Identification Request

<!DOCTYPE html> <html> <head> <meta charset="utf-8" /> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <title>Identification Request | BOLDSYSTEMS</title> <meta name="keywords" content="" /> <meta name="description" content="" /> <link rel="shortcut icon" type="image/x-icon" href="/favicon.ico" /> <link rel="apple-touch-icon" href="/favicons/apple-icon.png"/> <link rel="apple-touch-icon" sizes="57x57" href="/favicons/apple-icon-57x57.png"/> <link rel="apple-touch-icon" sizes="60x60" href="/favicons/apple-icon-60x60.png"/> <link rel="apple-touch-icon" sizes="72x72" href="/favicons/apple-icon-72x72.png"/> <link rel="apple-touch-icon" sizes="76x76" href="/favicons/apple-icon-76x76.png"/> <link rel="apple-touch-icon" sizes="114x114" href="/favicons/apple-icon-114x114.png"/> <link rel="apple-touch-icon" sizes="120x120" href="/favicons/apple-icon-120x120.png"/> <link rel="apple-touch-icon" sizes="144x144" href="/favicons/apple-icon-144x144.png"/> <link rel="apple-touch-icon" sizes="152x152" href="/favicons/apple-icon-152x152.png"/> <link rel="apple-touch-icon" sizes="180x180" href="/favicons/apple-icon-180x180.png"/> <meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=0" /> <link href="/libhtml_v4/css/bootstrap.css" rel="stylesheet" /> <link href="/libhtml_v4/css/style.css" rel="stylesheet" /> <link href="/libhtml_v4/css/animate.css" rel="stylesheet" /> <link href="/libhtml_v4/css/ionicons.min.css" rel="stylesheet" />  <link href="/libhtml_v3/font-awesome/css/font-awesome.css" rel="stylesheet"> <link href="https://fonts.googleapis.com/css?family=Open+Sans:400,600,800&subset=latin,latin-ext" rel="stylesheet" /> <link href="/libhtml_v4/css/print.css" rel="stylesheet" /> <script src="/libhtml_v4/js/modernizr-custom.min.js"></script> <script src="/libhtml_v4/js/jquery-2.1.0.min.js"></script> <script src="/libhtml_v4/js/bootstrap.js"></script> <script src="/libhtml_v4/js/plugins/toastr/toastr.min.js"></script> <script type="text/javascript" src="/libhtml_v3/js/modalWaitingBox.js"></script> <script> (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); 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} if($('a[data-lightbox]').index(next) > 0) { $('.prev-lightbox').show(); } }); } function submitSearch(){ //search box if (document.searchForm.searchMenu.value=="taxonomy") { document.searchForm.taxon.value = document.searchForm.query.value; //temp fix for now. document.searchForm.action="/index.php/Taxbrowser_Taxonpage?taxon="+document.searchForm.query.value+"&debug=1"; } else if (document.searchForm.searchMenu.value=="records") { document.searchForm.action="/index.php/Public_SearchTerms?"; } else if (document.searchForm.searchMenu.value=="bins") { document.searchForm.action="/index.php/Public_BINSearch?"; } } </script> <style> .ui-autocomplete { position: absolute; top: 100%; left: 0; z-index: 1000; float: left; display: none; min-width: 160px; _width: 160px; padding: 4px 0; margin: 2px 0 0 0; list-style: none; background-color: #ffffff; border-color: #ccc; border-color: rgba(0, 0, 0, 0.2); border-style: solid; border-width: 1px; -webkit-border-radius: 5px; -moz-border-radius: 5px; 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$('.alert-danger').show(); } $(".dbChange").on("click", function(event) { /* //Uncomment to disable the historical id engine. alert ("The historical DB feature has been temporarily taken offline for maintenance. Please check back shortly!"); */ event.preventDefault(); var histDB = $(this).attr("db"); updateView(histDB); $("#historicalDB").val(histDB); $("#species-radio").prop('checked', true); //$("#full-length-radio").prop('disabled', histDB==''); }) $('input[type="submit"]').click(function(event) { event.preventDefault(); var disableIDEngine = false; if (disableIDEngine == false) { var form = $(this).closest('form'); $('.alert-danger').hide(); var valid = validateForm(form); if (valid) { invokeAction(form, "", 'nopopup', 0, 0, '', 'Identification Request', 'Working'); } } else { alert("IDEngine features have been disabled temporarily for maintenance. Sorry for the inconvenience. Please check back later."); } }); $('a[data-toggle="tab"]').on('shown.bs.tab', function(e) { var target = $(e.target).attr("href") // activated tab $("#tabtype").val(target); console.log(target); }); if ($("#historicalDB").val() != '') { //console.log($("#historicalDB").val()); updateView($("#historicalDB").val()); //reset to the proper one } if ($("#tabtype").val() != "") { $('.nav-tabs a[href="' + $("#tabtype").val() + '"]').tab('show'); } }); function updateView(histDB) { $(".searchdb").each(function() { var oldValue = $(this).val(); var newValue = oldValue.split("-")[0] + histDB; $(this).val(newValue); }); $(".dbChange").each(function() { if ($(this).attr("db") != histDB) { $(this).removeClass("label-info"); } else { if (!$(this).hasClass("label-info")) { $(this).addClass("label-info"); } } }); $.ajax({ url: "/index.php/ids_openidengine/stats", method: 'GET', dataType: 'json', data: { year: histDB } }).done(function(data) { $("#COX1seqs").text(addCommas(data["COX1"][0])); $("#COX1_SPECIESseqs").text(addCommas(data["COX1_SPECIES"][0])); $("#COX1_SPECIESvalid").text(addCommas(data["COX1_SPECIES"][1])); $("#COX1_SPECIESspecies").text(addCommas(data["COX1_SPECIES"][2])); $("#COX1_SPECIES_PUBLICseqs").text(addCommas(data["COX1_SPECIES_PUBLIC"][0])); $("#COX1_SPECIES_PUBLICvalid").text(addCommas(data["COX1_SPECIES_PUBLIC"][1])); $("#COX1_SPECIES_PUBLICspecies").text(addCommas(data["COX1_SPECIES_PUBLIC"][2])); $("#COX1_L640bp_SPECIESseqs").text(addCommas(data["COX1_L640bp_SPECIES"][0])); $("#COX1_L640bp_SPECIESvalid").text(addCommas(data["COX1_L640bp_SPECIES"][1])); $("#COX1_L640bp_SPECIESspecies").text(addCommas(data["COX1_L640bp_SPECIES"][2])); }); } function addCommas(nStr) { nStr += ''; x = nStr.split('.'); x1 = x[0]; x2 = x.length > 1 ? '.' + x[1] : ''; var rgx = /(\d+)(\d{3})/; while (rgx.test(x1)) { x1 = x1.replace(rgx, '$1' + ',' + '$2'); } return x1 + x2; } function validateForm(tabForm) { var sequences = $(tabForm).find('textarea[name="sequence"]').val(); var msgError = ''; if (sequences == '') { msgError = "<li>Please enter sequences to be identified.</li>"; } else { var numSeq = sequences.split(">").length; if (userId == '' || userId == '8') { //no user if (numSeq > 2) { //Send error msgError = "<li>You must be logged in to submit multiple sequences.</li>"; } } else { // there is a user login if (numSeq > 51) { //Send error msgError = "<li>ID Engine requests are limited to 50 sequences per batch temporarily for system upgrades.</li>"; } } } var success = true; if (msgError != '') { $('#errorMsg ul').html(msgError); $('#errorMsg').show(); window.scrollTo(0, 0); success = false; } return success; } </script> </head> <body> <div class="page-container"> <div class="bloc sticky-nav bgc-dark-jungle-green d-bloc"> <div class="container bloc-xs"> <nav class="navbar row"> <div class="navbar-header"> <a class="navbar-brand" href="/index.php"> <img src="/libhtml_v4/images/BOLDlogo.png" alt="logo" /> </a> <button id="nav-toggle" type="button" class="ui-navbar-toggle navbar-toggle" data-toggle="collapse" data-target=".navbar-1"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <a href="#" class="search-toggle" data-toggle="collapse" data-target=".search-wrap"> <span class="fa fa-search fa-lg"></span> </a> </div> <div class="collapse navbar-collapse navbar-1"> <ul class="site-navigation nav navbar-nav">  <li><a href="/index.php/IDS_OpenIdEngine">Identification v4</a></li> <li><a href="/index.php/TaxBrowser_Home">Taxonomy</a></li> <li><a