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| | + | {{:Team:Shenzhen_BGIC_0101/Templates/Header}} |
| | <html> | | <html> |
| - | <head>
| + | <script src="https://2013.igem.org/Team:Shenzhen_BGIC_0101/aaa?action=raw&ctype=text/javascript"></script> |
| - | <!-- iGem wiki hacks -->
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| - | <script type="text/javascript">
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| - | $(document).ready(function() {
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| - | $("p").filter( function() {
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| - | return $.trim($(this).html()) == '';
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| - | </script>
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| - | <!-- Remove "team" from the menubar -->
| + | <body> |
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| - | $(document).ready(function() {
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| - | $("menubar > ul > li:last-child").remove();
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| - | </script>
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| - | <!-- Empty heading? - Then remove it.. -->
| + | <br/><br/> |
| - | <script type="text/javascript">
| + | <section class="container"> |
| - | $(document).ready(function() {
| + | <div class="one-third column"> |
| - | if ("" == "</html>{{{1}}}<html>") {
| + | |
| - | $("#heading").remove();
| + | <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Tutorial/neochr" target="_blank"> |
| - | }
| + | <img src="https://static.igem.org/mediawiki/2013/f/f9/Neochr_icon-purple.png" /> |
| - | });
| + | </a> |
| - | </script>
| + | |
| - | <script type="text/javascript">
| + | <h1>NeoChromosome</h1> |
| - | $(document).ready(function() {
| + | <a href="https://static.igem.org/mediawiki/2013/9/9e/Tutorial-Neochr.pdf" target="_self"><h4>Download</h4></a> |
| - | // document.getElementById("p-logo").style.display= "none";
| + | </div> |
| - | document.getElementsByClassName("right-menu noprint")[0].style.display= "none";
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| - | //document.getElementById("searchform").style.display= "none"; | + | |
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| - | });
| + | <div class="one-third column"> |
| - | </script>
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| | + | <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Tutorial/nucleomod" target="_blank"> |
| | + | <img src="https://static.igem.org/mediawiki/2013/e/e7/Nucleomod_icon-purple.png" /> |
| | + | </a> |
| | + | |
| | + | <h1>NucleoModifier</h1> |
| | + | |
| | + | <a href="https://static.igem.org/mediawiki/2013/9/96/Tutorial-NucleoMod.pdf" target="_self"><h4>Download</h4></a> |
| | + | </div> |
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| - | <script type="text/javascript" src="//use.typekit.net/jlr8wlp.js"></script> | + | <img src="https://static.igem.org/mediawiki/2013/9/9e/Segman_icon-purple.png" /> |
| - | <script type="text/javascript">try{Typekit.load();}catch(e){}</script> | + | </a> |
| | + | |
| | + | <h1>Segmentation</h1> |
| | + | |
| | + | <a href="https://static.igem.org/mediawiki/2013/a/a8/Tutorial-Segmentation.pdf" target="_self"><h4>Download</h4></a> |
| | + | <br/><br/><br/> |
| | + | </div> |
| | | | |
| - | <style>
| + | </section> |
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| - | #tabs {
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| - | overflow: hidden;
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| - | width: 70%;
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| - | margin: 0;
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| - | margin-left: 25%;
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| - | font-size: 1.3em;
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| - | font-weight: 800;
| + | <section class="container"> |
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| | + | <img src="https://static.igem.org/mediawiki/2013/e/ee/Olsdesigner.png" /> |
| | + | </a> |
| | | | |
| - | #tabs li {
| + | <h1>OLS Designer</h1> |
| - | float: left;
| + | |
| - | margin: 0 -15px 0 0;
| + | <a href="https://static.igem.org/mediawiki/2013/2/26/Tutorial-OLSDesigner.pdf" target="_self"><h4>Download</h4></a> |
| - | }
| + | </div> |
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| - | #tabs a {
| + | <div class="one-third column"> |
| - | float: left;
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| - | position: relative;
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| - | height: 0;
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| - | line-height: 30px;
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| + | <h1>Kgml2Jason</h1> |
| - | text-decoration: none;
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| - | color: #38f;
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| - | border-right: 30px solid transparent;
| + | </div> |
| - | border-bottom: 30px solid rgba(54, 49, 49, 0.71);
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| - | border-bottom-color: #777\9;
| + | |
| - | // opacity: .3;
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| - | filter: alpha(opacity=30);
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| - | }
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| - | #tabs a:hover,
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| - | #tabs a:focus {
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| - | border-bottom-color: #2ac7e1;
| + | <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Tutorial/videoturorial" target="_blank"> |
| - | opacity: 1;
| + | <img src="https://static.igem.org/mediawiki/2013/c/c1/Vedior.png" /> |
