MGI-Software Developer Tools for the Mouse Genome Informatics database resource

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "https://www.w3.org/TR/html4/loose.dtd"> <html> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />  <script async src="https://www.googletagmanager.com/gtag/js?id=G-8D61GHC97X"></script> <script> var c = document.cookie.split('; ').filter(c => c.startsWith('mgi_user_consent='))[0] if (!c || c === "mgi_user_consent=analytics") { window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-8D61GHC97X'); console.log("GA4 ok") } else { console.log("GA4 blocked") } </script>  <script type="text/javascript" src="https://www.informatics.jax.org/webshare/js/yui-2.8.custom.min.js"></script>  <script type="text/javascript" src="https://www.informatics.jax.org/webshare/js/jquery-1.10.2.min.js"></script> <script type="text/javascript" src="https://www.informatics.jax.org/webshare/js/jquery-ui-1.11.4.js"></script>   <link rel="stylesheet" type="text/css" href="https://www.informatics.jax.org/webshare/css/yui-reset.css">  <link rel="stylesheet" type="text/css" href="https://www.informatics.jax.org/webshare/css/yui-2.8-combo.css">  <link href="https://www.informatics.jax.org/webshare/css/mgi_template01.css" rel="stylesheet" type="text/css"/>  <title>MGI-Software Developer Tools for the Mouse Genome Informatics database resource</title> <meta name="description" content="Instructions for linking to MGI's web pages, description of downloadable files, and instructions for custom queries. " /> <meta name="keywords" content="MGI, mgi, mice, mouse, murine, mus musculus, genes, genome, genomic, link to MGI, web page links, download files, FTP, batch query, tab-delimited output, tab delimited output, FASTA output, SQL query, database schema, schema browser, custom query, custom report" /> <meta name="robots" content="NOODP" /> <meta name="robots" content="NOYDIR" />  </head> <body id="body" class="yui-skin-sam"> <div id="headerContainer"> <div id="topBannerContainer">  <div id="tabs" class="navtabs"> <span id="navRight"> <ul> <li id="minitab_Home"> <a href="https://www.informatics.jax.org/" onmouseover="return overlib('MGI Home Page',ANCHOR, 'tab_home', ANCHORALIGN, 'UL', 'LL', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_home">Home</span></a> </li> <li id="genes.shtml"> <a href="https://www.informatics.jax.org/genes.shtml" onmouseover="return overlib('Genes, Genome Features & Maps',ANCHOR, 'tab_gene', ANCHORALIGN, 'UL', 'LL', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_gene">Genes</span></a> </li> <li id="phenotypes.shtml"> <a href="https://www.informatics.jax.org/phenotypes.shtml" onmouseover="return overlib('Phenotypes, Alleles & Disease Models',ANCHOR, 'tab_pheno', ANCHORALIGN, 'UL', 'LL', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_pheno">Phenotypes</span></a> </li> <li id="humanDisease.shtml"> <a href="https://www.informatics.jax.org/diseasePortal" onmouseover="return overlib('Human-Mouse: Disease Connection',ANCHOR, 'tab_humanDisease', ANCHORALIGN, 'UL', 'LL', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_humanDisease">Human Disease</span></a> </li> <li id="expression.shtml"> <a href="https://www.informatics.jax.org/expression.shtml" onmouseover="return overlib('Gene Expression Database $GXD$',ANCHOR, 'tab_exp', ANCHORALIGN, 'UL', 'LL', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_exp">Expression</span></a> </li> <li id="home_recombinase"> <a href="https://www.informatics.jax.org/home/recombinase" onmouseover="return overlib('Recombinase Tissue Specificity',ANCHOR, 'tab_cre', ANCHORALIGN, 'UL', 'LL', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_cre">Recombinases</span></a> </li> <li id="function.shtml"> <a href="https://www.informatics.jax.org/function.shtml" onmouseover="return overlib('Functional Annotations $GO$',ANCHOR, 'tab_func', ANCHORALIGN, 'UL', 'LL', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_func">Function</span></a> </li> <li id="home_strains_SNPs"> <a href="https://www.informatics.jax.org/home/strain" onmouseover="return overlib('Strains, SNPs & Polymorphisms',ANCHOR, 'tab_snps', ANCHORALIGN, 'UL', 'LL', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_snps">Strains / SNPs</span></a> </li> <li id="homology.shtml"> <a href="https://www.informatics.jax.org/homology.shtml" onmouseover="return overlib('Vertebrate Homology',ANCHOR, 'tab_homo', ANCHORALIGN, 'UL', 'LL', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_homo">Homology</span></a> </li> <li id="minitab_Tumor"> <a href="http://tumor.informatics.jax.org/mtbwi/index.do" onmouseover="return