The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
Identifieur interne : 000124 ( Pmc/Corpus ); précédent : 000123; suivant : 000125The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
Auteurs : Xosé M. Fernández-Suárez ; Michael Y. GalperinSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2012.
Abstract
The 20th annual Database Issue of
Url:
DOI: 10.1093/nar/gks1297
PubMed: 23203983
PubMed Central: 3531151
Links to Exploration step
PMC:3531151Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The 2013 <italic>Nucleic Acids Research</italic> Database Issue and the online Molecular Biology Database Collection</title><author><name sortKey="Fernandez Suarez, Xose M" sort="Fernandez Suarez, Xose M" uniqKey="Fernandez Suarez X" first="Xosé M." last="Fernández-Suárez">Xosé M. Fernández-Suárez</name><affiliation><nlm:aff wicri:cut=" and" id="gks1297-AFF1">Cambridge, CB24 6DZ, UK</nlm:aff></affiliation></author><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 id="gks1297-AFF1">National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23203983</idno><idno type="pmc">3531151</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531151</idno><idno type="RBID">PMC:3531151</idno><idno type="doi">10.1093/nar/gks1297</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000124</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000124</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The 2013 <italic>Nucleic Acids Research</italic> Database Issue and the online Molecular Biology Database Collection</title><author><name sortKey="Fernandez Suarez, Xose M" sort="Fernandez Suarez, Xose M" uniqKey="Fernandez Suarez X" first="Xosé M." last="Fernández-Suárez">Xosé M. Fernández-Suárez</name><affiliation><nlm:aff wicri:cut=" and" id="gks1297-AFF1">Cambridge, CB24 6DZ, UK</nlm:aff></affiliation></author><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 id="gks1297-AFF1">National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA</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="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The 20th annual Database Issue of <italic>Nucleic Acids Research</italic> includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in <italic>NAR</italic> and other journals. This year’s highlights include two databases of DNA repeat elements; several databases of transcriptional factors and transcriptional factor-binding sites; databases on various aspects of protein structure and protein–protein interactions; databases for metagenomic and rRNA sequence analysis; and four databases specifically dedicated to <italic>Escherichia coli</italic>. The increased emphasis on using the genome data to improve human health is reflected in the development of the databases of genomic structural variation (NCBI’s dbVar and EBI’s DGVa), the NIH Genetic Testing Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein–ligand binding. Two new databases present genomic and RNAseq data for monkeys, providing wealth of data on our closest relatives for comparative genomics purposes. The <italic>NAR</italic> online Molecular Biology 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>, has been updated and currently lists 1512 online databases. The full content of the Database Issue is freely available online on the <italic>Nucleic Acids Research</italic> website (<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="Benson, D" uniqKey="Benson D">D Benson</name></author><author><name sortKey="Clark, K" uniqKey="Clark K">K Clark</name></author><author><name sortKey="Karsch Mizrachi, I" uniqKey="Karsch Mizrachi I">I Karsch-Mizrachi</name></author><author><name sortKey="Lipman, Dj" uniqKey="Lipman D">DJ Lipman</name></author><author><name sortKey="Ostell, J" uniqKey="Ostell J">J Ostell</name></author><author><name sortKey="Sayers, Ew" uniqKey="Sayers E">EW Sayers</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cochrane, G" uniqKey="Cochrane G">G Cochrane</name></author><author><name sortKey="Alako, B" uniqKey="Alako B">B 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">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">23203983</article-id><article-id pub-id-type="pmc">3531151</article-id><article-id pub-id-type="doi">10.1093/nar/gks1297</article-id><article-id pub-id-type="publisher-id">gks1297</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>The 2013 <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>Fernández-Suárez</surname><given-names>Xosé M.</given-names></name><xref ref-type="aff" rid="gks1297-AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="gks1297-COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Galperin</surname><given-names>Michael Y.</given-names></name><xref ref-type="aff" rid="gks1297-AFF1"><sup>2</sup></xref><xref ref-type="corresp" rid="gks1297-COR2">*</xref></contrib></contrib-group><aff id="gks1297-AFF1"><sup>1</sup>Cambridge, CB24 6DZ, UK and<sup>2</sup>National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA</aff><author-notes><corresp id="gks1297-COR1">*To whom correspondence should be addressed. Tel: <phone>+1 301 435 5910</phone>; Fax: <fax>+1 301 435 7793</fax>; Email: <email>nardatabase@gmail.com</email> or <email>galperin@ncbi.nlm.nih.gov</email></corresp><corresp id="gks1297-COR2">Correspondence may also be addressed to Xosé M. Fernández-Suárez. Email: <email>xose.m.fernandez@gmail.com</email></corresp></author-notes><pub-date pub-type="ppub"><month>1</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>30</day><month>11</month><year>2012</year></pub-date><pub-date pub-type="pmc-release"><day>30</day><month>11</month><year>2012</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>41</volume><issue>Database issue</issue><issue-title>Database issue</issue-title><fpage>D1</fpage><lpage>D7</lpage><history><date date-type="received"><day>14</day><month>11</month><year>2012</year></date><date date-type="accepted"><day>15</day><month>11</month><year>2012</year></date></history><permissions><copyright-statement>Published by Oxford University Press 2012.</copyright-statement><copyright-year>2012</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/">http://creativecommons.org/licenses/by-nc/3.0/</ext-link>), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.</license-p></license></permissions><abstract><p>The 20th annual Database Issue of <italic>Nucleic Acids Research</italic> includes 176 articles, half of which describe new online molecular biology databases and the other half provide updates on the databases previously featured in <italic>NAR</italic> and other journals. This year’s highlights include two databases of DNA repeat elements; several databases of transcriptional factors and transcriptional factor-binding sites; databases on various aspects of protein structure and protein–protein interactions; databases for metagenomic and rRNA sequence analysis; and four databases specifically dedicated to <italic>Escherichia coli</italic>. The increased emphasis on using the genome data to improve human health is reflected in the development of the databases of genomic structural variation (NCBI’s dbVar and EBI’s DGVa), the NIH Genetic Testing Registry and several other databases centered on the genetic basis of human disease, potential drugs, their targets and the mechanisms of protein–ligand binding. Two new databases present genomic and RNAseq data for monkeys, providing wealth of data on our closest relatives for comparative genomics purposes. The <italic>NAR</italic> online Molecular Biology 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>, has been updated and currently lists 1512 online databases. The full content of the Database Issue is freely available online on the <italic>Nucleic Acids Research</italic> website (<ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/">http://nar.oxfordjournals.org/</ext-link>).</p></abstract><counts><page-count count="7"></page-count></counts></article-meta></front><body><sec><title>NEW AND UPDATED DATABASES</title><p>This 1300-page virtual volume represents the 20th annual Database Issue of <italic>Nucleic Acids Research</italic> (<italic>NAR</italic>). It includes descriptions of 88 new online databases, 77 update articles on databases that have been previously featured in the <italic>NAR</italic> Database Issue (<xref ref-type="table" rid="gks1297-T1">Table 1</xref>) and 11 articles with updates on database resources whose descriptions have been previously published in other journals (<xref ref-type="table" rid="gks1297-T2">Table 2</xref>).
