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{{Loading|loadingimage=sprites.gif}}
<html>
<html>
<script language="javascript" type="text/javascript" src="/resource_browser/rb_js/flot/jquery.flot.js"></script>
<style type="text/css" title="currentStyle">
<script language="javascript" type="text/javascript" src="/resource_browser/rb_js/highcharts/highcharts.js""></script>
@import "/5/sstar/rb_js/html5button/datatables.css";
<script language="javascript" type="text/javascript" src="/resource_browser/rb_js/highcharts/modules/exporting.js"></script>
 
<style type="text/css">
table.details td { width:30%; background-color: #EAEBFF;}
#wrap{
table.details th { width:10%; background-color: #5A5FB5; color: white;}
clear: both;
div.a {
width: 1000px;
  width: 80%;
padding-bottom: 5px;
  float: left;
background:#fff;
  padding:5px;
overflow:hidden;
  margin:5px;
}
}
#left_col{
 
float: left;
div.b {
display:inline;
  width: 20%;
width:650px;
  float: right;
margin: 10px;
  padding:5px;
background:#fff;
  margin:5px;
}
}
#right_col{
float: right;
width: 350px;
padding-top: 10px;
margin:10px;
background:#fff;
}
</style>


<script type="text/javascript">
div.description
/*
{
The code below will take parameters from a page and create a Pie_Chart extracting
width:auto;
data from the values
height:auto;
*/
overflow:auto;
$(document).ready(function (){
 
/*
The code below is for chart settings
*/
var chart_title = "</html>{{{3}}}<html>";
var series_name = "</html>{{{4}}}<html>";
var chart_size  = "</html>{{{5}}}<html>";
if(chart_size.length <1){
chart_size=300;
}
}
</style>


var data = [];
</html>
var content = "</html>{{{1}}}<html>";
<div class="description">
var delimiter = "</html>{{{2}}}<html>";
<table>
var content_array = content.split(delimiter);
{{#if:{{{name}}}|<tr><th scope="row" align="right" valign="top">[[Property:Name|Name]]:</th><td>[[name::{{{name}}}]]</td></tr>|}}{{#if:{{{namespace}}}|<tr><th scope="row" align="right" valign="top">Namespace:</th><td>{{{namespace}}}</td></tr>|}}{{#if:{{{def}}}|<tr><th scope="row" align="right" valign="top">Definition:</th><td>{{{def}}}</td></tr>|}}{{#if:{{{xref}}}|<tr><th scope="row" align="right" valign="top">Xrefs:</th><td>{{XrefExternalRefs|{{{xref}}}|}}</td></tr>|}}{{#if:{{{synonym}}}|<tr><th scope="row" align="right" valign="top">Synonyms:</th><td>{{CollapsibleOntology|synonym|{{{synonym}}}|;;|<br>}}</td></tr>|}}
{{#if:{{{comment}}}|<tr><th scope="row" align="right" valign="top">Comments:</th><td>{{{comment}}}</td></tr>|}}{{#if:{{{alt_id}}}|<tr><th scope="row" align="right" valign="top">Alt_id:</th><td>{{CollapsibleOntology|alt_id|{{{alt_id}}}|;;|<br>}}</td></tr>|}}{{#if:{{{subset}}}|<tr><th scope="row" align="right" valign="top">Subset:</th><td>{{CollapsibleOntology|subset|{{{subset}}}|;;|<br>}}</td></tr>|}}{{#if:{{{created_by}}}|<tr><th scope="row" align="right" valign="top">Created by:</th><td>{{{created_by}}}</td></tr>|}}{{#if:{{{obo_creation_date}}}|<tr><th scope="row" align="right" valign="top">Creation date:</th><td>{{{obo_creation_date}}}</td></tr>|}}{{#if:{{{has_quality}}}|<tr><th scope="row" align="right" valign="top">Has quality:</th><td>{{{has_quality}}}</td></tr>|}}</table></div>
{{#if: {{#pos:{{{bp3d_img_id}}}|FMA:}}|<html><img width=100 height=100 src="http://lifesciencedb.jp/bp3d/API/image.cgi?%7B%22Common%22:%7B%22TreeName%22:%22partof%22%7D,%22Part%22:%5B%7B%22PartID%22:%22</html>{{#replace:{{{bp3d_img_id}}}|:|}}<html>%22%7D%5D%7D">
<!--
<img width=100 height=100 src="http://lifesciencedb.jp/bp3d/icon.cgi?i=</html>{{#replace:{{{bp3d_img_id}}}|:|}}<html>&p=front&v=3%2e0&t=conventional&c=1&m=bp3d&s=L">
-->
<span style="background:gainsboro;"> from <a href="http://lifesciencedb.jp/bp3d/">BodyParts3D</a></span>
</html>
{{#set:bp3d_img_id={{#replace:{{{bp3d_img_id}}}|:|}}}}
|{{#set:bp3d_img_id=}}
}}
<html>
<script type="text/javascript" language="javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script>
<script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.js"></script>
<script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script>
<script type="text/javascript" src="https://bioportal.bioontology.org/widgets/jquery.ncbo.tree-2.0.2.js"></script>
<script type="text/javascript" language="javascript" >