overlib('Mouse Tumor Biology',ANCHOR, 'tab_tumors', ANCHORALIGN, 'UR', 'LR', CSSCLASS, TEXTFONTCLASS, 'tabTipFont', BGCLASS, 'tabTipBoxBG', FGCLASS, 'tabTipBoxFG');" onmouseout="nd();"> <span id="tab_tumors">Tumors</span></a> </li> </ul> </span> </div>  <div id="logoContainer" style="position:absolute; left:0; top:0;"> <div> <a href="https://www.informatics.jax.org/" style="background-color: transparent"> <img src="https://www.informatics.jax.org/webshare/images/mgi_logo.gif" border=0> </a> </div> <span class="logoFooterContainer">   <a class="logoFooterAnchor" href="https://www.informatics.jax.org/mgihome/projects/aboutmgi.shtml">About</a>   <a class="logoFooterAnchor" href="https://www.informatics.jax.org/mgihome/homepages/help.shtml">Help</a>   <a class="logoFooterAnchor" href="https://www.informatics.jax.org/faq/FAQ.shtml">FAQ</a> </span> </div> <div id="agr_logo" style="float: right; padding-top: 3px; padding-right: 5px;"> <a href="https://globalbiodata.org/" target="_blank"><img src="https://www.informatics.jax.org/webshare/images/gcbr_logo.png" style="height:65px;margin-right:10px;margin-left:10px;"></a> <a href="https://www.alliancegenome.org/" target="_blank"><img src="https://www.informatics.jax.org/webshare/images/agr_logo_smallest.png" style="height:70px"></a> </div> <div id="templateSearchTool" style="float:right; top:15px; margin-right: 5px;"> <style> .lightYellow { background-color: #ffd; } .lightGray { background-color: #dadada; } .italic { font-style: italic; } </style> <form action="https://www.informatics.jax.org/quicksearch/summary" method="get"> <table> <tr> <td> <a onClick="return false;" href="https://www.informatics.jax.org/userhelp/searchtool_help.shtml" onMouseOver="if (window.jQuery) { setTimeout(function () { $('td[valign=TOP]').css({'background-color' : '#efefef'}); }, 750); }; return overlib('You can:<ul class=\'searchToolHelp\'><li>Search for genome features by name, symbol, synonym, homolog, allele, or accession ID:</li> <ul><li>p53 protein cell cycle DNA damage</li><li>Notch1</li><li>NM_053172</li><li>AT3</li></ul><li>Search for genome features and vocabulary terms by keywords or accession ID. Use several keywords to find the most relevant results:</li><ul><li>GO:0004713</li><li>resistance to fatty liver development</li><li>vitamin D receptor</li><li>lymphocyte function antigen immunodeficiency</li> </ul><li>Search for genome features by mouse genome location. Use a chromosome, point coordinate, or coordinate range:</li><ul><li>Chr1</li><li>Chr1:194732198</li><li>Chr1:194732198-294732198</li></ul> <li>Use asterisks (*) for wildcards at the end of partial words or genomic symbols:</li><ul><li>Pax*</li><li>embr* development</li><li>hippocamp* pyramid* cell layer</li></ul><li>Use quotation marks (" ") to indicate phrases:</li> <ul><li>"hair follicle" development</li><li>"amyotrophic lateral sclerosis"</li></ul><li>Use angle brackets to indicate superscript:</li><ul><li>Pax6<10Neu> for Pax6<sup>10Neu</sup></li></ul><li>Mix IDs, symbols, and keywords in a list:</li><ul><li>Nmt2, NM_013627, Acbd7, hair follicle development</li></ul></ul>Advanced searches are listed under the Search menu.<BR/>See <a href=\'https://www.informatics.jax.org/userhelp/QUICK_SEARCH_help.shtml\'>Using the Quick Search Tool</a> for more information.', STICKY, CAPTION, 'Quick Search Tips', CENTER, BELOW, WIDTH, 450, DELAY, 600, CLOSECLICK, CLOSETEXT, 'Close X');" onMouseOut="nd();"> <img src="https://www.informatics.jax.org/webshare/images/help_small_transp.gif" border="0"> </a> </td> <td> <select id="queryTypeTop" name="queryType" class="lightGray"> <option value="exactPhrase" selected="">Keywords, Symbols, or IDs (exact phrase)</option> <option value="keywords">Keywords, Symbols, or IDs</option> <option value="mouseLocation">Mouse Location</option> <option value="humanLocation">Human Location</option> </select> </td> <td> <input name="query" id="searchToolTextArea" class="lightYellow italic" value=" Type your search here" onFocus="if(this.defaultValue==this.value) this.value=''; $('#searchToolTextArea').removeClass('italic');" size="30"> </td> <td> <input name="submit" type="submit" class="searchToolButton" value="Quick Search" onclick="return verifySearchToolParms();"> </td> </tr> </table> </form> </div> <div style="position:absolute; top:4px; left:150px;"> <iframe style="border:none" src="/webshare/html/notice.html" width="400" height="40"></iframe> </div> </div>  <div id="navBarMenu" class="yuimenubar"> <div class="bd"> <ul class="first-of-type">  <li class="yuimenubaritem