<table-wrap id="gks1297-T1" position="float"><label>Table 1.</label><caption><p>New online databases featured in the 2013 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">APPRIS</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://appris.bioinfo.cnio.es/">http://appris.bioinfo.cnio.es/</ext-link></td><td rowspan="1" colspan="1">A system for annotating alternative splice isoforms</td></tr><tr><td rowspan="1" colspan="1">BioLiP</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://zhanglab.ccmb.med.umich.edu/BioLiP/">http://zhanglab.ccmb.med.umich.edu/BioLiP/</ext-link></td><td rowspan="1" colspan="1"><underline>Bio</underline>logically relevant <underline>li</underline>gand–<underline>p</underline>rotein interactions</td></tr><tr><td rowspan="1" colspan="1">BSRD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://kwanlab.bio.cuhk.edu.hk/BSRD">http://kwanlab.bio.cuhk.edu.hk/BSRD</ext-link></td><td rowspan="1" colspan="1">A repository of bacterial small regulatory RNA</td></tr><tr><td rowspan="1" colspan="1">CellLineNavigator</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.medicalgenomics.org/celllinenavigator">http://www.medicalgenomics.org/celllinenavigator</ext-link></td><td rowspan="1" colspan="1">Cell line expression profiles by microarray analysis</td></tr><tr><td rowspan="1" colspan="1">ChIPBase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://deepbase.sysu.edu.cn/chipbase/">http://deepbase.sysu.edu.cn/chipbase/</ext-link></td><td rowspan="1" colspan="1">Transcriptional regulation of lncRNA and microRNA genes from ChIP-Seq data</td></tr><tr><td rowspan="1" colspan="1">ChiTaRS</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://chimerasrch.bioinfo.cnio.es/">http://chimerasrch.bioinfo.cnio.es/</ext-link></td><td rowspan="1" colspan="1">Chimeric RNAs of two or more different transcripts</td></tr><tr><td rowspan="1" colspan="1">CIL-CCDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.cellimagelibrary.org/">http://www.cellimagelibrary.org/</ext-link></td><td rowspan="1" colspan="1">Images, videos and animations of various cell types from diverse organisms</td></tr><tr><td rowspan="1" colspan="1">CircaDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinf.itmat.upenn.edu/circa/">http://bioinf.itmat.upenn.edu/circa/</ext-link></td><td rowspan="1" colspan="1">Circadian gene expression profiles in human and mouse</td></tr><tr><td rowspan="1" colspan="1">CloneDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/clone/">http://www.ncbi.nlm.nih.gov/clone/</ext-link></td><td rowspan="1" colspan="1">Clones and libraries: sequence data, map positions and distributor information</td></tr><tr><td rowspan="1" colspan="1">ClusterMine360</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.sigma54.ca/microbialclusters/">http://www.sigma54.ca/microbialclusters/</ext-link></td><td rowspan="1" colspan="1">Microbial PKS/NRPS Biosynthesis</td></tr><tr><td rowspan="1" colspan="1">Cyanolyase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://cyanolyase.genouest.org/">http://cyanolyase.genouest.org/</ext-link></td><td rowspan="1" colspan="1">Sequences and motifs of the phycobilin lyase protein family</td></tr><tr><td rowspan="1" colspan="1">D2P2</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://d2p2.pro/">http://d2p2.pro/</ext-link></td><td rowspan="1" colspan="1"><underline>D</underline>atabase of <underline>D</underline>isordered <underline>P</underline>rotein <underline>P</underline>redictions</td></tr><tr><td rowspan="1" colspan="1">dbVar</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/dbvar">http://www.ncbi.nlm.nih.gov/dbvar</ext-link></td><td rowspan="2" colspan="1">Structural variation in chromosomes: inversions, translocations, insertions and deletions</td></tr><tr><td rowspan="1" colspan="1">DGVa</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/dgva/">http://www.ebi.ac.uk/dgva/</ext-link></td></tr><tr><td rowspan="1" colspan="1">dcGO</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://supfam.org/SUPERFAMILY/dcGO">http://supfam.org/SUPERFAMILY/dcGO</ext-link></td><td rowspan="1" colspan="1"><underline>d</underline>omain-<underline>c</underline>entric <underline>G</underline>ene <underline>O</underline>ntology</td></tr><tr><td rowspan="1" colspan="1">Dfam</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://dfam.janelia.org">http://dfam.janelia.org</ext-link></td><td rowspan="1" colspan="1">Human DNA repeat families</td></tr><tr><td rowspan="1" colspan="1">DGA</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://dga.nubic.northwestern.edu/">http://dga.nubic.northwestern.edu/</ext-link></td><td rowspan="1" colspan="1">Disease and Gene Annotations database</td></tr><tr><td rowspan="1" colspan="1">DIANA-LncBase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.microrna.gr/LncBase">http://www.microrna.gr/LncBase</ext-link></td><td rowspan="1" colspan="1">microRNA targets on long noncoding RNAs</td></tr><tr><td rowspan="1" colspan="1">DoBISCUIT</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.bio.nite.go.jp/pks/">http://www.bio.nite.go.jp/pks/</ext-link></td><td rowspan="1" colspan="1">Database Of BIoSynthesis clusters CUrated and InTegrated</td></tr><tr><td rowspan="1" colspan="1">EBI Enzyme Portal</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/enzymeportal">http://www.ebi.ac.uk/enzymeportal</ext-link></td><td rowspan="1" colspan="1">Various kinds of information about enzymes: small-molecule chemistry, biochemical pathways and drug compounds</td></tr><tr><td rowspan="1" colspan="1">ECMDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ecmdb.ca/">http://www.ecmdb.ca/</ext-link></td><td rowspan="1" colspan="1"><italic>Escherichia coli</italic> Metabolome Database</td></tr><tr><td rowspan="1" colspan="1">EENdb</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://eendb.zfgenetics.org/">http://eendb.zfgenetics.org/</ext-link></td><td rowspan="1" colspan="1"><underline>E</underline>ngineered <underline>e</underline>ndo<underline>n</underline>ucleases: zinc finger nucleases and transcription activator-like effector nucleases</td></tr><tr><td