var result_tmp = getDistinctElements(content_array);
$(document).ready(function() {


for(var i=0, l=result_tmp .length; i<l; i++){
if( $('.ont_enrich_ffcp').length ) {
var tmp =result_tmp [i];
var oTable= $('.ont_enrich_ffcp').DataTable({
var counted = countItems(content,tmp);
        dom: 'Blfrti',
var x = [tmp , counted];
scrollY: "300px",
data.push(x);
scrollCollapse: true,
paging: false,
order: [[0,'asc']],
        buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'],
        columnDefs: [{ width: "100px", targets: [0], type: "html-num"}],
        columns: [null,
{ render: function ( data, type, row, meta ) {
var title = data.split("#")[0];
return "<a href=\"/resource_browser/index.php/"+title+"\">"+title+"</a>";
},
},
null
]
});
}
else
{
}
}
 


    var chart;
} );
    // Build the chart
<!--
        chart = new Highcharts.Chart({
        chart: {
                renderTo: 'container',
                plotBackgroundColor: null,
                plotBorderWidth: null,
                plotShadow: false
            },
title: {
                text: chart_title 
            },
            tooltip: {
            pointFormat: '{series.name}:<b>{point.y}</b>',
            percentageDecimals: 0
            },
            plotOptions: {
                pie: {
                    allowPointSelect: true,
                    cursor: 'pointer',
                    dataLabels: {
                        enabled: true,
                        color: '#000000',
                        connectorColor: '#000000',
                        formatter: function() {
                            return '<b>'+ this.point.name +'</b>: '+ this.percentage.toFixed(1) +' %';
                        }
                    }
                }
            },
            series: [{
                type: 'pie',
                name: series_name,
                data: data
            }]
        });


});
function disp(url){
window.open(url, "window_name", "width=800,height=550,scrollbars=yes,menubar=no");
}