| - | filter: alpha(opacity=100);
| + | </a> |
| - | }
| + | |
| - | | + | <h1>Video Tutorial</h1> |
| - | #tabs a:focus {
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| - | outline: 0;
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| - | }
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| - | #tabs #current {
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| - | filter: alpha(opacity=100);
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| - | }
| + | |
| - | #tab1,#tab2,#tab3,#tab4{
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| - | font-size: 16px;
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| - | line-height: 19px;
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| - | font-family: Trebuchet MS;
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| - | font-weight: 600;
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| - | color: #ccc;
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| - | }
| + | |
| - | /* ----------- */
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| - | #content2 {
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| - | background: rgba(29, 28, 28, 0.79);
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| - | border-top: 2px solid #3d3d3d;
| + | |
| - | padding: 2em;
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| - | width :55%;
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| - | margin-left: 25%;
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| - |
| + | |
| - | }
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| - | | + | |
| - | #content2 h2,
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| - | #content h3,
| + | |
| - | #content p {
| + | |
| - | margin: 0 0 15px 0;
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| - | | + | |
| - | }
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| - | </style> | + | |
| - |
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| - | <script type="text/javascript">
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| - | function FloatMenu(){
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| - | var animationSpeed=1500;
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| - | var animationEasing='easeOutQuint';
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| - | var scrollAmount=$(document).scrollTop();
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| - | FloatMenu();
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| - | $(document).ready(function(){
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| - | var fadeSpeed=500;
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| - | $("#fl_menu").hover(function(){
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| - | $("#fl_menu .menu").fadeIn(fadeSpeed);
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| - | $("#fl_menu .menu").fadeOut(fadeSpeed);
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| - | <style>
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| - | .tit{
| + | |
| - | color: #6AA33D;
| + | |
| - | }
| + | |
| - | .container{
| + | |
| - | width:65%;
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| - | left: 5%;
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| - | }
| + | |
| - | /* fl_menu */
| + | |
| - | #fl_menu{position:absolute;top:150px;left:-2px;z-index:9999;
| + | |
| - | width:200px;
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| - | height:50px;
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| - | }
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| - | #fl_menu .label{line-height:50px;font-size:18px;font-weight:bold;background: #1B1B1B;color:#fff;letter-spacing:5px;text-align: center;box-shadow: 2px 1px 6px #272727;border-radius: 2px;opacity: 0.75;}
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| - | #fl_menu .label a{color:#83f;text-decoration: none;}
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| - | #fl_menu .label a:hover{color:#38f;}
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| - | <style type="text/css">.recentcomments a{display:inline !important;padding:0 !important;margin:0 !important;}</style>
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| - | </head>
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| - | <body class="blog developer-wanted">
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| - | <div id="fl_menu">
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| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software">Overview</a></div> | + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/ Modules">Modules</ a></div> | + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Next_version">Next version</a></div>
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| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Compatibility">Compatibility</a></div> | + | |
| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/NewStandard">New Standard</a></div>
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| - | <div class="label"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Tutorial#">Tutorial</a></div>
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| - | <nav class="menu-main-navigation-container"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Home" class="menu-item-20 menu-item menu-item-type-post_type menu-item-object-page">Home</a> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Team" class="menu-item-19 menu-item menu-item-type-post_type menu-item-object-page">Team</a> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software" class="menu-item-18 menu-item menu-item-type-post_type menu-item-object-page current-menu-item">Software</a> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Requirements" class="menu-item-17 menu-item menu-item-type-post_type menu-item-object-page">Requirements</a> <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Criteria" class="menu-item-15 menu-item menu-item-type-post_type menu-item-object-page">Criteria</a> </nav>