rowspan="1" colspan="1">eProS</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioservices.hs-mittweida.de/Epros/">http://bioservices.hs-mittweida.de/Epros/</ext-link></td><td rowspan="1" colspan="1">Energy profiles of protein structures</td></tr><tr><td rowspan="1" colspan="1">Factorbook</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.factorbook.org/">http://www.factorbook.org/</ext-link></td><td rowspan="1" colspan="1">Human transcription factor-binding data from ChIP-seq</td></tr><tr><td rowspan="1" colspan="1">G4LDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.g4ldb.org/">http://www.g4ldb.org/</ext-link></td><td rowspan="1" colspan="1">G-quadruplex Ligands Database</td></tr><tr><td rowspan="1" colspan="1">GDSC</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.cancerRxgene.org/">http://www.cancerRxgene.org/</ext-link></td><td rowspan="1" colspan="1">Genomics of Drug Sensitivity in Cancer: Sensitivity for anti-cancer drugs in various cell lines</td></tr><tr><td rowspan="1" colspan="1">GeneTack</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://topaz.gatech.edu/GeneTack/db.html">http://topaz.gatech.edu/GeneTack/db.html</ext-link></td><td rowspan="1" colspan="1">Genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences</td></tr><tr><td rowspan="1" colspan="1">Genome3D</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://genome3d.eu/">http://genome3d.eu/</ext-link></td><td rowspan="1" colspan="1">Domain structure predictions and 3D models for proteins from model genomes</td></tr><tr><td rowspan="1" colspan="1">Glycan Fragment DB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.glycanstructure.org/fragment-db">http://www.glycanstructure.org/fragment-db</ext-link></td><td rowspan="1" colspan="1">Database of glycan 3D structures</td></tr><tr><td rowspan="1" colspan="1">H2DB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://tga.nig.ac.jp/h2db/">http://tga.nig.ac.jp/h2db/</ext-link></td><td rowspan="1" colspan="1">Heritability data with trait-associated genomic loci</td></tr><tr><td rowspan="1" colspan="1">HBVdb</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://hbvdb.ibcp.fr/HBVdb/">http://hbvdb.ibcp.fr/HBVdb/</ext-link></td><td rowspan="1" colspan="1">A knowledge database for the Hepatitis B Virus</td></tr><tr><td rowspan="1" colspan="1">HemaExplorer</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://servers.binf.ku.dk/shs/">http://servers.binf.ku.dk/shs/</ext-link></td><td rowspan="1" colspan="1">Gene expression profiles in haematopoiesis</td></tr><tr><td rowspan="1" colspan="1">HEXEvent</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://hertellab.mmg.uci.edu/cgi-bin/HEXEvent/HEXEventWEB.cgi">http://hertellab.mmg.uci.edu/cgi-bin/HEXEvent/HEXEventWEB.cgi</ext-link></td><td rowspan="1" colspan="1"><underline>H</underline>uman <underline>E</underline>xone <underline>S</underline>plicing <underline>E</underline>vents</td></tr><tr><td rowspan="1" colspan="1">HOCOMOCO</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://autosome.ru/HOCOMOCO">http://autosome.ru/HOCOMOCO</ext-link>, <ext-link ext-link-type="uri" xlink:href="http://cbrc.kaust.edu.sa/hocomoco/">http://cbrc.kaust.edu.sa/hocomoco/</ext-link></td><td rowspan="1" colspan="1">HOmo sapiens COmprehensive MOdel COllection of hand-curated transcription factor-binding site models</td></tr><tr><td rowspan="1" colspan="1">KIDFamMap</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://gemdock.life.nctu.edu.tw/KIDFamMap/">http://gemdock.life.nctu.edu.tw/KIDFamMap/</ext-link></td><td rowspan="1" colspan="1"><underline>K</underline>inase-<underline>I</underline>nhibitor-<underline>D</underline>isease <underline>Fam</underline>ily <underline>Map</underline></td></tr><tr><td rowspan="1" colspan="1">LAMP</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.llamp.net/">http://www.llamp.net/</ext-link></td><td rowspan="1" colspan="1"><underline>L</underline>ibrary of <underline>A</underline>picomplexan <underline>M</underline>etabolic <underline>P</underline>athways</td></tr><tr><td rowspan="1" colspan="1">Lncipedia</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.lncipedia.org/">http://www.lncipedia.org/</ext-link></td><td rowspan="1" colspan="1">Human lncRNA gene sequences and structures</td></tr><tr><td rowspan="1" colspan="1">LncRNADisease</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://cmbi.bjmu.edu.cn/lncrnadisease">http://cmbi.bjmu.edu.cn/lncrnadisease</ext-link></td><td rowspan="1" colspan="1">Long non-coding RNA-associated diseases</td></tr><tr><td rowspan="1" colspan="1">LUCApedia</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://eeb.princeton.edu/lucapedia/">http://eeb.princeton.edu/lucapedia/</ext-link></td><td rowspan="1" colspan="1">Predicted genome of Last Universal Common Ancestor</td></tr><tr><td rowspan="1" colspan="1">meta.MicrobesOnline</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://meta.MicrobesOnline.org/">http://meta.MicrobesOnline.org/</ext-link></td><td rowspan="1" colspan="1">Comparative genomic tools for metagenome analysis</td></tr><tr><td rowspan="1" colspan="1">MetaboLights</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/metabolights">http://www.ebi.ac.uk/metabolights</ext-link></td><td rowspan="1" colspan="1">Metabolomics experiments and associated metadata</td></tr><tr><td rowspan="1" colspan="1">MetalPDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://metalweb.cerm.unifi.it/">http://metalweb.cerm.unifi.it/</ext-link></td><td rowspan="1" colspan="1">Metal-binding sites in macromolecular structures</td></tr><tr><td rowspan="1" colspan="1">METscout</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://metscout.mpg.de">http://metscout.mpg.de</ext-link></td><td rowspan="1" colspan="1">Spatial organization of <underline>met</underline>abolic reactions in the mouse</td></tr><tr><td rowspan="1" colspan="1">MonarchBase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://monarchbase.umassmed.edu/">http://monarchbase.umassmed.edu/</ext-link></td><td rowspan="1" colspan="1">Genome biology of the monarch butterfly <italic>Danaus plexippus</italic></td></tr><tr><td