first-of-type"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/allsearch.shtml">Search</a> <div id="navBarSearch" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/allsearch.shtml" title="">All Search Tools</a></li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Genes</a> <div id="navBarGenes" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/marker/" onMouseOver="return overlib('Search for genes and genome features by symbol, name, location, gene ontology classification or phenotype.',ANCHOR, 'navBarGenes', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Genes & Markers Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Input a list of gene IDs or symbols and retrieve other database IDs and gene attributes (e.g. phenotypes, GO).',ANCHOR, 'navBarGenes', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Batch Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="http://jbrowse.informatics.jax.org/?data=data/GRCm39" onMouseOver="return overlib('Create a graphical display of genome features from regions of the mouse genome.',ANCHOR, 'navBarGenes', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> JBrowse Genome Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgv/" onMouseOver="return overlib('Compare genome features of de novo sequenced mouse strains.',ANCHOR, 'navBarGenes', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Multiple Genome Viewer (MGV)</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/genes.shtml">More</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Phenotypes</a> <div id="navBarPhenotypes" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/allele/" onMouseOver="return overlib('Search for mutations or QTL based on phenotype, human disease, mutation type, gene, or genome location.',ANCHOR, 'navBarPhenotypes', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Phenotypes, Alleles & Diseases Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/mp_ontology" onMouseOver="return overlib('Search for a phenotype term to find relevant mutant genotypes.',ANCHOR, 'navBarPhenotypes', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Mammalian Phenotype (MP) Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/disease" onMouseOver="return overlib('Browse for a human disease or condition term to find mouse models.',ANCHOR, 'navBarPhenotypes', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Human Disease (DO) Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/hp_ontology" onMouseOver="return overlib('Search for a human phenotype ontology term to find relevant human diseases.',ANCHOR, 'navBarPhenotypes', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Human Phenotype (HPO) Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/phenotypes.shtml">More</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a id="navBarHMDC" class="yuimenuitemlabel" href="https://www.informatics.jax.org/diseasePortal" onMouseOver="return overlib('Human-Mouse: Disease Connection', ANCHOR, 'navBarHMDC', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> Human Disease</a> </li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Expression</a> <div id="navBarExpression" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/gxd/" onMouseOver="return overlib('Search for detailed gene expression assay results.',ANCHOR, 'navBarExpression', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Gene Expression Data Search</a></li> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/gxdlit" onMouseOver="return overlib('Search for references on gene expression during development.',ANCHOR, 'navBarExpression', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Gene Expression Literature Search</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16039" onMouseOver="return overlib('Search or browse for anatomical structures; includes links to associated expression results.',ANCHOR, 'navBarExpression', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Mouse Developmental Anatomy Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/gxd/htexp_index" onMouseOver="return overlib('Search for experiments using sample metadata annotations.',ANCHOR, 'navBarExpression', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> RNA-Seq and Microarray Experiment Search</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/expression.shtml">More</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a id="navBarCre" class="yuimenuitemlabel" href="https://www.informatics.jax.org/home/recombinase" onMouseOver="return overlib('Get recombinase (cre) activity data for knock-in and transgene alleles.',ANCHOR, 