// -->
</script>
</html>


{{Fontsize|3|Ontology association}}{{#info:<br>Each term has an is_a parent in the Uberon Ontology, which has a linkage to an another entity and FANTOM5 samples.Libraries were grouped into mutually exclusive facets according to the FANTOM5 sample ontology mapping to UBERON ontologies.
<br>
<br>link to ontology dataset
<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ff-phase1-prerelease-20130717.obo  data]
}}
----
{{Fontsize|3|Parents}}
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{is_a}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{disjoint_from}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{union_of}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{derives_from}}}|:|0}}|1|0}} +{{#if:{{#pos:{{{has_quality}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{located_in}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{part_of}}}|:|0}}|1|0}} }} |NA|<table>
{{#if:{{{is_a}}}|<tr><th width=100 align="right">is_a:</th><td>{{#arraymap:{{{is_a}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{disjoint_from}}}|<tr><th width=100 align="right">disjoint_from:</th><td>{{#arraymap:{{{disjoint_from}}}|;;|$|[[$]]({{#show:$|?name}})|,}}</td></tr>}}{{#if:{{{union_of}}}|<tr><th width=100 align="right">union_of:</th><td>{{#arraymap:{{{union_of}}}|;;|$|[[$]]({{#show:$|?name}})|,}}</td></tr>}}{{#if:{{{derives_from}}}|<tr><th width=100 align="right">derives_from:</th><td>{{#arraymap:{{{derives_from}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{develops_from}}}|<tr><th width=100 align="right">develops_from:</th><td>{{#arraymap:{{{develops_from}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{has_quality}}}|<tr><th width=100 align="right">has_quality:</th><td>{{#arraymap:{{{has_quality}}}|;;|$|[[$]]({{#show:$|?name}})|,}}</td></tr>}}{{#if:{{{located_in}}}|<tr><th width=100 align="right">located_in:</th><td>{{#arraymap:{{{located_in}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}{{#if:{{{part_of}}}|<tr><th width=100 align="right">part_of:</th><td>{{#arraymap:{{{part_of}}}|;;|$|[[$]]({{#show:$|?name}})|, }}</td></tr>}}
</table>}}
<br><br>
{{Fontsize|3|Children}}
{{#vardefine:is_a_count|{{#ask:[[is_a::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:disjoint_from_count|{{#ask:[[disjoint_from::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:adjacent_to_count|{{#ask:[[adjacent_to::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:derives_from_count|{{#ask:[[derives_from::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:develops_from_count|{{#ask:[[develops_from::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:has_quality_count|{{#ask:[[has_quality::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:located_in_count|{{#ask:[[located_in::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:part_of_count|{{#ask:[[part_of::{{FULLPAGENAME}}]]|format=count}}}}{{#vardefine:total_element_count|{{#expr:{{#var:is_a_count}}+{{#var:disjoint_from_count}}+{{#var:adjacent_to_count}}+{{#var:derives_from_count}}+{{#var:develops_from_count}}+{{#var:has_quality_count}}+{{#var:located_in_count}}+{{#var:part_of_count}} }} }}{{#ifexpr: {{#var:total_element_count}} > 0 | <table>
{{#ask:[[is_a::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">is_a:</th><td>|outro=</td></tr>}}{{#ask:[[disjoint_from::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">disjoint_from:</th><td>|outro=</td></tr>}}{{#ask:[[adjacent_to::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">adjacent_to:</th><td>|outro=</td></tr>}}{{#ask:[[derives_from::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">derives_from:</th><td>|outro=</td></tr>}}{{#ask:[[develops_from::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">develops_from:</th><td>|outro=</td></tr>}}{{#ask:[[has_quality::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">has_quality:</th><td>|outro=</td></tr>}}{{#ask:[[located_in::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">located_in:</th><td>|outro=</td></tr>}}{{#ask:[[part_of::{{FULLPAGENAME}}]]|mainlabel=-|?id|?name=|format=template|template=query_result_list_with_namespace|sep=,|intro=<tr><th width=100 align="right">part_of:</th><td>|outro=</td></tr>}}</table>|NA}}
== Ontology Tree: Loaded from [http://purl.bioontology.org/ontology/UBERON BioPortal] ==
<html><a style='cursor: pointer' onClick="disp('http://fantoms.gsc.riken.jp/5/sstar/ontologytree.php?a=</html>{{#explode:{{{id}}}|:|0}}<html>&b=</html>{{#explode:{{{id}}}|:|1}}')<html>">Ontorolgy tree</a>(Small window open)</html><br>
<!--
<html><object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" id="FlexoViz" width="100%" height="100%" codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><param name="movie" value="/resource_browser/rb_js/BasicFlexoViz.swf" /><param name="quality" value="high" /><param name="bgcolor" value="#ffffff" /><param name="allowScriptAccess" value="always" /><embed src="/resource_browser/rb_js/BasicFlexoViz.swf" bgcolor="#ffffff" width="750px" height="600px" name="FlexoViz" align="middle" play="true" loop="false" quality="high" allowScriptAccess="always" type="application/x-shockwave-flash" flashVars="widget=true&ontology=49804&nodeid=</html>{{{id}}}<html>&server=http://rest.bioontology.org/bioportal" pluginspage="http://www.adobe.com/go/getflashplayer"></embed></object></html>
-->
<br>
{{Fontsize|3|FF samples}}{{#info:<br>It includes FANTOM5 samples that overlay the [http://uberon.org/  Uberon] ontology}}
----
{{#ifexpr: 0 ={{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]][[sample_species::Human (Homo sapiens)]][[name::+]][[datafreeze_phase::2]]|?name=|format=count}}||{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Human (Homo sapiens)]][[name::+]][[datafreeze_phase::2]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Human (Homo sapiens)</b>}} }}
{{#ifexpr: 0 ={{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]][[sample_species::Mouse (Mus musculus)]][[name::+]][[datafreeze_phase::2]]|?name=|format=count}}||{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Mouse (Mus musculus)]][[name::+]][[datafreeze_phase::2]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Mouse (Mus musculus)</b>}} }}
<!--{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Rat (Rattus rattus)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Rat (Rattus rattus)</b>}}
{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Dog (Canis lupus familaris)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Dog (Canis lupus familaris)</b>}}
{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Chicken (Gallus gallus)]][[name::+]][[datafreeze_phase::1]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Chicken (Gallus gallus)</b>}} -->
<br>
{{Fontsize|3|Enrichment analysis: top 100 FFCP enriched with this ontology term }}{{#info:TOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji
<br><br>
link to source dataset <br>
human : [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/hg19exp_uberon_general_term_excluded.txt.gz data]  <br>
mouse : [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/mm9exp_uberon_general_term_excluded.txt.gz data]
}}
----
{{#ifexpr: 0 = {{#ask:[[ffcp_ontology_enrichment_uberon_id::{{{id}}}]]|?#|format=count}} | No analysis results |{{#ask:[[ffcp_ontology_enrichment_uberon_id::{{{id}}}]]
|?ffcp_ontology_enrichment_uberon_p-value|format=template|template=Triplecolumn_to_tbrow|link=none|intro=<html><span id="export_tool"></span><table class="ont_enrich_ffcp stripe cell-border order-column compact"><thead><tr><th>P-value</th><th>FFCP</th><th>Short description</th></tr></thead><tbody></html>|outro=<html></tbody></table></html>|sort=ffcp_ontology_enrichment_uberon_p-value|order=asc|limit=100|searchlabel=}}  }}