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| - | </header>
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| - | <div id="page-header" style="background: url(https://static.igem.org/mediawiki/igem.org/b/b0/Za.jpg);height: 300px;box-shadow: 4px 3px 25px #000;">
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| - | <h1></h1>
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| - | </div>
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| - | <br/>
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| - | <h2 style="font-family: 'Tangerine', serif;font-size: 48px; text-shadow: 4px 4px 4px #aaa; color: #38f;
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| - | letter-spacing: 0.1em;
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| - | word-spacing: 0.3em;
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| - | font-weight: 700;
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| - | width: 30%;
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| - | line-height: 36px;
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| - | margin: 0;
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| - | margin-left: 20%;">Tutorial</h2><br/>
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| - | <ul id="tabs">
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| - | <li><a href="#" name="#tab1">Neochr</a></li>
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| - | <li><a href="#" name="#tab2">NucleoMod</a></li>
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| - | <li><a href="#" name="#tab3">SegmMan</a></li>
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| - | <li><a href="#" name="#tab4">Others</a></li>
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| - | </ul>
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| - | <div id="content2">
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| - | <div id="tab1">
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| - | <p class="tit">1. NeoChr </p>
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| - | <p>
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| - | NeoChr module would assist users to grab related genes in different pathways manually, to rewire genes’ relationship logically*, and to replace genes with ortholog that score higher*. Firstly, it would allow users to define gene order and orientation in DRAG&DROP way. Secondly, decoupled these genes if have overlap and make all genes are non-redundancy. Finally, add chromosome features to build a new chromosome and show in the JBrowse. Moreover, users can drag a window in the JBrowse and delete any gene in the window.<br/>
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| - | Note: <br/>
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| - | *These function are unavailable now, please wait for version 2.<br/>
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| - | **You can also add any thing here including your own water mark.<br/></p>
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| - | <p class="tit">2. Plugin Scripts </p>
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| - | <p>This module contains three plugins: Decouple.pl, Add.pl and Delete.pl.</p>
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| - | <p class="tit">2.1 Decouple.pl</p>
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| - | <p>This plugin is to decouple the genes which have overlap gene regions. These overlapping genes can be decoupled if meet the following conditions: (1)If two genes have overlap gene regions, the latter gene 5’UTR does not cover the former gene initial codon (ATG); (2)Overlapping region initial coordinate is in the coding DNA sequences(CDS) of gene which is need to be decoupled; (3)The decouple site of CDS have synonymous substitute codon to replace; After decoupling, we use these non-redundancy genes to generate a GFF file and a FASTA file.</p>
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| - | <p class="tit">2.1.1 Internal operation </p>
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| - | <p>First, this plugin extracts base sequence from the genome file according to the gene order list, and records the gene order in the list. And then plugin records the annotation information according to the specie GFF file, moreover, plugin extends gene CDS upstream 600bp as 5’-UTR and downstream 100bp as 3’-UTR if the GFF file does not contain annotated these two features.<br/>
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| - | Second, this plugin detects the overlapping genes in the same chromosome. In case the overlapping genes are detected, it will judge whether the overlapping initial site is located in the CDS region, and identify the site is belong to phase0/1/2.<br/>
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| - | Third, the plugin attempts to synonymous substitute codon to break the initial codon intra the CDS. Printing information whether or not be decoupled successfully, such as:<br/>
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| - | <img src="https://static.igem.org/mediawiki/2013/e/e0/T1-1.png" alt="data" style="width: 750px" /><br/>
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| - | And non-redundancy genes are generated.<br/>
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| - | Finally, the plugin links non-redundancy genes to construct a new chromosome according to the gene order.