href="/index.php/MAS_Management_UserConsole">Workbench</a></li>  <li><a href="/index.php/MAS_Management_UserConsole">Login</a></li> <li class="nav-search"> <a href="#" data-toggle="collapse" data-target=".search-wrap"> <span class="fa fa-search icon-sm"></span> </a> </li> </ul> </div> </nav> </div> <div class="search-wrap collapse"> <form id="site-search" name ="searchForm" onSubmit="submitSearch();"> <div class="col-sm-3 col-md-2"> <label class="sr-only" for="search_type">Type</label> <select id="search_type" class="form-control" name="searchMenu"> <option value="taxonomy">Taxonomy</option> <option value="records">Public Data</option> <option value="bins">BINs</option> </select> </div> <div class="col-sm-9 col-md-10"> <label class="sr-only" for="search_keyword">Keyword</label> <input id="query" class="form-control" name="query" placeholder="Search" /> <input type="hidden" name="taxon"/> </div> </form> </div> </div> <div class="bloc bgc-cadet-blue d-bloc" id="lead-in"> <div class="container bloc-md"> <div class="row"> <div class="col-sm-12"> <h3>IDENTIFICATION ENGINE</h3> </div> </div> </div> </div> <div class="bloc l-bloc bgc-white"> <div class="container bloc-md"> <div class="ibox"> <div class="ibox-content">  <div class="alert alert-danger" id="errorMsg"> <strong>There was an error with your request:</strong> <ul> </ul> </div> <div class="tabs-container"> <ul class="nav nav-tabs"> <li class="active"><a href="#animalTabPane" data-toggle="tab">Animal Identification [COI]</a></li> <li><a href="#fungiTabPane" data-toggle="tab">Fungal Identification [ITS]</a></li> <li><a href="#plantTabPane" data-toggle="tab">Plant Identification [rbcL & matK]</a></li> </ul> <div class="tab-content">  <div id="animalTabPane" class="tab-pane active"> <div class="panel-body"> <p> The BOLD Identification System (IDS) for COI accepts sequences from the 5' region of the mitochondrial Cytochrome c oxidase subunit I gene and returns a species-level identification when one is possible. Further validation with independent genetic markers will be desirable in some forensic applications. </p> <p> <strong>Historical Databases:</strong> <a db="" class="dbChange label label-info m-r">Current</a><a db="-JUL2019" class="dbChange label m-r">Jul-2019</a><a db="-JUL2018" class="dbChange label m-r">Jul-2018</a><a db="-JUL2017" class="dbChange label m-r">Jul-2017</a><a db="-JUL2016" class="dbChange label m-r">Jul-2016</a><a db="-JUL2015" class="dbChange label m-r">Jul-2015</a><a db="-JUL2014" class="dbChange label m-r">Jul-2014</a><a db="-JUL2013" class="dbChange label m-r">Jul-2013</a><a db="-JUL2012" class="dbChange label m-r">Jul-2012</a><a db="-JUL2011" class="dbChange label m-r">Jul-2011</a><a db="-JUL2010" class="dbChange label m-r">Jul-2010</a><a db="-JUL2009" class="dbChange label m-r">Jul-2009</a> </p> <form action="/index.php/IDS_IdentificationRequest" method="post" name="sequencesubForm" id="animalForm"> <input name="tabtype" id="tabtype" type="hidden" value="animalTabPane"><input type="hidden" name="historicalDB" id="historicalDB" value="" /> <p>Search Databases:</p> <table class="table"> <tr> <td><input class="searchdb" name="searchdb" type="radio" value="COX1"></td> <td> <strong>All Barcode Records on BOLD (<span id="COX1seqs">14,781,716</span> Sequences)</strong> <br> <p style="font-size: 12px"> Every COI barcode record on BOLD with a minimum sequence length of 500bp. Records classified as Diptera, Coleoptera, Lepidoptera, and Hymenoptera, without further taxonomic resolution, have been excluded to enhance the utility of the results. This search only returns a list of the nearest matches and does not provide a probability of placement to a taxon.