{{#arraymap:{{{namespace}}}|;;|$|{{#set:namespace=$}}}}
{{#arraymap:{{{xref}}}|;;|$|{{#set:xref=$}}}}
{{#arraymap:{{{def}}}|;;|$|{{#set:def=$}}}}
{{#arraymap:{{{is_a}}}|;;|$|{{#set:is_a=$}}}}
{{#arraymap:{{{synonym}}}|;;|$|{{#set:synonym=$}}}}
{{#arraymap:{{{comment}}}|;;|$|{{#set:comment=$}}}}
{{#arraymap:{{{alt_id}}}|;;|$|{{#set:alt_id=$}}}}
{{#arraymap:{{{disjoint_from}}}|;;|$|{{#set:disjoint_from=$}}}}
{{#arraymap:{{{union_of}}}|;;|$|{{#set:union_of=$}}}}
{{#arraymap:{{{created_by}}}|;;|$|{{#set:created_by=$}}}}
{{#arraymap:{{{subset}}}|;;|$|{{#set:subset=$}}}}
{{#arraymap:{{{obo_creation_date}}}|;;|$|{{#set:obo_creation_date=$}}}}
{{#arraymap:{{{adjacent_to}}}|;;|$|{{#set:adjacent_to=$}}}}
{{#arraymap:{{{derives_from}}}|;;|$|{{#set:derives_from=$}}}}
{{#arraymap:{{{develops_from}}}|;;|$|{{#set:develops_from=$}}}}
{{#arraymap:{{{has_quality}}}|;;|$|{{#set:has_quality=$}}}}
{{#arraymap:{{{located_in}}}|;;|$|{{#set:located_in=$}}}}
{{#arraymap:{{{part_of}}}|;;|$|{{#set:part_of=$}}}}
{{#arraymap:{{{property_value}}}|;;|$|{{#set:property_value=$}}}}
{{#set:id={{{id}}}}}


function getDistinctElements(anArray) {
[[Category:Uber_Anatomy_Ontology]]
      var result = [];
      $.each(anArray, function(i,v){
          if ($.inArray(v, result) == -1) result.push(v);
      });
      return result;
    }
 
 
function countItems(arr, what){
    var count= 0, i;
    while((i= arr.indexOf(what, i))!= -1){
        ++count;
        ++i;
    }
    return count;
}
 
</script>
</html>
<div id ="wrap" style="background-color:White; {round corners}} padding: 0.5em 1em;">
<div id="left_col">
<div  id="container" style="min-width:300px; height: 300px; margin: 0 auto"></div>
</div>
</div>

Latest revision as of 10:25, 13 February 2020

Name:{{{name}}}
Namespace:{{{namespace}}}
Definition:{{{def}}}
Xrefs:
links:
{{{xref}}}:[1]
Synonyms: {{{synonym}}}
Comments:{{{comment}}}
Alt_id: {{{alt_id}}}
Subset: {{{subset}}}
Created by:{{{created_by}}}
Creation date:{{{obo_creation_date}}}
Has quality:{{{has_quality}}}

Ontology association<br>Each term has an is_a parent in the Uberon Ontology, which has a linkage to an another entity and FANTOM5 samples.Libraries were grouped into mutually exclusive facets according to the FANTOM5 sample ontology mapping to UBERON ontologies.<br><br>link to ontology dataset<br>data

Parents NA

Children NA

Ontology Tree: Loaded from BioPortal

Ontorolgy tree(Small window open)

FF samples<br>It includes FANTOM5 samples that overlay the Uberon ontology



Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with {{{id}}} ({{{name}}}), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

No analysis results







"{{{obo_creation_date}}}" contains an extrinsic dash or other characters that are invalid for a date interpretation.




Property "Property value" (as page type) with input value "{{{property_value}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.

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