'navBarCre', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> Recombinase (cre)</a></li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Function</a> <div id="navBarFunction" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gene_ontology" onMouseOver="return overlib('Browse the Gene Ontology and mouse annotations in MGI.',ANCHOR, 'navBarFunction', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> GO Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/marker/" onMouseOver="return overlib('Search for genes and genome features by symbol, name, location, gene ontology classification or phenotype.',ANCHOR, 'navBarFunction', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Genes & Markers Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Obtain sets of MGI IDs for use in GO tools.',ANCHOR, 'navBarFunction', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Batch Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/function.shtml">More</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Strains / SNPs</a> <div id="navBarStrains" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/home/strain" onMouseOver="return overlib('Search for strains by name, synonyms, or attributes.',ANCHOR, 'navBarStrains', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();">Strain Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/snp" onMouseOver="return overlib('Search for SNPs by strain(s), SNP attributes, genomic position, or associated genes.',ANCHOR, 'navBarStrains', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> SNP Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgv/" onMouseOver="return overlib('Compare genome features of de novo sequenced mouse strains.',ANCHOR, 'navBarStrains', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Multiple Genome Viewer (MGV)</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/home/strain">More</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a id="navBarHomology" class="yuimenuitemlabel" href="https://www.informatics.jax.org/homology.shtml" onMouseOver="return overlib('Find out more about Homology relationships in MGI.',ANCHOR, 'navBarHomology', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> Homology</a></li>  <li class="yuimenuitem"><a id="navBarMTB" class="yuimenuitemlabel" href="https://tumor.informatics.jax.org/mtbwi/index.do" onMouseOver="return overlib('MTB provides information on the frequency, pathology, and genetics of spontaneous and induced tumors in mice.',ANCHOR, 'navBarMTB', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> Tumors</a></li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Sequence Searches</a> <div id="navBarSequences" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi" onMouseOver="return overlib('Search for sequence similarity using BLAST at NCBI.',ANCHOR, 'navBarSequences', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> BLAST at NCBI</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="http://jbrowse.informatics.jax.org/?data=data/GRCm39" onMouseOver="return overlib('Create a graphical display of genome features from regions of the mouse genome.',ANCHOR, 'navBarSequences', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> JBrowse Genome Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Input a list of gene IDs or symbols and retrieve other database IDs and gene attributes (e.g. phenotypes, GO).',ANCHOR, 'navBarSequences', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Batch Query</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">References</a> <div id="navBarReferences" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/reference" onMouseOver="return overlib('Search for references (with abstracts) by title, author, journal, year, or abstract.',ANCHOR, 'navBarReferences', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Reference Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/gxdlit" onMouseOver="return overlib('Search for references on gene expression during development.',ANCHOR, 'navBarReferences', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Gene Expression Literature Query</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Ontologies</a> <div id="navBarVocabularies" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gene_ontology" onMouseOver="return overlib('Browse the Gene Ontology and mouse annotations in MGI.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> GO Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/disease" onMouseOver="return overlib('Browse for a human disease or condition term to find mouse models.