rowspan="1" colspan="1">NetwoRx</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://ophid.utoronto.ca/networx/">http://ophid.utoronto.ca/networx/</ext-link></td><td rowspan="1" colspan="1">Chemogenomic experiments in yeast: connection of drug response to biological pathways, phenotypes, and networks</td></tr><tr><td rowspan="1" colspan="1">NCBI Bookshelf</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/books">http://www.ncbi.nlm.nih.gov/books</ext-link></td><td rowspan="1" colspan="1">Free online books on the NCBI website</td></tr><tr><td rowspan="1" colspan="1">NHPRTR</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://nhprtr.org/">http://nhprtr.org/</ext-link></td><td rowspan="1" colspan="1"><underline>N</underline>on-<underline>h</underline>uman <underline>P</underline>rimate <underline>R</underline>eference <underline>T</underline>ranscriptome <underline>R</underline>esource</td></tr><tr><td rowspan="1" colspan="1">NIH Genetic Testing Registry</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/gtr/">http://www.ncbi.nlm.nih.gov/gtr/</ext-link></td><td rowspan="1" colspan="1">Genetic tests and laboratories that perform them</td></tr><tr><td rowspan="1" colspan="1">NPACT</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://crdd.osdd.net/raghava/npact/">http://crdd.osdd.net/raghava/npact/</ext-link></td><td rowspan="1" colspan="1"><underline>N</underline>aturally occurring <underline>P</underline>lant-based <underline>A</underline>nticancer <underline>C</underline>ompound <underline>T</underline>argets</td></tr><tr><td rowspan="1" colspan="1">OikoBase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://oikoarrays.biology.uiowa.edu/Oiko/">http://oikoarrays.biology.uiowa.edu/Oiko/</ext-link></td><td rowspan="1" colspan="1">Genome expression database of <italic>Oikopleura dioica</italic></td></tr><tr><td rowspan="1" colspan="1">OrtholugeDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.pathogenomics.sfu.ca/ortholugedb/">http://www.pathogenomics.sfu.ca/ortholugedb/</ext-link></td><td rowspan="1" colspan="1">Microbial orthology resource</td></tr><tr><td rowspan="1" colspan="1">OrysPSSP</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://genoportal.org/SPD/index.do">http://genoportal.org/SPD/index.do</ext-link></td><td rowspan="1" colspan="1">Small secreted proteins from rice</td></tr><tr><td rowspan="1" colspan="1">Papillomavirus Episteme</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://PaVE.niaid.nih.gov/">http://PaVE.niaid.nih.gov/</ext-link></td><td rowspan="1" colspan="1">A database of Papillomaviridae family of viruses</td></tr><tr><td rowspan="1" colspan="1">PGDD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://chibba.agtec.uga.edu/duplication/">http://chibba.agtec.uga.edu/duplication/</ext-link></td><td rowspan="1" colspan="1"><underline>P</underline>lant <underline>G</underline>enome <underline>D</underline>uplication <underline>D</underline>atabase</td></tr><tr><td rowspan="1" colspan="1">PIECE</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://probes.pw.usda.gov/piece/">http://probes.pw.usda.gov/piece/</ext-link></td><td rowspan="1" colspan="1"><underline>P</underline>lant <underline>I</underline>ntron <underline>E</underline>xon <underline>C</underline>omparison and <underline>E</underline>volution</td></tr><tr><td rowspan="1" colspan="1">PlantRNA</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://plantrna.ibmp.cnrs.fr/">http://plantrna.ibmp.cnrs.fr/</ext-link></td><td rowspan="1" colspan="1">tRNAs of plants and algae</td></tr><tr><td rowspan="1" colspan="1">PR2</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://ssu-rrna.org/">http://ssu-rrna.org/</ext-link></td><td rowspan="1" colspan="1"><underline>P</underline>rotist <underline>R</underline>ibosomal <underline>r</underline>eference database</td></tr><tr><td rowspan="1" colspan="1">prePPI</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bhapp.c2b2.columbia.edu/PrePPI">http://bhapp.c2b2.columbia.edu/PrePPI</ext-link></td><td rowspan="1" colspan="1">Predicted and experimentally determined protein–protein interactions for yeast and human</td></tr><tr><td rowspan="1" colspan="1">PTMcode</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://ptmcode.embl.de/">http://ptmcode.embl.de/</ext-link></td><td rowspan="1" colspan="1">Functional associations between posttranslational modifications within proteins</td></tr><tr><td rowspan="1" colspan="1">Quorumpeps</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://quorumpeps.ugent.be/">http://quorumpeps.ugent.be/</ext-link></td><td rowspan="1" colspan="1">A database of quorum-sensing peptides</td></tr><tr><td rowspan="1" colspan="1">RhesusBase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.rhesusbase.org/">http://www.rhesusbase.org/</ext-link></td><td rowspan="1" colspan="1">A Knowledgebase for the Monkey Research Community</td></tr><tr><td rowspan="1" colspan="1">RiceFREND</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://ricefrend.dna.affrc.go.jp/">http://ricefrend.dna.affrc.go.jp/</ext-link></td><td rowspan="1" colspan="1">Rice Functionally Related gene Expression Network Database</td></tr><tr><td rowspan="1" colspan="1">RNApathwaysDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://rnb.genesilico.pl/">http://rnb.genesilico.pl/</ext-link></td><td rowspan="1" colspan="1">A database of RNA processing pathways</td></tr><tr><td rowspan="1" colspan="1">SecReT4</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://db-mml.sjtu.edu.cn/SecReT4/">http://db-mml.sjtu.edu.cn/SecReT4/</ext-link></td><td rowspan="1" colspan="1">Type IV Secretion system Resource</td></tr><tr><td rowspan="1" colspan="1">SEVA</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://seva.cnb.csic.es/SEVA/">http://seva.cnb.csic.es/SEVA/</ext-link></td><td rowspan="1" colspan="1">Standard European Vector Architecture: a collection of plasmids to analyse complex prokaryotic phenotypes</td></tr><tr><td rowspan="1" colspan="1">SIFTS</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/pdbe/docs/sifts/">http://www.ebi.ac.uk/pdbe/docs/sifts/</ext-link></td><td rowspan="1" colspan="1">Structure Integration with Function, Taxonomy