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| - | </p>
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| - | <p class="tit">2.2.1 Example</p>
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| - | <p>We have two input forms to execute the plugin:<br/>
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| - | 1. Using string format as gene order list input form:<br/>
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| - | perl GeneDecouple.pl --species saccharomyces_cerevisiae_chr --list_format string --gene_order="YAL054C -,YAL038W +,YBR019C -,YBR145W +,YCL040W +,YCR012W +,YCR105W +,YDL168W +,YPL017C -,YIL177C -,YIL177W-A +,YIL172C -,YIL171W-A +,” --geneset_dir ../gene_set --upstream_extend 600 --downstream_extend 100 --neo_chr_gff neochr.gff --neo_chr_fa neochr.fa<br/>
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| - | 2. Using file format as gene order list input form:<br/>
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| - | erl GeneDecouple.pl --species saccharomyces_cerevisiae_chr --list_format file --gene_order gene_ordre.list --geneset_dir ../gene_set --upstream_extend 600 --downstream_extend 100 --neo_chr_gff neochr.gff --neo_chr_fa neochr.fa
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| - | </p>
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| - | <p class="tit">2.1.3 Parameters </p>
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| - | <table border="1">
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| - | <tr>
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| - | <th>Parameter</th>
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| - | <th>Description</th>
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| - | <th></th>
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| - | <th></th>
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| - | </tr>
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| - | <tr>
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| - | <th>list_format</th>
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| - | <th>set the input form of gene order list</th>
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| - | <th>string</th>
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| - | <th>string/file</th>
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| - | </tr>
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| - | <tr>
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| - | <th>gene_order</th>
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| - | <th>set the input gene order list file(include pathway genes and addition genes)</th>
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| - | <th></th>
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| - | <th></th>
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| - | </tr>
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| - | <tr>
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| - | <th>Parameter</th>
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| - | <th>Description</th>
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| - | <th>Default</th>
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| - | <th>Selectable range</th>
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| - | </tr>
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| - | <tr>
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| - | <th>geneset_dir</th>
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| - | <th>set the species annotation directory</th>
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| - | <th>600</th>
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| - | <th></th>
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| - | </tr>
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| - | <tr>
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| - | <th>upstream_extend</th>
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| - | <th>set the length of gene downstram(bp)</th>
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| - | <th>100</th>
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| - | <th></th>
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| - | </tr>
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| - | <tr>
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| - | <th>neo_chr_gff</th>
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| - | <th>set the name of output neochr gff file</th>
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| - | <th></th>
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| - | <th></th>
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| - | </tr>
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| - | <tr>
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| - | <th>neo_chr_fa</th>
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| - | <th>set the name of output neochr fasta file</th>
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| - | <th></th>
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| - | <th></th>
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| - | </tr>
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| - | <tr>
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| - | <th>help</th>
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| - | <th>Show help information</th>
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| - | <th></th>
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| - | <th></th>
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| - | </tr>
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| - | </table>
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| - | </p><br/>
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| - | <p class="tit">2.4.1 The format of output file</p>
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| - | <p>The output files are standard GFF and FASTA format files which are decoupled.<br/>
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| - | 1. decoupled GFF file<br/>
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| - | <img src="https://static.igem.org/mediawiki/2013/e/e5/T1-2.png" alt="data" style="width: 750px" /><br/>
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| - | 2.decoupled FASTA file<br/>
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| - | <img src="https://static.igem.org/mediawiki/2013/b/b2/T1-3.png" alt="data" style="width: 750px" /><br/>
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| - |
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| - | <p class="tit">2.2 Add.pl </p>
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| - | <p>This plugin will add the LoxPsym sequence and the customized left and right telomeres, centromere and autonomously replicating sequence (ARS) into the FASTA file and GFF file which are generated by Decouple.pl.</p>
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| - | <p class="tit">2.2.1 Internal operation </p>
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| - | <p>The plugin adds LoxPsym behind the first 3bp of 3’-UTR in each gene and adds telomere, centromere and ARS according this mode:<br/>
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| - | <b>left_telomere + gene1 + centromere + gene2 + ARS + gene3 + right_telomere</b><br/>
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| - | The distance between centromere and ARS is less than 30Kb.<br/>
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| - | Finally, user can see the new added features chromosome according to the JBrowse.