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Human Disease (DO) Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/mp_ontology" onMouseOver="return overlib('Search for a phenotype term to find relevant mutant genotypes.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Mammalian Phenotype (MP) Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16039" onMouseOver="return overlib('Search or browse for anatomical structures; includes links to associated expression results.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Mouse Developmental Anatomy Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gxd/ma_ontology" onMouseOver="return overlib('An extensive ontology of anatomical structures for the postnatal mouse.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Adult Mouse Anatomy Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/hp_ontology" onMouseOver="return overlib('Search for a human phenotype ontology term to find relevant human diseases.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Human Phenotype (HPO) Browser</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a id="navBarBatch" class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Input a list of gene IDs or symbols and retrieve other database IDs and gene attributes (e.g. phenotypes, GO).',ANCHOR, 'navBarBatch', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> Batch Query</a></li> <li class="yuimenuitem"><a id="navBarMine" class="yuimenuitemlabel" href="https://www.mousemine.org" onMouseOver="return overlib('Access MGI data via InterMine.',ANCHOR, 'navBarMine', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> MouseMine</a></li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Mouse Genome Browsers</a> <div id="navBarGenomeBrowsers" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem"><a id="navBarJBrowse" class="yuimenuitemlabel" href="http://jbrowse.informatics.jax.org/?data=data/GRCm39" onMouseOver="return overlib('Create a graphical display of genome features from regions of the mouse genome.',ANCHOR, 'navBarJBrowse', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> JBrowse Genome Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgv/" onMouseOver="return overlib('Compare genome features of de novo sequenced mouse strains.',ANCHOR, 'navBarJBrowse', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Multiple Genome Viewer (MGV)</a></li> </ul> </div> </div> </li> </ul> </div> </div> </li>   <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html">Download</a> <div id="navBarDownload" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html">All MGI Reports</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch">Batch Query</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#marker">Genes & Markers</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#seq">Sequence Data</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#homology">Vertebrate Homology</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#go">Gene Ontology Data</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#strain">Strains & Polymorphisms</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#expression">Gene Expression</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#pheno">Phenotypic Data</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#cre">Recombinase (cre)</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#nomen">Nomenclature</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#refs">References</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#clonecoll">Clone Collections</a> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html#dnamap">DNA Mapping Panels</a> </li> </ul> </div> </div> </li>   <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/resources.shtml">More Resources</a> <div id="navBarResources" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/resources.shtml">More Resources Index</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgihome/lists/lists.shtml">Research Community E-mail Lists</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/resources.shtml#res_books">Online Books</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgihome/nomen/index.shtml">Nomenclature Home Page</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/glossary">MGI Glossary</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://phenome.jax.org">Mouse Phenome Database (MPD)</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="http://www.informatics.jax.org/knockout_mice/">Deltagen and Lexicon Knockout Mice</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.mousephenotype.org/" id="navBarKomp" onMouseOver="return