and Sequences</td></tr><tr><td rowspan="1" colspan="1">SINEBase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://sines.eimb.ru">http://sines.eimb.ru</ext-link></td><td rowspan="1" colspan="1">A database of short interspersed elements (SINEs)</td></tr><tr><td rowspan="1" colspan="1">SomamiR</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://compbio.uthsc.edu/SomamiR/">http://compbio.uthsc.edu/SomamiR/</ext-link></td><td rowspan="1" colspan="1">Somatic mutations that impact microRNA targeting in cancer</td></tr><tr><td rowspan="1" colspan="1">Spermatogenesis Online</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://mcg.ustc.edu.cn/sdap1/spermgenes/">http://mcg.ustc.edu.cn/sdap1/spermgenes/</ext-link></td><td rowspan="1" colspan="1">Spermatogenesis-related genes</td></tr><tr><td rowspan="1" colspan="1">SpliceAid-F</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://mi.caspur.it/SpliceAidF/">http://mi.caspur.it/SpliceAidF/</ext-link></td><td rowspan="1" colspan="1">Human splicing factors and their RNA-binding sites</td></tr><tr><td rowspan="1" colspan="1">Spliceosome Database</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://spliceosomedb.ucsc.edu/">http://spliceosomedb.ucsc.edu/</ext-link></td><td rowspan="1" colspan="1">Spliceosome genes and proteins, splicing complexes</td></tr><tr><td rowspan="1" colspan="1">StreptomeDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://streptomedb.pharmaceutical-bioinformatics.de">http://streptomedb.pharmaceutical-bioinformatics.de</ext-link></td><td rowspan="1" colspan="1">Antibiotic, anti-tumour and immunosuppressant drugs produced by <italic>Streptomyces</italic> spp.</td></tr><tr><td rowspan="1" colspan="1">SwissBioisostere</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.swissbioisostere.ch/">http://www.swissbioisostere.ch/</ext-link></td><td rowspan="1" colspan="1">Molecular replacements for ligand design</td></tr><tr><td rowspan="1" colspan="1">SwissSidechain</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.swisssidechain.ch/">http://www.swisssidechain.ch/</ext-link></td><td rowspan="1" colspan="1">Non-natural amino acid sidechains for protein engineering</td></tr><tr><td rowspan="1" colspan="1">SynSysNet</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinformatics.charite.de/synsysnet/">http://bioinformatics.charite.de/synsysnet/</ext-link></td><td rowspan="1" colspan="1">Synapse proteins, their structures and interactions</td></tr><tr><td rowspan="1" colspan="1">TCMID</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.megabionet.org/tcmid/">http://www.megabionet.org/tcmid/</ext-link></td><td rowspan="1" colspan="1">Traditional Chinese Medicine Integrated Database</td></tr><tr><td rowspan="1" colspan="1">TFClass</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.edgar-wingender.de/huTF_classification.html">http://www.edgar-wingender.de/huTF_classification.html</ext-link></td><td rowspan="1" colspan="1">Human <underline>t</underline>ranscription <underline>f</underline>actors <underline>class</underline>ified according to their DNA-binding domains</td></tr><tr><td rowspan="1" colspan="1">TissueNet</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://netbio.bgu.ac.il/tissuenet/">http://netbio.bgu.ac.il/tissuenet/</ext-link></td><td rowspan="1" colspan="1">Tissue distribution of protein–protein interactions</td></tr><tr><td rowspan="1" colspan="1">TOPPR</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://iomics.ugent.be/toppr/">http://iomics.ugent.be/toppr/</ext-link></td><td rowspan="1" colspan="1">The Online Protein Processing Resource</td></tr><tr><td rowspan="1" colspan="1">TSGene</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://bioinfo.mc.vanderbilt.edu/TSGene/">http://bioinfo.mc.vanderbilt.edu/TSGene/</ext-link></td><td rowspan="1" colspan="1">Tumor Suppressor Gene database</td></tr><tr><td rowspan="1" colspan="1">UCNEbase</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://ccg.vital-it.ch/UCNEbase/">http://ccg.vital-it.ch/UCNEbase/</ext-link></td><td rowspan="1" colspan="1"><underline>U</underline>ltra<underline>c</underline>onserved <underline>n</underline>on-coding <underline>e</underline>lements and gene regulatory blocks</td></tr><tr><td rowspan="1" colspan="1">UUCD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://uucd.biocuckoo.org/">http://uucd.biocuckoo.org/</ext-link></td><td rowspan="1" colspan="1">Ubiquitin and ubiquitin-like conjugation database</td></tr><tr><td rowspan="1" colspan="1">ValidNESs</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://validness.ym.edu.tw/">http://validness.ym.edu.tw/</ext-link></td><td rowspan="1" colspan="1">Validated <underline>n</underline>uclear <underline>e</underline>xport <underline>s</underline>ignal<underline>s</underline>-containing proteins</td></tr><tr><td rowspan="1" colspan="1">Voronoia4RNA</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://proteinformatics.charite.de/voronoia4rna/tools/v4rna/index">http://proteinformatics.charite.de/voronoia4rna/tools/v4rna/index</ext-link></td><td rowspan="1" colspan="1">Packing of RNA molecules and complexes</td></tr><tr><td rowspan="1" colspan="1">WDDD</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://so.qbic.riken.jp/wddd/">http://so.qbic.riken.jp/wddd/</ext-link></td><td rowspan="1" colspan="1"><underline>W</underline>orm <underline>D</underline>evelopmental <underline>D</underline>ynamics <underline>D</underline>atabase</td></tr><tr><td rowspan="1" colspan="1">WholeCellKB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://wholecellkb.stanford.edu/">http://wholecellkb.stanford.edu/</ext-link></td><td rowspan="1" colspan="1">Pathway and genome database of <italic>Mycoplasma genitalium</italic> for whole-cell modelling</td></tr><tr><td rowspan="1" colspan="1">WormQTL</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.wormqtl.org">http://www.wormqtl.org</ext-link></td><td rowspan="1" colspan="1">Natural variation data in <italic>Caenorhabditis</italic> spp.