| |
| - | </p>
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| - | <p class="tit">2.2.2 Example </p>
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| - | <p>perl 04.Add.pl --loxp loxPsym.feat --left_telomere UTC_left.feat --right_telomere UTC_right.feat --ars chromosome_I_ARS108.feature --centromere chromosome_I_centromere.feat --chr_gff neochr.gff --chr_seq neochr.fa --neochr_seq neochr.final.fa --neochr_gff neochr.final.gff<br/><br/>
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| - | All the feature file format is 4 lines format, for example:<br/>
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| - | name = site_specific_recombination_target_region<br/>
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| - | type = loxPsym<br/>
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| - | source = BIO<br/>
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| - | sequence = ATAACTTCGTATAATGTACATTATACGAAGTTAT<br/>
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| - | Note: the first line is the detail name of feature, the second line is the type of feature, the third line is the source of feature and the last line is the sequence of feature.
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| - | </p>
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| - | <p class="tit">2.2.3 Parameters</p>
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| - | <pre>
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| - | Parameter Description Default Selectable range
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| - | loxp set the sequence of loxp ATAACTTCGTATAATGTATGCTATACGAAGTTAT
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| - | left_telomere set the sequence of left telomere
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| - | right_telomere set the sequence of right telomere
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| - | chr_gff set the input neorchr_gff file
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| - | chr_seq set the input neorchr_gff file
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| - | neochr_seq set the name of output added loxps and telomeres neochr_fa file
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| - | neochr_gff set the name of output added loxps and telomeres neochr_gff file
| |
| - | </pre>
| |
| - |
| |
| - | <p class="tit">2.2.4 The format of output</p>
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| - | <p>The output files are standard GFF and FASTA format of adding features chromosome.<br/>
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| - | 1. added features GFF file<br/>
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| - | <img src="https://static.igem.org/mediawiki/2013/e/e0/T1-4.png" alt="data" style="width: 750px" ></a>
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| - | </p>
| |
| - |
| |
| - | <p class="tit">2.3 Delete.pl </p>
| |
| - | <p>This plugin can modify the GFF and FASTA file which are generated by Add.pl according to the user drags a window in the JBrowse and delete any gene in the window.</p>
| |
| - | <p class="tit">2.3.1 Internal operation </p>
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| - | <p>Firstly, user uses mouse to drag a window in the added features FASTA file which is showed in the JBrowse and JBrowse displays all the genes in this window.Secondly, user decides which genes is need to be delected from the new chromosome and plugin deletes genes from GFF file and modify FASTA in the same time.</p>
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| - | <p class="tit">2.3.2 Example </p>
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| - | <p>perl 05.delete.pl --delete="YAL054C,YAL038W" --neochr_gff neochr.refine.final.gff --neochr_fa neochr.refine.final.fa --slim_gff neochr.refine.delete.gff --slim_fa neochr.refine.delete.fa </p>
| |
| - | <p class="tit">2.3.3 Parameters </p>
| |
| - | <p><pre>
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| - | Parameter Description Default Selectable range
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| - | delete Set the to be deleted gene list
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| - | neochr_gff Set the input GFF file which is generated by Add.pl
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| - | neochr_fa Set the input FASTA file which is generated by Add.pl
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| - | slim_gff Set the output GFF file
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| - | slim_fa Set the output FASTA file </pre></p>
| |
| - |
| |
| - | <p class="tit">2.3.4 The format of ouput</p>
| |
| - | <p>The output files are standard GFF and FASTA format of deleted genes chromosome.</p>
| |
| - |
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| - | </div>
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| - | <div id="tab2">
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| - |
| |
| - | <p>test</p>
| |
| - |