overlib('Producing and phenotyping knockout mice from the IKMC mutant ES cell line resource.',ANCHOR, 'navBarKomp', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();">International Mouse Phenotyping Consortium (IMPC)</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.jax.org/mgi-coronavirus-info">Mouse Resources For COVID-19 Research</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/datasets/index.html">Contributed Data Sets</a></li> <li class="yuimenuitem"> <a class="yuimenuitemlabel">Community Links</a> <div id="navBarLinks" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgihome/other/mouse_facts4.shtml">Mouse Resources & Model Organism Links</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgihome/other/phenoallele_commun_resource.shtml">Phenotypes & Mutants Community Resources</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.oxfordjournals.org/nar/database/a/" id="navBarNAR" onMouseOver="return overlib('An index of over 1500 biological databases compiled by the journal of Nucleic Acids Research. Includes links for other model organisms and species, diseases, DNA, RNA, and protein resources.',ANCHOR, 'navBarNAR', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();">Nucleic Acids Research (Journal) Database Summary</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgihome/other/mouse_facts1.shtml">Mouse Facts</a></li> </ul> </div> </div> </li> <li class="yuimenuitem"> <a class="yuimenuitemlabel" href="#">Software Developer Tools</a> <div id="navBarSoftware" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgihome/other/link_instructions.shtml">Creating Web Links to MGI</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.mousemine.org">MouseMine</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/software.shtml#sql">Direct SQL Account</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/schema_pg/">Database Schema Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html">All MGI Reports</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/software.shtml">More</a></li> </ul> </div> </div> </li> </ul> </div> </div> </li>   <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/submit.shtml">Submit Data</a></li> <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.findmice.org/index.jsp" title="International Mouse Strain Resource (IMSR)">Find Mice (IMSR)</a></li> <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/tools.shtml" title="Analysis Tools"><img src="https://www.informatics.jax.org/webshare/images/tools.gif" alt="Analysis Tools"> Analysis Tools</a></li> <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml" title="Contact user support">Contact Us</a></li> <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/mgihome/homepages/browser_compatibility.shtml" title="Browser compatibility">Browsers</a></li> </ul> </div> </div>  </div> <div id="templateBodyInsert">   <div id="titleBarWrapper"> <span class="titleBarMainTitle">Bulk Data Access, APIs and Linking to MGI</span> </div>    <table width="75%" cellpadding="2" align="center"> <tr><td>  <table class="toc" width="100%"> <tr> <td> <ul> <li><a href="#batch">Batch Queries</a> | </li> <li><a href="#sw_links">Creating Web Links to MGI</a> | </li> <li><a href="#data">Data Files for Download</a> | </li> <li><a href="#mgiws">MGI Web Service</a> | </li> <li><a href="#sql">Direct SQL Account</a> </li>  </td> </tr> </table> </td></tr> <tr><td> <table class="outline" width="100%"> <tr> <td class="enhance"> Join the <a href="https://www.informatics.jax.org/mgihome/lists/lists.shtml">MGI Developer's Forum</a> Mailing List </td> </tr> <tr> <td> <ul> <li>Please join to be notified of any changes to the mechanisms listed here.</li> </ul> </tr> </table> </td></tr> <tr><td>  <a id="batch"></a> <table class="outline" width="100%"> <tr> <td class="enhance"> Batch Queries </td> </tr> <tr > <td> <dl class="linkedList"> <dt>• <a href="https://www.informatics.jax.org/batch">Batch Query</a></dt> <dd>Input a list of IDs or gene symbols and retrieve other database IDs and gene attributes (e.g. phenotypes, GO, expression data).