</td></tr><tr><td rowspan="1" colspan="1">YM500</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://ngs.ym.edu.tw/ym500/">http://ngs.ym.edu.tw/ym500/</ext-link></td><td rowspan="1" colspan="1">smRNA-seq database for miRNA research</td></tr><tr><td rowspan="1" colspan="1">ZInC</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://research.nhgri.nih.gov/zinc">http://research.nhgri.nih.gov/zinc</ext-link></td><td rowspan="1" colspan="1">Zebrafish Insertions Collection</td></tr></tbody></table></table-wrap><table-wrap id="gks1297-T2" position="float"><label>Table 2.</label><caption><p>Database updates new for the 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">Previous article</th><th rowspan="1" colspan="1">Brief description</th></tr></thead><tbody align="left"><tr><td rowspan="1" colspan="1">2P2Idb</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://dimr.cnrs-mrs.fr">http://dimr.cnrs-mrs.fr</ext-link></td><td rowspan="1" colspan="1">2010</td><td rowspan="1" colspan="1">Structural data on <underline>p</underline>rotein–<underline>p</underline>rotein <underline>i</underline>nteractions and their <underline>i</underline>nhibitors</td></tr><tr><td rowspan="1" colspan="1">Allen Brain Atlas</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.brain-map.org">http://www.brain-map.org</ext-link></td><td rowspan="1" colspan="1">2009</td><td rowspan="1" colspan="1">Gene expression and neuroanatomical data on human and mouse brain</td></tr><tr><td rowspan="1" colspan="1">BioGPS</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://biogps.org">http://biogps.org</ext-link></td><td rowspan="1" colspan="1">2009</td><td rowspan="1" colspan="1">Gene annotation portal and a resource on gene and protein function</td></tr><tr><td rowspan="1" colspan="1">DARNED</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://beamish.ucc.ie/">http://beamish.ucc.ie/</ext-link></td><td rowspan="1" colspan="1">2010</td><td rowspan="1" colspan="1"><underline>Da</underline>tabase of <underline>RN</underline>A <underline>Ed</underline>iting</td></tr><tr><td rowspan="1" colspan="1">DoriC</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://tubic.tju.edu.cn/doric/">http://tubic.tju.edu.cn/doric/</ext-link></td><td rowspan="1" colspan="1">2007</td><td rowspan="1" colspan="1">Replication origin (<italic>oriC</italic>) regions in bacterial and archaeal genomes</td></tr><tr><td rowspan="1" colspan="1">FlyAtlas</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://flyatlas.org/">http://flyatlas.org/</ext-link></td><td rowspan="1" colspan="1">2007</td><td rowspan="1" colspan="1"><italic>Drosophila</italic> gene expression atlas</td></tr><tr><td rowspan="1" colspan="1">GenColors</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://sgb.fli-leibniz.de/">http://sgb.fli-leibniz.de/</ext-link></td><td rowspan="1" colspan="1">2005</td><td rowspan="1" colspan="1">Genome annotation and comparison database for small genomes</td></tr><tr><td rowspan="1" colspan="1">Genomicus</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.dyogen.ens.fr/genomicus">http://www.dyogen.ens.fr/genomicus</ext-link></td><td rowspan="1" colspan="1">2010</td><td rowspan="1" colspan="1">Syntenic relationships between eukaryote genomes</td></tr><tr><td rowspan="1" colspan="1">InnateDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.innatedb.com/">http://www.innatedb.com/</ext-link></td><td rowspan="1" colspan="1">2008</td><td rowspan="1" colspan="1">A database of mammalian innate immune response</td></tr><tr><td rowspan="1" colspan="1">MicroScope</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.genoscope.cns.fr/agc/microscope/">http://www.genoscope.cns.fr/agc/microscope/</ext-link></td><td rowspan="1" colspan="1">2009</td><td rowspan="1" colspan="1">Microbial genome annotation and analysis platform</td></tr><tr><td rowspan="1" colspan="1">NPIDB</td><td rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://npidb.belozersky.msu.ru/">http://npidb.belozersky.msu.ru/</ext-link></td><td rowspan="1" colspan="1">2007</td><td rowspan="1" colspan="1"><underline>N</underline>ucleic acids–<underline>p</underline>rotein <underline>i</underline>nteraction <underline>d</underline>ata<underline>b</underline>ase</td></tr></tbody></table></table-wrap></p><p>At this point it might be instructive to look back at the origin and evolution of the <italic>NAR</italic> Database Issue. Its history started from two supplementary issues that were published in <italic>NAR</italic> in April of 1991 and in May of 1992 and consisted of 18 and 19 articles, respectively (see <ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/content/19/supplement.toc">http://nar.oxfordjournals.org/content/19/supplement.toc</ext-link> and <ext-link ext-link-type="uri" xlink:href="http://nar.oxfordjournals.org/content/20/supplement.toc">http://nar.oxfordjournals.org/content/20/supplement.toc</ext-link>). These articles offered descriptions of several nucleotide sequence databases, such as GenBank, the EMBL Data Library, compilations of small RNA, tRNA, and 5S, 16S, and 23S rRNA sequences (including the Ribosomal Database Project), DNA sequences from <italic>Escherichia coli</italic> and a human genome database (GDB). Those first issues also included descriptions of several protein databases, such as S<sc>wiss-Prot</sc>, PIR, P<sc>rosite</sc>, Restriction Enzyme Database (REBASE), Transcription Factors Database (TFD) and Histone database. There was also a medical genetics database, Haemophilia B, listing point mutations and indels in the coagulation factor IX (<italic>F9</italic>) gene that caused this blood clotting disorder, which has affected the royal families of several European countries.</p><p>The next issue, published on July 1, 1993, was the first one formally labelled as the Database Issue. It consisted of 24 articles, which added databases of RNA and protein structure and the E<sc>nzyme</sc> database. It was followed by <italic>NAR</italic> Database Issues in September 1994, then in January 1996, and each January after that.