td><td rowspan="1" colspan="1">PeroxiRedoxin classification indEX</td></tr><tr><td rowspan="1" colspan="1">PRIDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bindr.gdcb.iastate.edu/PRIDB">http://bindr.gdcb.iastate.edu/PRIDB</ext-link></td><td rowspan="1" colspan="1">Protein–RNA Interface Database</td></tr><tr><td rowspan="1" colspan="1">PRO</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://pir.georgetown.edu/pro">http://pir.georgetown.edu/pro</ext-link></td><td rowspan="1" colspan="1">Protein Ontology based on evolutionary relatedness</td></tr><tr><td rowspan="1" colspan="1">PROMISCUOUS</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinformatics.charite.de/promiscuous">http://bioinformatics.charite.de/promiscuous</ext-link></td><td rowspan="1" colspan="1">Protein interactions data for studies of drug repositioning</td></tr><tr><td rowspan="1" colspan="1">ProtCID</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://dunbrack2.fccc.edu/protcid">http://dunbrack2.fccc.edu/protcid</ext-link></td><td rowspan="1" colspan="1">Protein Common Interface Database</td></tr><tr><td rowspan="1" colspan="1">PSSRdb</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://210.212.215.200/PSSR/pssr_frame.html">http://210.212.215.200/PSSR/pssr_frame.html</ext-link></td><td rowspan="1" colspan="1">Polymorphic Simple Sequence Repeats in bacteria</td></tr><tr><td rowspan="1" colspan="1">RBPDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://rbpdb.ccbr.utoronto.ca/">http://rbpdb.ccbr.utoronto.ca/</ext-link></td><td rowspan="1" colspan="1">RNA-binding proteins and their specificities</td></tr><tr><td rowspan="1" colspan="1">RegPhos</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://RegPhos.mbc.nctu.edu.tw">http://RegPhos.mbc.nctu.edu.tw</ext-link></td><td rowspan="1" colspan="1">Regulatory Network in Protein Phosphorylation</td></tr><tr><td rowspan="1" colspan="1">REPAIRtoire</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://repairtoire.genesilico.pl">http://repairtoire.genesilico.pl</ext-link></td><td rowspan="1" colspan="1">DNA repair pathways of human, yeast and <italic>E. coli</italic></td></tr><tr><td rowspan="1" colspan="1">RepTar</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://reptar.ekmd.huji.ac.il/">http://reptar.ekmd.huji.ac.il/</ext-link></td><td rowspan="1" colspan="1">Predicted targets of host and viral miRNAs</td></tr><tr><td rowspan="1" colspan="1">RiceXPro</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://ricexpro.dna.affrc.go.jp/">http://ricexpro.dna.affrc.go.jp/</ext-link></td><td rowspan="1" colspan="1">High-resolution analysis of rice transcriptome</td></tr><tr><td rowspan="1" colspan="1">RIKEN mammals</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://scines.org/db/mammal">http://scines.org/db/mammal</ext-link></td><td rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1">SAHG</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bird.cbrc.jp/sahg">http://bird.cbrc.jp/sahg</ext-link></td><td rowspan="1" colspan="1">Structural Atlas of Human Genome</td></tr><tr><td rowspan="1" colspan="1">SCLD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://scld.mcb.uconn.edu">http://scld.mcb.uconn.edu</ext-link></td><td rowspan="1" colspan="1">Stem Cell Lineage Database</td></tr><tr><td rowspan="1" colspan="1">SolGenomics<xref ref-type="table-fn" rid="TF1"><sup>a</sup></xref></td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://solgenomics.net/">http://solgenomics.net/</ext-link></td><td rowspan="1" colspan="1">Solanaceae Genomics Network</td></tr><tr><td rowspan="1" colspan="1">SPIKE</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.cs.tau.ac.il/~spike/">http://www.cs.tau.ac.il/∼spike/</ext-link></td><td rowspan="1" colspan="1">Signaling Pathways Integrated Knowledge Engine</td></tr><tr><td rowspan="1" colspan="1">Starbase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://starbase.sysu.edu.cn/">http://starbase.sysu.edu.cn/</ext-link></td><td rowspan="1" colspan="1">microRNA–mRNA interaction maps</td></tr><tr><td rowspan="1" colspan="1">SuperSweet</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinformatics.charite.de/sweet">http://bioinformatics.charite.de/sweet</ext-link></td><td rowspan="1" colspan="1">Natural and artificial sweetening agents</td></tr><tr><td rowspan="1" colspan="1">TADB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinfo-mml.sjtu.edu.cn/TADB/">http://bioinfo-mml.sjtu.edu.cn/TADB/</ext-link></td><td rowspan="1" colspan="1">Type II Toxin-Antitoxin loci in bacteria and archaea</td></tr><tr><td rowspan="1" colspan="1">TcoF-DB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://cbrc.kaust.edu.sa/tcof">http://cbrc.kaust.edu.sa/tcof</ext-link></td><td