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| - | </div>
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| - | <div id="tab3">
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| - |
| |
| - | <p>test</p>
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| - | </div>
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| - | <div id="tab4">
| |
| - | <p class="tit">Presentation from KGML</p>
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| - | <p> This module will grab genes’ details in different pathways, which from KEGG with KEGG Makeup Language (KGML) file and export genes list and relationship of genes. The goal here is to visualize the pathway and rebuild it in the level of genes.</p>
| |
| - | <p class="tit">Scripts<br/>1. keggid_convert_gene.pl</p>
| |
| - | <p> This utility can convert KEGGID which in KGML file into genes’ name and rewrite KGML file.</p>
| |
| - | <p class="tit">Internal operation</p>
| |
| - | <p> First, this utility will change the pathway’s name into KEGG database names, and then open the file with the entire list of genes, push them in hash.<br/>
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| - | Second, this utility will read the original pathway’s xml file in and replace KEGGID with gene’s name one by one. Furthermore, it will change type element all into “gene”.<br/>
| |
| - | Thirdly, it will be the substitution of original pathway’s xml file.</p>
| |
| - | <p class="tit">Example</p>
| |
| - | <p> perl keggid_convert_gene.pl ko04010</p>
| |
| - | <p class="tit">The format of output:</p>
| |
| - | <p>It will rewrite the original pathway’s xml file, if we have following statement:<br/>
| |
| - | <entry id="30" name="ko:K08018" type="ortholog"<br/>
| |
| - | After running this scripts, it will turn into:<br/><entry id="30" name=" RAPGEF2, PDZGEF1" type="gene" </p>
| |
| - | <p class="tit">convert.py</p>
| |
| - | <p> This utility will read in KGML file which have been rewritten before, and grab genes’ information, such as genes’ name, genes’ relationship and then convert these into JSON.</p>
| |
| - | <p class="tit">Internal operation</p>
| |
| - | <p> First, this utility will use the parameter –f to determine the specified file and read it in. The output file will use the file name that put forward.<br/>
| |
| - | Second, this utility convert KGML file into JSON and grab the information of genes, such as the reactions of genes and the relationship between genes.<br/>
| |
| - | Third, this utility continue to integrate the information above into two files, ‘gene.json’ and ‘relation.json’, which can be use directly in rewrite gene’s pathway.</p>
| |
| - | <p class="tit">Example</p>
| |
| - | <p> python convert.py –f sce04111</p>
| |
| - | <p class="tit">Parameters:</p>
| |
| - | <p>-f/--file read KGML from FILENAME(omit '.xml'), produce two files: gene list and relation</p>
| |
| - | <p class="tit">The format of output:</p>
| |
| - | <p>The output file is stored in the path where you running this program.<br/>
| |
| - | 1. _gene.json <br/>
| |
| - | <img src="https://static.igem.org/mediawiki/2013/1/1b/T4-1.png" />
| |
| - | type:
| |
| - | <pre>
| |
| - | ortholog KO (orthology group)
| |
| - | enzyme Enzyme
| |
| - | reaction Reaction
| |
| - | gene gene product (mostly a protein)
| |
| - | group a complex of gene products (mostly a protein complex)
| |
| - | </pre>
| |
| - | geneID:the unique identification of gene
| |
| - | <pre>
| |
| - | name the KEGGID of this gene
| |
| - | type the type of this gene
| |
| - | </pre>
| |
| - | reaction:
| |
| - | <pre>
| |
| - | name the KEGGID of this reaction
| |
| - | reversible true: reversible reaction; false: irreversible reaction
| |
| - | substrates KEGGID of substrate node
| |
| - | products the KEGGID of product node
| |
| - | related-reactions relate to another pathway or gene
| |
| - | </pre>
| |
| - | 2. _relation.json
| |
| - | <img src="https://static.igem.org/mediawiki/2013/c/c1/T4-2.png" />
| |
| - | relations:
| |
| - | <pre>
| |
| - | type The type of this relation[ ECrel, PPrel. GErel, PCrel, maplink]
| |
| - | subtype Interaction/relation information[activation/inhibition]
| |
| - | entry1 The first (from) entry that defines this relation
| |
| - | entry2 The second (to) entry that defines this relation
| |
| - | </pre>
| |
| - | entry1&2:
| |
| - | <pre>
| |
| - | entry ID The KEGGID of node which takes part in this relation
| |
| - | type Have only two options: [gene/group]
| |
| - | name The KEGGID of this gene
| |
| - | group The node is a complex of gene products (mostly a protein complex)
| |
| - | </pre>
| |
| - | </p>
| |
| - | <br/> <p class="tit">Shortcoming</p>
| |
| - | <p>We can’t automatic acquisition KGML file in the KEGG API, all the demo we have show need to be downloaded before. You can get the entire list of one database genes through KEGG API, just like http://rest.kegg.jp/list/ko , it shows the entire list of orthology genes. The download method about KGML files shows in “How to finish this plun-in” part.