</p><p>In the past 20 years, the Database Issue has gradually grown in size before stabilizing at the level of ∼180 articles. However, despite the almost 10-fold increase in the number of published articles, the key topics of the current issue remain largely the same as 20 years ago. This issue again features articles from GenBank and the European Nucleotide Archive (formerly the EMBL Data Library), which, together with the DNA Data Bank of Japan, form the International Nucleotide Sequence Database collaboration, INSDC (<xref rid="gks1297-B1" ref-type="bibr">1–4</xref>). Just as 20 years ago, there are updates from S<sc>wiss-Prot</sc> and PIR (now combined into UniProt) and P<sc>rosite</sc> (<xref rid="gks1297-B5" ref-type="bibr">5</xref>,<xref rid="gks1297-B6" ref-type="bibr">6</xref>).</p><p>Continuing the tradition of featuring well-curated databases of RNA sequences, this issue includes an update on SILVA, a widely used comprehensive database of bacterial, archaeal and eukaryotic 16S/18S and 23S/28S rRNA sequences (<xref rid="gks1297-B7" ref-type="bibr">7</xref>), and a description of Protist Ribosomal Reference database (PR2), a new database that catalogs small subunit rRNA sequences from unicellular eukaryotes (<xref rid="gks1297-B8" ref-type="bibr">8</xref>). An update on the Ribosomal Database Project, a constant feature of the <italic>NAR</italic> Database Issue since 1991 (<xref rid="gks1297-B9" ref-type="bibr">9</xref>), was last published in 2009 (<xref rid="gks1297-B10" ref-type="bibr">10</xref>). Other RNA databases in this issue include an update on Rfam (<xref rid="gks1297-B11" ref-type="bibr">11</xref>), the universally acclaimed database of RNA families, as well as several databases on long non-coding RNA, microRNA and their targets. An update of M<sc>odomics</sc>, a database on RNA modification, is now supplemented by RNApathwaysDB, a database of RNA maturation and decay pathways developed by the same group (<xref rid="gks1297-B12" ref-type="bibr">12</xref>,<xref rid="gks1297-B13" ref-type="bibr">13</xref>).</p><p>As before, this issue presents several transcription factor (TF) databases. Two of them cover TFs themselves: TFClass offers a classification of human TFs, while NPIDB presents structural information on DNA–protein and RNA–protein complexes (<xref rid="gks1297-B14" ref-type="bibr">14</xref>,<xref rid="gks1297-B15" ref-type="bibr">15</xref>). Several other databases collect information on the TF-binding sites. These include Factorbook, a database of TF-binding data from the ENCODE project; HOCOMOCO, a collection of human TF-binding sites; CTCFBSDB, a database of CCCTC-binding factor (CTCF)-binding sites; RegulonDB, a database of transcriptional regulation in <italic>E. </italic><italic>coli</italic>; and SwissRegulon, a database of regulatory sites in human, mouse and yeast genomes and in model bacteria (<xref rid="gks1297-B16" ref-type="bibr">16–20</xref>).</p><p>The structural databases featured in this issue all show a trend towards a better integration and cross-referencing tools. This refers both to the updates of well-known databases, such as the RCSB Protein Data Bank (PDB), CATH and PDBTM, and to such databases as EBI’s SIFTS, a joint effort of UniProt and PDBe to provide a residue level mapping of their entries and supplement it with annotation from other public databases; Genome3D, a recent collaborative project aiming to provide structural annotation from CATH and SCOP to the genomic sequences; and dcGO, which develops domain-centric ontologies to link protein domains with functions, phenotypes and diseases (<xref rid="gks1297-B21" ref-type="bibr">21–23</xref>).</p><p>Likewise, with <italic>E. </italic><italic>coli</italic> remaining the workhorse of molecular biology, this issue includes update articles on the EcoGene (the first one since 2000), EcoCyc and RegulonDB databases, as well as a description of the newly developed <italic>E. coli</italic> Metabolome Database (<xref rid="gks1297-B20" ref-type="bibr">20</xref>,<xref rid="gks1297-B24" ref-type="bibr">24–26</xref>).</p></sec><sec><title>HUMAN DISEASE GENOMICS—THE NEXT FRONTIER?</title><p>As discussed earlier (<xref rid="gks1297-B27" ref-type="bibr">27</xref>), the original GDB did not survive the influx of the new data and multiple changes of ownership. Nevertheless, we now have a wide variety of databases that cover different aspects of human genome and genomes of model organisms. This issue features annual updates from Ensembl and ENCODE projects and from the UCSC Genome Browser and the Japanese H-InvDB database (<xref rid="gks1297-B28" ref-type="bibr">28–31</xref>). The model organism databases are represented by the updates to FlyBase, Mouse Genome database, Xenbase and ZFIN (<xref rid="gks1297-B32" ref-type="bibr">32–35</xref>).</p><p>Two new databases, RhesusBase and NHPRTR, present extensive genome and RNAseq data for non-human primates, including great apes, old world monkeys, new world monkeys and prosimians (<xref rid="gks1297-B36" ref-type="bibr">36</xref>,<xref rid="gks1297-B37" ref-type="bibr">37</xref>). These data could go a long way towards establishing monkeys as model organisms for comparative genomics studies. One more database is dedicated to a more distant relative of human, the urochordate <italic>Oikopleura dioica</italic> (<xref rid="gks1297-B38" ref-type="bibr">38</xref>).</p><p>A potentially important development is the construction of two new databases of repetitive DNA elements, Dfam and SINEBase (<xref rid="gks1297-B39" ref-type="bibr">39</xref>,<xref rid="gks1297-B40" ref-type="bibr">40</xref>). Along with the industry standard Repbase Update (<xref rid="gks1297-B41" ref-type="bibr">41</xref>,<xref rid="gks1297-B42" ref-type="bibr">42</xref>) and monthly RepBase Reports (<ext-link ext-link-type="uri" xlink:href="http://www.girinst.org/repbase/reports/">http://www.girinst.org/repbase/reports/</ext-link>), these databases promise to contribute to a better understanding of eukaryotic repeat elements.