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<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="content-type" content="text/html; charset=utf-8" /> <meta http-equiv="content-script-type" content="text/javascript" /> <title>DBGET Search</title> <link rel="stylesheet" href="/css/gn2.css" type="text/css" /> </head> <body bgcolor="#ffffff" link="#003399" vlink="#003399" onload="document.forms[0].keywords.focus()"> <table width="720"> <tr> <td width="180" align="center"> <a href="/"><img src="/Fig/gntop2.gif" alt="GenomeNet icon" border="0" /></a> </td> <td> <h2 class="title2">DBGET Search</h2> </td> </tr> </table> <br /> <table width="720" cellpadding="2" class="frame2"> <tr><td align="center" class="td20"> <table width="700"> <tr> <th><font class="current">DBGET</font></th> <th><a href="/linkdb/">LinkDB</a></th> <th><a href="/kegg/kegg2.html">KEGG2</a></th> </tr> </table> </td></tr> <tr><td align="center">  <br /> <table width="680"> <tr><td> <table cellpadding="0" cellspacing="0"> <tr><td nowrap="nowrap"> <form method="get" action="/dbget-bin/www_bfind_sub"> <input type="hidden" name="mode" value="bfind" /> <input type="hidden" name="max_hit" value="1000" /> <b>Search</b> <select name="dbkey"> <option value="alldb" selected="selected">All databases</option> <option value="ontology">Ontology</option> <option value="brite">  KEGG BRITE</option> <option value="go">  GO</option> <option value="pathway_all">Pathway</option> <option value="pathway">  KEGG PATHWAY</option> <option value="module">  KEGG MODULE</option> <option value="network_all">Network</option> <option value="network">  KEGG Network</option> <option value="variant">  KEGG Variant</option> <option value="disease_all">Disease</option> <option value="disease">  KEGG DISEASE</option> <option value="drug_all">Drug</option> <option value="drug">  KEGG DRUG</option> <option value="dgroup">  KEGG DGROUP</option> <option value="ligandbox">  LigandBox</option> <option value="sider">  SIDER</option> <option value="substance_all">Chemical substance</option> <option value="compound">  KEGG COMPOUND</option> <option value="glycan">  KEGG GLYCAN</option> <option value="pubchem">  PubChem</option> <option value="chebi">  ChEBI</option> <option value="pdb-ccd">  PDB-CCD</option> <option value="lipidmaps">  LIPIDMAPS</option> <option value="knapsack">  KNApSAcK</option> <option value="hmdb">  HMDB</option> <option value="reaction_all">Chemical reaction</option> <option value="enzyme">  KEGG ENZYME</option> <option value="reaction">  KEGG REACTION</option> <option value="rclass">  KEGG RCLASS</option> <option value="genome_all">Genome</option> <option value="genome">  KEGG GENOME</option> <option value="mgenome">  KEGG MGENOME</option> <option value="genes_all">Gene</option> <option value="orthology">  KEGG ORTHOLOGY</option> <option value="genes">  KEGG GENES</option> <option value="mgenes">  KEGG MGENES</option> <option value="refgene">  RefGene</option> <option value="ncbi-geneid">  NCBI-Gene</option> <option value="ensembl">  Ensembl</option> <option value="hgnc">  HGNC</option> <option value="brc-dna">  RIKEN BRC-DNA</option> <option value="brc-epd">  RIKEN BRC-EPD</option> <option value="aaseq_all">Protein sequence</option> <option value="uniprot">  UniProt</option> <option value="refpep">  RefSeq</option> <option value="ntseq_all">DNA sequence</option> <option value="refnuc">  RefSeq</option> <option value="dna-today-nonst">  INSDC</option> <option value="structure_all">3D Structure</option> <option value="pdb">  PDB</option> <option value="motifdic">Protein domain</option> <option value="interpro">  InterPro</option> <option value="pfam">  Pfam</option> <option value="prosite">  PROSITE</option> <option value="ncbi-cdd">  NCBI-CDD</option> <option value="expression">Gene expression</option> <option value="expression">  