| |
| - | Some genes will relate to another pathway but it doesn’t shows in the pathway so we are failed to grab the relationships between genes and pathways automatically. So we added two gene-pathway relations in ko04010 demo manually, TP53 gene connected with ko04115: P53 signaling pathway and NLK gene connected with ko04310: WNT signaling pathway.
| |
| - | We look forward to the improvement of this plun-in through these disadvantages. </p>
| |
| - | <p class="tit">How to finish this plun-in?</p>
| |
| - | <p> KEGG is a database resource for understanding high-level functions and utilities of the biological system, and KGML is an XML presentation of the KEGG pathway database, which enables automatic drawing of KEGG pathways and provides facilities for computational analysis and modeling of gene/protein networks and chemical networks. Here is the data structure of KGML.<br/>
| |
| - | <img src="https://static.igem.org/mediawiki/2013/f/fa/T4-3.png" />
| |
| - | It’s really complex and it will bother you to understand the KGML file! Do not worry, I will show you how to understand a KGML file and then how to convert it into JSON.<br/>
| |
| - | First, how to find or download KGML file?<br/>
| |
| - | Method: <br/>
| |
| - | Download KGML" link for each pathway map.<br/>
| |
| - | If you choose a pathway with prefix “map”, you can’t find the download link in the page, that’s
| |
| - | because it can be generating almost ko/rn/ec/org files. <br/>
| |
| - | Such as “map04111”, it has no link for download. But if you change the “map” into “sce” in
| |
| - | the URL, you can get the file.<br/>
| |
| - | <a href="http://www.kegg.jp/kegg/rest/keggapi.html">KEGG API:</a>
| |
| - | Take “sce04111” as an example, you can download the KGML file via the <a href="http://rest.kegg.jp/get/sce04111/KGML">this</a>.<br/>
| |
| - | Second, the KGML file is difficult to find out the relationship through the data structure show above.<br/>
| |
| - | Here is the simple but straightforward tutorial to teach you how to understand a KGML file.<br/>
| |
| - | Take “sce04111.xml” as an example. We can simplify the data structure as:<br/>
| |
| - | <img src="https://static.igem.org/mediawiki/2013/c/c5/T4-4.png" />
| |
| - | The entry element can be path/ko/ec/rn/cpd/gl/org/group, enzyme/protein/gene will have relation and gene will also have compound and reactions. We choose one relation to be example:<br/>
| |
| - | <img src="https://static.igem.org/mediawiki/2013/2/27/T4-5.png" />
| |
| - | It means that gene (YCL061C) have activation effect in gene (YPL153C).By the way, through the graphics elements, we can definitely rewrite the connection between these two genes.<br/>
| |
| - |
| |
| - | Third, thought we know how to get KGML file and can understand it but the crucial problem is, how to grab the information of genes and convert it into JSON.<br/>
| |
| - | Here we use Python programming Language, install the library “lxml” for processing XML and HTML, and we import JSON library for convert.<br/>
| |
| - |
| |
| - | Fourth, you may ask: If there have any other software to do such job, that is read KGML files, convert it and rewrite it? <br/>
| |
| - | Of course, and we indeed tried but failed for it’s not open source or the original source is difficult for modification.
| |
| - | Actually, if you want to do some visualize pathway job, Cytoscape is a good choice and it also have cytoscape.js for drawing.<br/>
| |
| - |
| |
| - | Finally, we indeed done plentiful preparatory work, maybe in the end it’s not useful in this software but it can expand our horizons.
| |
| - | <br/>
| |
| - | </p>
| |
| - |
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| - | <p>BGI-Shenzhen, Beishan Industrial Zone<br />
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| - | Yantian District, Shenzhen, 518083, China</p>
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