</p><p>With the abundance of databases providing valuable tools for genome analysis, there is a clear trend towards bringing genomics ‘from the bench to the bedside’, i.e. using genomic data for a better understanding and, hopefully, better treatment of human disease. A number of projects, including ClinSeq (<ext-link ext-link-type="uri" xlink:href="http://www.genome.gov/20519355">http://www.genome.gov/20519355</ext-link>), DDD (<ext-link ext-link-type="uri" xlink:href="http://www.ddduk.org/">http://www.ddduk.org/</ext-link>) and UK10K (<ext-link ext-link-type="uri" xlink:href="http://www.uk10k.org/">http://www.uk10k.org/</ext-link>) are working towards these goals, and several databases featured in this issue represent important steps in this direction. Last year’s issue introduced the GWASdb database of human genetic variants identified by genome-wide association studies (<xref rid="gks1297-B43" ref-type="bibr">43</xref>). GWAS Central, established in 2007 as HGVbaseG2P (<xref rid="gks1297-B44" ref-type="bibr">44</xref>), has been revamped and now includes data from over 1000 studies. Now, a joint article from NCBI and EBI describes their databases of genomic structural variation, dbVar and DGVa (<xref rid="gks1297-B45" ref-type="bibr">45</xref>). These databases cover diverse variation data including inversions, insertions and translocations that are >50 bp in length. NCBI is also developing ClinVar (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/clinvar/">http://www.ncbi.nlm.nih.gov/clinvar/</ext-link>), a database of relationships between human gene variation and the observed health status (<xref rid="gks1297-B46" ref-type="bibr">46</xref>). The task of streamlining the genetic tests that provide such information is taken up by the recently created NIH Genetic Testing Registry, a database of genetic tests and laboratories that perform them, with detailed information about what exactly is measured in each test and its analytic and clinical validity (<xref rid="gks1297-B47" ref-type="bibr">47</xref>).</p><p>The impact of the genomic data on developing targeted approaches for fighting disease is particularly evident in the case of cancer. This issue features updates from three great databases, the UCSC Cancer Genome Browser (<xref rid="gks1297-B48" ref-type="bibr">48</xref>), the Atlas of Genetics and Cytogenetics in Oncology and Haematology (<xref rid="gks1297-B49" ref-type="bibr">49</xref>) and the TP53 website [(<xref rid="gks1297-B50" ref-type="bibr">50</xref>), the first update of the database on tumor factor p53 mutations since 1997]. In addition, there are two new databases dedicated to studying cancer at the level of specific cell lines. The CellLineNavigator database provides gene expression profiles of different cancer cell lines in different pathological states (<xref rid="gks1297-B51" ref-type="bibr">51</xref>), whereas the Genomics of Drug Sensitivity in Cancer (GDSC) collects the results of high-throughput studies examining the sensitivity for anti-cancer drugs in various cell lines (<xref rid="gks1297-B52" ref-type="bibr">52</xref>).</p></sec><sec><title>CURATION OF THE <italic>NAR</italic> DATABASE COLLECTION</title><p>During the past 20 years, all databases featured in the <italic>NAR</italic> Database Issues were added to the <italic>NAR</italic> online Molecular Biology 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>. With the annual attrition rate of <5%, this Collection has been steadily growing and, in 2012, exceeded 1400 database entries (<xref rid="gks1297-B53" ref-type="bibr">53</xref>). It was clear that the list was due for a serious clean-up, and one of the authors (XMFS) devised and set in motion a semi-automated procedure to identify obsolete and non-responsive websites. Remarkably, >90% of the databases listed in the last year’s release of the online Collection were found to be functional. Corresponding authors of close to a hundred non-responsive resources had been contacted and 44 websites (∼3.2% of the total) have been approved for deletion. About 100 entries in the Collection have been updated by receiving corrected URLs, summaries highlighting recent developments, or some other changes in the deposited data.</p><p>Although deletion of 40 databases was well within the average drop-off rate and was hardly surprising, further analysis revealed that most of these resources were not lost. Instead, in the normal course of database evolution, they have been integrated into larger projects. For example, a couple of segmental duplications databases were merged into the Database of Genomic Variants (<xref rid="gks1297-B54" ref-type="bibr">54</xref>), <italic>NAR</italic> Database Collection entry no. 655, while the NCBI’s Cancer Chromosomes database has been merged into dbVar [described in detail in this issue, (<xref rid="gks1297-B45" ref-type="bibr">45</xref>)]. Further, improved annotation of the human genome made redundant a number of resources that covered specific areas of the genome (e.g. the IXDB with its physical maps of human chromosome X).</p><p>In one instance, the ExDom database of exon–intron structures of genes in seven eukaryotic genomes (<xref rid="gks1297-B55" ref-type="bibr">55</xref>) had to be removed from the Collection, as it has taken the commercial route and does not provide a free version anymore, although the author’s company offered a discounted version for academic users. Unfortunately, the tightening budgets (<xref rid="gks1297-B56" ref-type="bibr">56</xref>) might force other databases to follow the same path.</p><p>In total, the <italic>NAR</italic> online Molecular Biology Database Collection now includes 1512 databases sorted into 14 categories and 41 subcategories. The authors wishing to have their databases, published elsewhere, to be included in the Collection are welcome to contact XMFS directly.</p></sec><sec><title>FUNDING</title><p>Intramural Research Program of the <funding-source>U.S. National Institutes of Health</funding-source> at the <funding-source>National Library of Medicine</funding-source> [to M.Y.G.]. 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 Drs Javier Herrero and Michael Schuster for helpful comments and the Oxford University Press team led by Jennifer Boyd and Andrew Malvern for their help in compiling this issue.</p></ack><ref-list><title>REFERENCES</title><ref id="gks1297-B1"><label>1</label><element-citation publication-type="journal"><person-group 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