</dd> <dt>• <a href="https://www.informatics.jax.org/gxd/batchSearch">Gene Expression Batch Search</a></dt> <dd>Input a list of IDs or gene symbols and retrieve associated gene expression assay data. Search results include a tissue-by-gene matrix view to enable the comparison of expression patterns between genes. </dd> <dt>• <a href="http://www.mousemine.org/">MouseMine</a></dt> <dd>Powered by InterMine, MouseMine offers flexible querying, numerous predefined query templates, iterative refinement of results, and linking to other model organism Mines. MouseMine: </dd> <blockquote> <ul> <li> offers many useful "canned" queries, plus point-and-click query editing</li> <li> supports uploading and manipulating lists of objects</li> <li> allows any query result to be downloaded (text, xml, json) or forwarded to Galaxy</li> </ul> </blockquote> </dl> </td> </tr> </table> </td></tr> <tr><td>  <a id="sw_links"></a> <table class="outline" width="100%"> <tr> <td class="enhance"> Creating Web Links to MGI </td> </tr> <tr > <td> <ul> <li>MGI supports external links to our Web Interface using Accession IDs.</li> <li>See <a href="https://www.informatics.jax.org/mgihome/other/link_instructions.shtml">Creating Web Links to MGI</a> for instructions and examples.</li> <li>Public reports generated weekly are available for obtaining Accession IDs. See <a href="https://www.informatics.jax.org/downloads/reports/index.html">MGI Data and Statistical Reports</a> for an index of the reports available.</li> </ul> </td> </tr> </table> </td></tr> <tr><td>  <a id="data"></a> <table class="outline" width="100%"> <tr> <td class="enhance"> Data Files for Download </td> </tr> <tr > <td> <b><i>Public Reports via FTP</i></b> <ul> <li>Over 65 data files are generated weekly and available for download.</li> <li>See <a href="https://www.informatics.jax.org/downloads/reports/index.html">MGI Data and Statistical Reports</a> for the list of reports and their field descriptions.</li> </ul> <b><i>Database Dumps via FTP</i></b> <ul> <li>Database backups are available from our ftp site at: <a href="https://www.informatics.jax.org/downloads/database_backups/">http://www.informatics.jax.org/downloads/database_backups/</a></li> <ul> <li>Backups are available for MySQL 5.0.67 and PostgreSQL 9.3.5.</li> <li>These backups assume you have a compatible version of MySQL or PostgreSQL installed, that you have created a database, and that you have adequate user permissions to load that database.</li> <li>Backups are updated on Mondays between 12:30 AM and 1:30 AM EST, so please avoid downloading the files during that time, or your file may not download successfully.</li> </ul> <li>To load the MySQL backup:</li> <ul> <li>First, uncompress it: gunzip mgd.mysql.dump.gz</li> <li>Then load it: mysql -e "mgd.mysql.dump" <i>databaseName</i></li> </ul> <li>To load the PostgreSQL backup:</li> <ul> <li>Load it: pg_restore -c -d <i>databaseName</i> -j jobCount -O -h host -U user mgd.postgres.dump-Fc</li> <li>jobCount should be an integer, representing the number of subprocesses. If you have a multiprocessor machine, using a jobCount between 2 and 4 will likely speed your restore significantly.</li> </ul> </ul> <b><i>Tab Delimited Output from our Web Interface</i></b> <ul> <li>User-defined results for references, gene and SNP data are available in tab delimited format.</li> <li>You can modify the output format on the query form from <i>Web</i> to <i>Tab-delimited</i>.</li> <li>The Quick Search, as well as these query forms, offer tab-delimited outputs:</li> <ul class="softwareUL"> <li><a href="https://www.informatics.jax.org/batch">MGI Batch Query</a><br> <i>Download gene/marker data for a batch of IDs or symbols</i></li> <li><a href="https://www.informatics.jax.org/marker">Genes and Markers Query Form</a><br> <i>Search by symbol, location, gene ontology classification, or phenotype.</i></li> <li><a href="https://www.informatics.jax.org/allele">Phenotypes, Alleles & Disease Models Query</a><br> <i>Search for mutations or QTL based on phenotype, human disease, mutation type, gene, or genome location.</i></li> <li><a href="https://www.informatics.jax.org/humanDisease.shtml">Human—Mouse: Disease Connection</a><br> <i>Search for phenotype and disease associations by human and mouse genes and genome regions.</i></li> <li><a href="https://www.informatics.jax.org/gxd">Gene Expression Data Query</a><br> <i>Search for detailed gene expression assay results.</i></li> <li><a href="https://www.informatics.jax.org/reference">References</a><br> <i>Search curated references by author, journal or text. The output to this form provides the text export option</i></li> <li><a href="https://www.informatics.jax.org/snp">Mouse SNP Query Form</a><br> <i>Search for SNPS by strain(s), SNP attributes, genomic position, or associated genes</i></li> </ul> </ul> <b><i>FASTA Output from our Web Interface</i></b> <ul> <li>The FASTA format is available on reports where sequences are returned for a specific gene or when querying sequences.</li> <li>Click on the checkboxes next to each sequence to select it for FASTA download and click GO.