rowspan="1" colspan="1">Database for Human Transcription Co-Factors</td></tr><tr><td rowspan="1" colspan="1">TFGD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://ted.bti.cornell.edu">http://ted.bti.cornell.edu</ext-link></td><td rowspan="1" colspan="1">Tomato Functional Genomics Database</td></tr><tr><td rowspan="1" colspan="1">ThYme</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.enzyme.cbirc.iastate.edu">http://www.enzyme.cbirc.iastate.edu</ext-link></td><td rowspan="1" colspan="1">Thioester-active enzymes</td></tr><tr><td rowspan="1" colspan="1">TIARA</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.gmi.ac.kr">http://www.gmi.ac.kr</ext-link></td><td rowspan="1" colspan="1">Totally Integrated Array data and high-throughput sequencing Read data Archive for human whole genomes</td></tr><tr><td rowspan="1" colspan="1">TMPad</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bio-cluster.iis.sinica.edu.tw/TMPad/">http://bio-cluster.iis.sinica.edu.tw/TMPad/</ext-link></td><td rowspan="1" colspan="1">Helix-packing folds in transmembrane proteins</td></tr><tr><td rowspan="1" colspan="1">TOPSAN</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.topsan.org">http://www.topsan.org</ext-link></td><td rowspan="1" colspan="1">The Open Protein Structure Annotation Network</td></tr><tr><td rowspan="1" colspan="1">TRIP</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.trpchannel.org">http://www.trpchannel.org</ext-link></td><td rowspan="1" colspan="1">Protein–protein interactions in mammalian TRP channels</td></tr><tr><td rowspan="1" colspan="1">UCSC Cancer Genomics Browser</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://genome-cancer.cse.ucsc.edu">http://genome-cancer.cse.ucsc.edu</ext-link></td><td rowspan="1" colspan="1">Web-based tools to integrate, visualize and analyze cancer genomics and clinical data</td></tr><tr><td rowspan="1" colspan="1">UK PubMed Central</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://ukpmc.ac.uk/">http://ukpmc.ac.uk/</ext-link></td><td rowspan="1" colspan="1">UK PubMed Central database</td></tr><tr><td rowspan="1" colspan="1">ViralZone</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.expasy.org/viralzone">http://www.expasy.org/viralzone</ext-link></td><td rowspan="1" colspan="1">Molecular and epidemiological data on viral genera and families</td></tr><tr><td rowspan="1" colspan="1">VnD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://210.218.222.221:8080/VnD/">http://210.218.222.221:8080/VnD/</ext-link></td><td rowspan="1" colspan="1">Variation and Disease: disease-related SNPs and drugs</td></tr><tr><td rowspan="1" colspan="1">WebGeSTer DB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://pallab.serc.iisc.ernet.in/gester/">http://pallab.serc.iisc.ernet.in/gester/</ext-link></td><td rowspan="1" colspan="1">Genome Scanner for bacterial transcriptional Terminators</td></tr><tr><td rowspan="1" colspan="1">YPA</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://service.csbb.ntu.edu.tw/ypa/">http://service.csbb.ntu.edu.tw/ypa/</ext-link></td><td rowspan="1" colspan="1">Yeast promoter atlas</td></tr></tbody></table><table-wrap-foot><fn id="TF1"><p><sup>a</sup>A description of this database has been previously published elsewhere.</p></fn></table-wrap-foot></table-wrap></p><p>In addition to this editorial comment, the current issue includes two more editorials. The first of them (<xref ref-type="bibr" rid="B1">1</xref>) is a collective statement by a large consortium of scientists, including the authors of this article, who are concerned with the proliferation of new databases that are rarely able to talk to each other. As a result, instead of contributing to building a single body of knowledge, these databases risk functioning increasingly as isolated islands in a sea of disparate biological data. This article proposes creating a community-defined, uniform, generic description of the core attributes of biological databases, BioDBcore, a kind of ‘minimal information about a biological database’, and provides a preliminary checklist to describe basic specifications of each new database (<xref ref-type="bibr" rid="B1">1</xref>). We would ask the authors of future submissions to the NAR Database Issue to fill out that checklist (or its latest version posted at <ext-link ext-link-type="uri" xlink:href="http://biocurator.org/biodbcore.shtml">http://biocurator.org/biodbcore.shtml</ext-link>) and provide it as Supplementary Data to their manuscripts. In addition, we will explore ways in which the NAR online Molecular Biology Database Collection might ultimately support the standard.