EXPRESSION</option> </select> <b>for</b> <input type="text" size="40" name="keywords" /> <input type="submit" value="Go" /> <input type="reset" value="Clear" /> </form> </td></tr> </table> <br /> <hr class="frame2" /> <b>DBGET</b> is an integrated database retrieval system for major biological databases, which are classified into five categories: <blockquote> <table border="1" cellpadding="2" cellspacing="0"> <tr><td rowspan="2">Category</td><td colspan="3" align="center">Main commands</td><td rowspan="2">Remark</td></tr> <tr><td align="center">bget</td><td align="center">bfind</td><td align="center">blink</td></tr> <tr><td>1. KEGG databases in DBGET</td><td align="center">yes</td><td align="center">yes</td><td align="center">yes</td><td rowspan="2">Mirrored at GenomeNet</td></tr> <tr><td>2. Other DBGET databases</td><td align="center">yes</td><td align="center">yes</td><td align="center">yes</td></tr> <tr><td>3. Searchable databases on the Web</td><td align="center">no</td><td align="center">yes</td><td align="center">yes</td><td rowspan="3">Used as Web resources</td></tr> <tr><td>4. Link-only databases on the Web</td><td align="center">no</td><td align="center">no</td><td align="center">yes</td></tr> <tr><td>5. PubMed database</td><td align="center">yes</td><td align="center">no</td><td align="center">yes</td></tr> </table> </blockquote> Databases in the third category are integrated for keyword seach, but the actual data are to be obtained from the original sites. Databases in the fourth category are available only in the LinkDB system. PubMed is a link-only database, but the bget page is generated using the NCBI service in order to better integrate with KEGG and other DBGET databases. DBGET search targets are described on <a href="/dbget/targets.html">this page</a>. <p />  <hr class="frame2" /> <h4 class="title2">1. KEGG Databases in DBGET (18+1 databases)</h4> <blockquote> <table border="1" cellpadding="2" cellspacing="0"> <tr> <th colspan="3">Database name</th> <th>Abbre-<br />viation</th> <th>Content</th> <th>Remark</th> </tr> <tr> <th rowspan="21"><a href="/dbget-bin/www_bfind?kegg">kegg</a></th> <th colspan="2"><a href="/dbget-bin/www_bfind?pathway">pathway</a></th> <td align="center">path</td> <td>KEGG pathways</td> <td><a href="/kegg/pathway.html">KEGG PATHWAY</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?brite">brite</a></th> <td align="center">br</td> <td>Functional hierarchies</td> <td><a href="/kegg/brite.html">KEGG BRITE</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?module">module</a></th> <td align="center">md</td> <td>KEGG modules</td> <td><a href="/kegg/module.html">KEGG MODULE</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?orthology">orthology</a></th> <td align="center">ko</td> <td>KEGG orthology</td> <td nowrap="nowrap"><a href="/kegg/ko.html">KEGG ORTHOLOGY</a></td> </tr> <tr> <th rowspan="4"><a href="/dbget-bin/www_bfind?genes">genes</a></th> <td align="center"><a href="/kegg/catalog/org_list.html">Organisms</a></td> <td align="center">org<br />code</td> <td>Genes in KEGG organisms</td> <td rowspan="4"><a href="/kegg/genes.html">KEGG GENES</a></td> </tr> <tr> <td align="center"><a href="/dbget-bin/www_bfind?Viruses">Viruses</a></td> <td align="center">vg</td> <td>Genes in viruses category</td> </tr> <tr> <td align="center"><a href="/dbget-bin/www_bfind?Vpept">Vpept</a></td> <td align="center">vp</td> <td>Mature peptides in viruses</td> </tr> <tr> <td align="center"><a href="/dbget-fbin/www_bfind?Addendum">Addendum</a></td> <td align="center">ag</td> <td>Genes in addendum category</td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?genome">genome</a></th> <td align="center">gn</td> <td>KEGG organisms and selected viruses</td> <td><a href="/kegg/genome/">KEGG Organism</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?mgenes">mgenes</a></th> <td