</p> </td> </tr> <tr> <td><input id="species-radio" class="searchdb" name="searchdb" type="radio" value="COX1_SPECIES" checked></td> <td><strong>Species Level Barcode Records (<span id="COX1_SPECIESseqs">5,040,349</span> Sequences/<span id="COX1_SPECIESvalid">246,329</span> Species/<span id="COX1_SPECIESspecies">120,909</span> Interim Species)</strong> <br> <p style="font-size: 12px">Every COI barcode record with a species level identification and a minimum sequence length of 500bp. This includes many species represented by only one or two specimens as well as all species with interim taxonomy. </p> </td> </tr> <tr> <td><input class="searchdb" name="searchdb" type="radio" value="COX1_SPECIES_PUBLIC"></td> <td><strong>Public Record Barcode Database (<span id="COX1_SPECIES_PUBLICseqs">2,565,899</span> Sequences/<span id="COX1_SPECIES_PUBLICvalid">157,071</span> Species/<span id="COX1_SPECIES_PUBLICspecies">69,898</span> Interim Species)</strong> <br> <p style="font-size: 12px"> All published COI records from BOLD and GenBank with a minimum sequence length of 500bp. This library is a collection of records from the published projects section of BOLD. </p> </td> </tr> <tr> <td><input id="full-length-radio" class="searchdb" name="searchdb" type="radio" value="COX1_L640bp_SPECIES"></td> <td><strong>Full Length Record Barcode Database (<span id="COX1_L640bp_SPECIESseqs">3,583,153</span> Sequences/<span id="COX1_L640bp_SPECIESvalid">222,163</span> Species/<span id="COX1_L640bp_SPECIESspecies">100,022</span> Interim Species)</strong> <br> <p style="font-size: 12px"> Subset of the Species library with a minimum sequence length of 640bp and containing both public and private records. This library is intended for short sequence identification as it provides maximum overlap with short reads from the barcode region of COI. </p> </td> </tr> </table> <p>Enter fasta formatted sequences in the forward orientation:</p> <textarea name="sequence" rows="15" class="form-control" id="sequence"></textarea> <div class="col-sm-12 text-right"> <input name="Submit" id="submitAnimal" type="submit" class="btn btn-primary btn-sm" value="Submit"> </div> </form> </div> </div>  <div id="fungiTabPane" class="tab-pane"> <div class="panel-body"> <p style="font-size: 12px">The BOLD Identification System (IDS) for ITS is the default identification tool for Fungal barcodes and accepts sequences from the Internal Transcribed Spacer Region and returns a species-level identification when possible. Further validation with independent genetic markers will be desirable in some forensic applications.</p> <p style="font-size: 12px">The BLAST algorithm is employed in place of the standard BOLD identification engine for ITS sequences. </p> <p style="font-size: 12px">There are very few ITS records on BOLD so most queries will likely not return a successful match.</p> <form action="/index.php/IDS_BlastRequest" method="post" name="sequencesubForm" id="fungiForm"> <input name="tabtype" id="tabtype" type="hidden" value="fungiTabPane"> <p>Search Database:</p> <table class="table"> <tr> <td><input name="searchdb" type="radio" value="ITS" checked></td> <td> <strong>ITS Sequences </strong> <br> <p style="font-size: 12px"> Every ITS barcode record on BOLD with a minimum sequence length of 100bp (warning: unvalidated database that includes records without species level identification). This includes many species represented by only one or two specimens as well as all species with interim taxonomy. This search only returns a list of the nearest matches and does not provide a probability of placement to a taxon. </p> </td> </tr> </table> <p>Enter sequences in fasta format:</p> <textarea name="sequence" rows="15" class="form-control" id="sequence"></textarea> <div class="col-sm-12 text-right"> <input name="Submit" id="submitFungal" type="submit" class="btn btn-sm btn-primary" value="Submit"> </div> </form> </div> </div>  <div id="plantTabPane" class="tab-pane"> <div class="panel-body"> <p style="font-size: 12px">The BOLD Identification System (IDS) for rbcL and matK is the default identification tool for Plant barcodes and accepts sequences from the Ribulose-bisphosphate carboxylase and Maturase K genes. It returns a species-level identification when possible. Further validation with independent genetic markers will be desirable in some forensic applications.