</li> <li>From a gene detail page, FASTA is available for:</li> <ul class="softwareUL"> <li>Representative genomic, transcript, and polypeptide sequences</li> <li>All mouse sequences</li> <li>RefSeq transcript sequences for their human, rat, and zebrafish homologs</li> <li>Protein sequences for human, rat, and zebrafish homologs.</li> </ul> </ul> </td> </tr> </table> </td></tr> <tr><td>  <a id="mgiws"></a> <table class="outline" width="100%"> <tr> <td class="enhance"> MGI Web Service </td> </tr> <tr > <td> <ul> <li>The <a href="http://www.mousemine.org/">MouseMine</a> web services API offers robust and comprehensive programmatic access to MGI data. For assistance using MouseMine web services, see: <ul> <li>InterMine Web Services <a href="https://intermine.readthedocs.io/en/latest/web-services/">Documentation</a></li> <li><a href="http://iodocs.labs.intermine.org/mgi/docs#/">MGI API</a> Documentation</li> <li>Or <a href="https://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml">Contact User Support.</li> </ul></li> </ul> </td> </tr> </table> </td></tr> <tr><td>  <a id="sql"></a> <table class="outline" width="100%"> <tr> <td class="enhance"> Direct SQL Account </td> </tr> <tr > <td> <ul> <li>The MGI Public Ad Hoc SQL Server is available for running custom SQL queries against the MGI database. </li> <li>MGI uses PostgreSQL relational databases to store information.</li> <li>You must install client software that can connect to a PostgreSQL server in order to query the database. You can use free clients such as JDBC (Java), ODBC (Windows) or SQuirreL SQL (<a href="https://squirrel-sql.sourceforge.io">https://squirrel-sql.sourceforge.io</a>).</li> <li>See our example <a href="https://www.informatics.jax.org/mgihome//other/MGIConnect.txt">JDBC Client</a>. You can also use this to verify that your SQL account is active. </li> </ul> <blockquote> <b><i>Schema Browser</i></b> <ul> <li>In order to write your own custom SQL query, you must be familiar with SQL and the MGI database schema. </li> <li>For help with the database schema, use the <a href="https://www.informatics.jax.org/schema_pg/">Schema Browser</a> available in the Web Interface.</li> </ul> <b><i>Login & Configuration</i></b> <ul> <li><a href="https://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml">Contact User Support</a> to request an SQL account. You will receive a login, password and connection parameters.</li> </ul> <b><i>Custom SQL Reports from MGI</i></b> <ul><li><a href="https://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml">Contact User Support</a> for custom SQL queries if you prefer not to write them yourself.</li></ul> </blockquote> </td> </tr> </table>   </table> </div>  <table style="font-size:12" border=0 width="99%"> <tr> <td colspan="3"><HR noshade="noshade"/ color="#d0e0f0" width="100%"> <center style="font-size:10px;"> <span style="float: left;">Contributing Projects:</span> <br> Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO) </center> </td> </tr> <tr> <td width="33%" style="font-size:9px;"> <A HREF="https://www.informatics.jax.org/mgihome/other/citation.shtml"> Citing These Resources</A> <BR> <A HREF="https://www.informatics.jax.org/mgihome/other/mgi_funding.shtml"> Funding Information</A> <BR> <A HREF="https://www.informatics.jax.org/mgihome/other/copyright.shtml"> Warranty Disclaimer, Privacy Notice, Licensing, & Copyright</A> <BR> Send questions and comments to <A HREF="https://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml"> User Support</A>. </td> <td WIDTH="34%" ALIGN=center style="font-size:9px;"> last database update<BR> 11/19/2024<BR> MGI 6.24 </td> <td WIDTH="33%" ALIGN=right style="font-size:9px;"> <A HREF="https://www.jax.org/" border=0 style="background-color: transparent"> <IMG SRC="https://www.informatics.jax.org/webshare/images/jax_logo_small.png" BORDER=0 ALT="The Jackson Laboratory"></A> </td> </tr> <tr> <td colspan="3"> <HR noshade="noshade"/ color="#d0e0f0" width="100%"> </td> </tr> </table>  <script type="text/javascript" src="https://www.informatics.jax.org/webshare/js/mgi_template01.js"></script> <script type="text/javascript" src="https://www.informatics.jax.org/webshare/js/mgi_ga.js"></script> <script> // For some pages (like HMDC Home) that don't have a templateBodyInsert element, we don't want to do this as it // presents an odd error popup. if (document.getElementById('templateBodyInsert') != null) { setTimeout(function() { overlib('Building initial tooltip...',ANCHOR, 'templateBodyInsert', ANCHORALIGN, 'UR', 'UL'); 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