</p><p>Another editorial (<xref ref-type="bibr" rid="B2">2</xref>) describes COMBREX, an exciting project that is aimed at figuring out the functions of the ‘conserved hypothetical’ and poorly or incorrectly annotated proteins, identified through genome sequencing [see also refs (<xref ref-type="bibr" rid="B3">3</xref>,<xref ref-type="bibr" rid="B4">4</xref>)]. This project is designed to serve as a clearinghouse, collecting functional predictions from specialists in bioinformatics and functional genomics and then sending these predictions for testing by experimentalists. COMBREX offers an entirely new arrangement for research funding, whereby relatively small amounts of money are offered on a competitive basis to the experimental groups that are willing to test those predictions, employing the techniques and equipment that already exist in their laboratories. This arrangement dramatically decreases the costs of functional analysis of the uncharacterized proteins and gives hope that many of them could be assigned a biochemical—and/or general biological—function.</p><p>A bright example of databases that do talk to each other is the International Nucleotide Sequence Database Collaboration (INSDC), which consists of three participating databases, the DNA Data Bank of Japan (DDBJ), the European Nucleotide Archive (ENA) at the European Bioinformatics Institute (EMBL-EBI), and GenBank at the US National Center for Biotechnology Information (NCBI). This issue features separate papers from each of these three databases (<xref ref-type="bibr" rid="B5 B6 B7">5–7</xref>), as well as a joint paper describing the principles of data maintenance and exchange within the collaboration (<xref ref-type="bibr" rid="B8">8</xref>). A separate paper describes the functioning of the Sequence Read Archive (SRA), recently established by the three INSDC partners (<xref ref-type="bibr" rid="B9">9</xref>).</p><p>Another area where database collaboration proved extremely successful is storage and dissemination of published research. This issue features a detailed description of the UK PubMed Central, an extremely important project that, in collaboration with PubMed Central projects in USA and Canada, provides a permanent online record for the research sponsored by British funding agencies, such as MRC, BBSRC, Wellcome Trust and the National Institute for Health Research (<xref ref-type="bibr" rid="B10">10</xref>).</p><p>In addition to the archival databases such as those of the INSDC, this issue includes curated databases of DNA sequence motifs, such as AREsite, a collection of AU-rich elements in vertebrate mRNA UTR sequences, and non-B DB, a repository of DNA sequences that form cruciform, triplex, slipped (hairpin) structures, tetraplex (G-quadruplex), left-handed Z-DNA and other DNA structures (<xref ref-type="bibr" rid="B11">11</xref>,<xref ref-type="bibr" rid="B12">12</xref>).</p><p>The RNA database papers featured in this issue include updates on Rfam and miRBase, two gold-standard databases of RNA sequences (<xref ref-type="bibr" rid="B13">13</xref>,<xref ref-type="bibr" rid="B14">14</xref>), a description of lncRNAdb, a new resource on experimentally characterized long non-coding RNA (<xref ref-type="bibr" rid="B15">15</xref>), as well as descriptions of several databases of predicted and/or experimentally validated microRNA targets (<xref ref-type="bibr" rid="B16 B17 B18 B19 B20 B21">16–21</xref>). This issue also includes an update on the status of the RNA Modification Database, which was regularly featured in the NAR Database Issue in the 1990s (<xref ref-type="bibr" rid="B22 B23 B24 B25">22–25</xref>) but not in the past 12 years. The current version lists 107 types of posttranscriptional modifications of nucleosides in RNA, primarily in various tRNAs (<xref ref-type="bibr" rid="B26">26</xref>). Two new databases present data on the RNA-binding proteins [RBPDB, <ext-link ext-link-type="uri" xlink:href="http://rbpdb.ccbr.utoronto.ca/">http://rbpdb.ccbr.utoronto.ca/</ext-link> (<xref ref-type="bibr" rid="B27">27</xref>)] and the specific structures of their RNA-binding sites [PRIDB, <ext-link ext-link-type="uri" xlink:href="http://bindr.gdcb.iastate.edu/PRIDB">http://bindr.gdcb.iastate.edu/PRIDB</ext-link> (<xref ref-type="bibr" rid="B28">28</xref>)].