align="center"> </td> <td>Gene catalogs in metagenomes</td> <td rowspan="2"><a href="/kegg/catalog/org_list3.html">KEGG Metagenomes</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?mgenome">mgenome</a></th> <td align="center">mgnm</td> <td>Metagenomes</td> </tr> <tr> <th rowspan="5"><a href="/dbget-bin/www_bfind?ligand">ligand</a></th> <th><a href="/dbget-bin/www_bfind?compound">compound</a></th> <td align="center">cpd</td> <td>Chemical compounds</td> <td rowspan="5"><a href="/kegg/ligand.html">KEGG LIGAND</a></td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?glycan">glycan</a></th> <td align="center">gl</td> <td>Glycans</td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?reaction">reaction</a></th> <td align="center">rn</td> <td>Chemical Reactions</td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?rclass">rclass</a></th> <td align="center">rc</td> <td>Reaction class</td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?enzyme">enzyme</a></th> <td align="center">ec</td> <td>Enzyme nomenclature</td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?network">network</a></th> <td align="center">ne</td> <td>Network elements</td> <td rowspan="2"><a href="/kegg/network.html">KEGG NETWORK</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?variant">variant</a></th> <td align="center">hsa_var</td> <td>Human gene variants</td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?disease">disease</a></th> <td align="center">ds</td> <td>Human diseases</td> <td><a href="/kegg/disease/">KEGG DISEASE</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?drug">drug</a></th> <td align="center">dr</td> <td>Drugs</td> <td rowspan="2"><a href="/kegg/drug/">KEGG DRUG</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?dgroup">dgroup</a></th> <td align="center">dg</td> <td>Drug groups</td> </tr> <tr> <td> </td> <th colspan="2"><a href="/dbget-bin/www_bfind?expression">expression</a></th> <td align="center">ex</td> <td>Gene expression profiles</td> <td>Submitted by authors</td> </tr> </table> </blockquote> <h4 class="title2">2. Other DBGET Databases (19 databases)</h4> <blockquote> <table border="1" cellpadding="2" cellspacing="0"> <tr> <th colspan="2">Database name</th> <th colspan="2">Abbre-<br />viation</th> <th>Content</th> <th>Original site</th> </tr> <tr> <th rowspan="2"><a href="/dbget-bin/www_bfind?refseq">refseq</a></th> <th><a href="/dbget-bin/www_bfind?refnuc">refnuc</a></th> <td rowspan="2" align="center">rs</td> <td align="center">rsnt</td> <td rowspan="2">NCBI Reference Sequence Database</td> <td rowspan="2"><a href="https://www.ncbi.nlm.nih.gov/RefSeq/">NCBI</a></td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?refpep">refpep</a></th> <td align="center">rsaa</td> </tr> <tr> <th rowspan="2"><a href="/dbget-bin/www_bfind?uniprot">uniprot</a></th> <th><a href="/dbget-bin/www_bfind?swissprot">swissprot</a></th> <td rowspan="2" align="center">up</td> <td align="center">sp</td> <td rowspan="2">UniProt (Universal Protein Resource) protein sequence database</td> <td rowspan="2"><a href="https://www.uniprot.org/">SIB</a> / <a href="https://www.ebi.ac.uk/uniprot">EBI</a></td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?trembl">trembl</a></th> <td align="center">tr</td> </tr> <tr> <th rowspan="3"><a href="/dbget-bin/www_bfind?refgene">refgene</a></th> <th><a href="/dbget-bin/www_bfind?rg001">rg001</a></th> <td rowspan="3" colspan="2" align="center"> </td> <td>OM-RGC: Ocean microbial reference gene catalog</td> <td><a href="http://ocean-microbiome.embl.de/companion.html#OM-RGC">EMBL</a></td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?rg002">rg002</a></th> <td>IGC: Integrated reference catalog of the human gut microbiome</td> <td><a href="http://meta.genomics.cn/meta/home">BGI</a> / EMBL</td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?rg003">rg003</a></th> <td>MATOU: Marine Atlas of Tara Oceans Unigenes</td> <td><a href="https://www.genoscope.cns.fr/tara/">Tara Oceans</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?pdb">pdb</a></th> <td colspan="2" align="center">pdb</td> <td>PDB (Protein Data Bank) 3D structure database</td> <td><a href="https://www.rcsb.org/">RCSB</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?epd">epd</a></th> <td colspan="2" align="center">epd</td> <td>Eukaryotic promoters</td> <td><a href="https://epd.vital-it.ch/">ISREC</a></td> </tr> <tr> <th rowspan="3"><a href="/dbget-bin/www_bfind?motifdic">motifdic</a></th> <th><a href="/dbget-bin/www_bfind?prosite">prosite</a></th> <td colspan="2" align="center">ps</td> <td rowspan="3">Protein domains and families</td> <td><a href="https://prosite.expasy.org/">ExPASy</a></td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?pfam">pfam</a></th> <td colspan="2" align="center">pf</td> <td><a href="http://pfam-legacy.xfam.org/">EBI</a></td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?ncbi-cdd">ncbi-cdd</a></th> <td colspan="2" align="center">ncbi-cdd</td> <td><a href="https://www.ncbi.nlm.nih.gov/cdd/">NCBI</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?pmd">pmd</a></th> <td colspan="2" align="center">pmd</td> <td>Protein mutants</td> <td><a href="http://pmd.ddbj.nig.ac.jp/~pmd/pmd.html">DDBJ</a></td> </tr> <tr> <th rowspan="3"><a href="/dbget-bin/www_bfind?aaindex">aaindex</a></th> <th><a href="/dbget-bin/www_bfind?aaindex1">aaindex1</a></th> <td colspan="2" align="center">aax1</td> <td rowspan="3">Amino acid indices</td> <td rowspan="3"><a href="/aaindex/">Kyoto</a></td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?aaindex2">aaindex2</a></th> <td colspan="2" align="center">aax2</td> </tr> <tr> <th><a href="/dbget-bin/www_bfind?aaindex3">aaindex3</a></th> <td colspan="2" align="center">aax3</td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?pdbstr">pdbstr</a></th> <td colspan="2" align="center">pdbstr</td> <td>Protein sequences generated from PDB</td> <td>Kyoto</td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?carbbank">carbbank</a></th> <td colspan="2" align="center">ccsd</td> <td>Carbohydrate structures</td> <td>Teikyo U /<br> U Georgia</td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?prosdoc">prosdoc</a></th> <td colspan="2" align="center">pdoc</td> <td>Prosite literature</td> <td><a href="https://prosite.expasy.org/">ExPASy</a></td> </tr> </table> </blockquote> <h4 class="title2">3. Searchable Databases on the Web (19 databases)</h4> <blockquote> <table border="1" cellpadding="2" cellspacing="0"> <tr> <th colspan="2">Database name</th> <th colspan="2">Abbre-<br />viation</th> <th>Content</th> <th>Original site</th> </tr> <tr> <th rowspan="3"><a href="/dbget-bin/www_bfind?dna-today-nonst">insdc</a></th> <th>genbank</th> <td colspan="2" align="center">gb</td> <td rowspan="3">Nonredundant database of International Nucleotide Sequence Database Collaboration</td> <td><a href="https://www.ncbi.nlm.nih.gov/Genbank/">NCBI</a></td> </tr> <tr> <th>embl</th> <td colspan="2" align="center">emb</td> <td><a href="https://www.ebi.ac.uk/ena">EBI</a></td> </tr> <tr> <th>ddbj</th> <td colspan="2" align="center"> </td> <td><a href="https://www.ddbj.nig.ac.jp/">DDBJ</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?ncbi-geneid">ncbi-gene</a></th> <td colspan="2" align="center"> </td> <td>NCBI Entrez Gene database</td> <td><a href="https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene">NCBI</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?ensembl">ensembl</a></th> <td colspan="2" align="center"> </td> <td>Eukaryotic genome annotation database</td> <td><a href="https://www.ensembl.org/">Ensembl</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?hgnc">hgnc</a></th> <td