</p> <p style="font-size: 12px">The BLAST algorithm is employed in place of the standard BOLD identification engine for rbcL and matK sequences. </p> <p style="font-size: 12px">There are very few rbcL and matK records on BOLD so most queries will likely not return a successful match.</p> <form action="/index.php/IDS_BlastRequest" method="post" name="sequencesubForm" id="plantForm"> <input name="tabtype" id="tabtype" type="hidden" value="plantTabPane"> <p>Search Database:</p> <table class="table"> <tr> <td><input name="searchdb" type="radio" value="MATK_RBCL" checked></td> <td> <strong>Plant Sequences </strong> <br> <p style="font-size: 12px"> Every rbcL and matK barcode record on BOLD with a minimum sequence length of 500bp (warning: unvalidated database that includes records without species level identification). This includes many species represented by only one or two specimens as well as all species with interim taxonomy. This search only returns a list of the nearest matches and does not provide a probability of placement to a taxon. </p> </td> </tr> </table> <p>Enter sequences in fasta format:</p> <textarea name="sequence" rows="15" class="form-control" id="sequence"></textarea> <div class="col-sm-12 text-right"> <input name="Submit" id="submitPlant" type="submit" class="btn btn-sm btn-primary" value="Submit"> </div> </form> </div> </div> </div> </div> </div> </div> </div> </div> <div class="bloc bgc-platinum l-bloc" id="footer"> <div class="container bloc-md"> <div class="row">                    <div class="col-sm-3"> <h3 class="mg-md">Organization</h3> <ul class="list-unstyled"> <li><a href="/index.php/Resources/whatIsBOLD">About Us</a></li> <li><a href="/index.php/Resources/ContactUs">Contact Us</a></li> <li><a href="/index.php/NewsFeed">News & Events</a></li> </ul> </div> <div class="col-sm-3"> <h3 class="mg-md">Partners</h3> <ul class="list-unstyled"> <li><a href="http://www.ibol.org">iBOL</a></li> <li><a href="http://biodiversitygenomics.net/">CBG</a></li> <li><a href="http://ccdb.ca">CCDB</a></li> <li><a href="http://www.ncbi.nlm.nih.gov">GenBank</a></li> <li><a href="http://www.eol.org">EOL</a></li> <li><a href="http://www.gbif.org">GBIF</a></li> </ul> </div> </div> </div> </div> <div class="bloc bgc-floral-white l-bloc" id="affiliates"> <div class="container bloc-md"> <div class="row"> <div class="col-sm-2"> <img class="img-responsive center-block" style="margin-top:20px" src="/libhtml_v4/img/ibol-50v.png" /> </div> <div class="col-sm-2"> <img class="img-responsive center-block" style="margin-top:20px" src="/libhtml_v4/img/CFREF.png" /> </div> <div class="col-sm-2"> <img class="img-responsive center-block" src="/libhtml_v4/img/MRI_logo.png" /> </div> <div class="col-sm-2"> <img class="img-responsive center-block" style="margin-top:20px" src="/libhtml_v4/img/CFINN.png"/> </div> <div class="col-sm-2"> <img class="img-responsive center-block" style="margin-top:20px" src="/libhtml_v4/img/NSERC.png" /> </div> <div class="col-sm-2"> <img class="img-responsive center-block" src="/libhtml_v4/img/UoGuelph_image18-100x100.png" /> </div> </div> <div class="row"> <div class="col-xs-12"><br/><h5><small><strong>Copyright</strong> BOLD © 2014-2024</small></h5></div> </div> </div> </div> </div> </body> </html>

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