</p><p>This issue also features a block of 15 papers describing recent progress in protein structure databases, such as Protein DataBank (PDB), PDB in Europe (PDBe), CATH, SUPERFAMILY (<xref ref-type="bibr" rid="B29 B30 B31 B32">29–32</xref>), as well as a selection of databases on protein building blocks, protein–protein interactions, protein structure modeling, and the organization of inter-protein contact sites (<xref ref-type="bibr" rid="B33 B34 B35 B36 B37 B38">33–38</xref>). Among new databases, it is worth mentioning EMDataBank.org, a database of 3D cryo-electron microscopy maps (<xref ref-type="bibr" rid="B39">39</xref>), a database of protein circular dichroism data (<xref ref-type="bibr" rid="B40">40</xref>) and three databases that are dedicated to the conformational dynamics of proteins (<xref ref-type="bibr" rid="B41 B42 B43">41–43</xref>). In addition, a paper from Gert Vriend’s group (<xref ref-type="bibr" rid="B44">44</xref>) presents their PDB-facilities web site with several useful PDB-derived databases for the analysis of protein structures. These include the famous Definition of Secondary Structure of Proteins (DSSP) and Homology-derived Secondary Structure of Proteins (HSSP) databases, which were last featured in the NAR Database Issue >12 years ago (<xref ref-type="bibr" rid="B45">45</xref>,<xref ref-type="bibr" rid="B46">46</xref>).</p><p>Progress in the analysis of the human genome prompted the creation of databases that list genes implicated in a variety of human diseases, including coronary artery disease (<xref ref-type="bibr" rid="B47">47</xref>), type I diabetes (<xref ref-type="bibr" rid="B48">48</xref>) and cancer. Cancer databases in this issue are represented by an update paper on the Catalogue of Somatic Mutations In Cancer [COSMIC, <ext-link ext-link-type="uri" xlink:href="http://www.sanger.ac.uk/cosmic">http://www.sanger.ac.uk/cosmic</ext-link> (<xref ref-type="bibr" rid="B49">49</xref>)], a description of the University of California Santa Cruz (UCSC) Cancer Genomics Browser [<ext-link ext-link-type="uri" xlink:href="http://genome-cancer.cse.ucsc.edu">http://genome-cancer.cse.ucsc.edu</ext-link> (<xref ref-type="bibr" rid="B50">50</xref>)], a new resource tightly integrated with the popular UCSC Genome Browser and the ENCODE database (<xref ref-type="bibr" rid="B51">51</xref>,<xref ref-type="bibr" rid="B52">52</xref>), and three more databases, dedicated, respectively, to cervical cancer, prostate cancer and potential cancer drug targets (<xref ref-type="bibr" rid="B53 B54 B55">53–55</xref>).</p><p>There are many other excellent databases that could not be mentioned here because of the space restrictions. In fact, we expect every single database featured in this issue to be useful to a wide audience of students and researchers in various areas of molecular biology.</p><p>As explained in last year’s editorial (<xref ref-type="bibr" rid="B56">56</xref>), moving to an online-only format for the NAR Database Issue has allowed us to accommodate longer papers and to offer the authors of the most popular data resources an opportunity to describe their resources in more detail, providing a deeper insight into the organization and goals of their respective resources and putting the recent updates of these resources into a broader context. This year, such extended papers were invited for a much larger number of databases, resulting in comprehensive descriptions of the PDB, PDBe, EMDataBank, MODBASE, GPCRDB, RegulonDB, STRING and other well-known databases (<xref ref-type="bibr" rid="B29">29</xref>,<xref ref-type="bibr" rid="B30">30</xref>,<xref ref-type="bibr" rid="B35">35</xref>,<xref ref-type="bibr" rid="B39">39</xref>,<xref ref-type="bibr" rid="B57 B58 B59">57–59</xref>). In some cases, longer descriptions were accepted for first-time descriptions of several new databases (<xref ref-type="bibr" rid="B36">36</xref>,<xref ref-type="bibr" rid="B60">60</xref>,<xref ref-type="bibr" rid="B61">61</xref>). We intend to continue accepting long(er) database papers in the future.</p></sec><sec><title>FUNDING</title><p><funding-source>Intramural Research Program of the US National Institutes of Health</funding-source> (to M.Y.G.); European Molecular Biology Laboratory (to G.R.C.). Funding for open access charge: Waived by Oxford University Press.</p><p><italic>Conflict of interest statement</italic>. The authors' opinions do not necessarily reflect the views of their respective institutions.</p></sec></body><back><ack><title>ACKNOWLEDGEMENTS</title><p>The authors thank Sir Richard Roberts and Dr Alex Bateman, Dr David Landsman and Dr Francis Ouellette for helpful comments; Patricia Anderson, Dr Martine Bernardes-Silva and Gail Welsh for excellent editorial assistance, the Oxford University Press team lead by Claire Bird and Jennifer Boyd and Sheila Plaister at EMBL-EBI for their help in compiling this issue and the online Molecular Biology Database Collection.</p></ack><ref-list><title>REFERENCES</title><ref id="B1"><label>1</label><element-citation publication-type="journal"><person-group 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