colspan="2" align="center"> </td> <td>Human gene nomenclature</td> <td><a href="https://www.genenames.org/">HGNC</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?brc-dna">brc-dna</a></th> <td colspan="2" align="center"> </td> <td>RIKEN BRC cDNA Cloned Library</td> <td rowspan="2"><a href="http://dna.brc.riken.jp/en/">RIKEN BRC</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?brc-epd">brc-epd</a></th> <td colspan="2" align="center"> </td> <td>RIKEN BRC cDNA Cloned Library for Plants</td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?go">go</a></th> <td colspan="2" align="center"> </td> <td>Gene Ontology</td> <td><a href="http://www.geneontology.org/">GO</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?interpro">interpro</a></th> <td colspan="2" align="center"> </td> <td>Protein domains and families</td> <td><a href="https://www.ebi.ac.uk/interpro/">EBI</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?pubchem">pubchem</a></th> <td colspan="2" align="center"> </td> <td>NCBI PubChem (small molecules) database</td> <td><a href="https://pubchem.ncbi.nlm.nih.gov/">NCBI</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?chebi">chebi</a></th> <td colspan="2" align="center"> </td> <td>EBI ChEBI (small molecules) database</td> <td><a href="https://www.ebi.ac.uk/chebi/">EBI</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?pdb-ccd">pdb-ccd</a></th> <td colspan="2" align="center"> </td> <td>PDB Chemical Component Dictionary</td> <td><a href="http://remediation.wwpdb.org/data/ccd">PDB</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?lipidmaps">lipidmaps</a></th> <td colspan="2" align="center"> </td> <td>LIPID Metabolites And Pathways Strategy </td> <td><a href="http://www.lipidmaps.org/">LIPIDMAPS</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?knapsack">knapsack</a></th> <td colspan="2" align="center"> </td> <td>Secondary metabolite database</td> <td><a href="http://kanaya.naist.jp/KNApSAcK/">KNApSAcK</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?hmdb">hmdb</a></th> <td colspan="2" align="center"> </td> <td>Human metabolome database</td> <td><a href="http://www.hmdb.ca/">HMDB</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?ligandbox">ligandbox</a></th> <td colspan="2" align="center"> </td> <td>Ligand data base open and extensible</td> <td><a href="http://ligandbox.protein.osaka-u.ac.jp/ligandbox/">LigandBox</a></td> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?sider">sider</a></th> <td colspan="2" align="center"> </td> <td>Side effect resource</td> <td><a href="http://sideeffects.embl.de/">SIDER</a></td> </tr> </table> </blockquote> <h4 class="title2">4. Link-only Databases on the Web (85 databases)</h4> <blockquote> <table border="1" cellpadding="2" cellspacing="0"> <tr> <td>The databases in this category can be found in <a href="/linkdb/link_only.html">LinkDB</a></td> </tr> </table> </blockquote> <h4 class="title2">5. PubMed Database</h4> <blockquote> <table border="1" cellpadding="2" cellspacing="0"> <tr> <th colspan="2">Database name</th> <th colspan="2">Abbre-<br />viation</th> <th>Content</th> <th>Original site</th> </tr> <tr> <th colspan="2"><a href="/dbget-bin/www_bfind?medline">pubmed</a></th> <td colspan="2" align="center">pmid</td> <td>Biomedical literature</td> <td><a href="https://www.ncbi.nlm.nih.gov/pubmed/">NCBI</a></td> </tr> </table> </blockquote>  <br /> <i>Last updated: July 7, 2021</i> </td></tr></table>  </td></tr> <tr><td align="center" class="td20"> <table width="680"> <tr> <th><a href="https://www.genome.jp/feedback/?category=dbget">Feedback</a></th> <th><a href="https://www.genome.jp/kegg/">KEGG</a></th> <th><a href="https://www.genome.jp/">GenomeNet</a></th> <td align="center"><a href="http://www.bic.kyoto-u.ac.jp/">Kyoto University Bioinformatics Center</a></td> </tr> </table> </td></tr> </table> </body> </html>