Personal tools

Template:UBERON: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
mNo edit summary
 
(98 intermediate revisions by 4 users not shown)
Line 1: Line 1:
<table>
{{Loading|loadingimage=sprites.gif}}
<tr><th scope="row" align="right"> [[Property:name|name]]:</th><td>[[name::{{{name}}}]]</td></tr>
<html>
<tr><th scope="row" align="right"> [[Property:def|def]]:</th><td>{{#show:{{FULLPAGENAME}}|?def}}|}}</td></tr>
<style type="text/css" title="currentStyle">
@import "/5/sstar/rb_js/html5button/datatables.css";
table.details td { width:30%; background-color: #EAEBFF;}
table.details th { width:10%; background-color: #5A5FB5; color: white;}
div.a {
  width: 80%;
  float: left;
  padding:5px;
  margin:5px;
}


</table>
div.b {
  width: 20%;
  float: right;
  padding:5px;
  margin:5px;
}


div.description
{
width:auto;
height:auto;
overflow:auto;
}
</style>
</html>
<div class="description">
<table>
{{#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" language="javascript" >


*id: [[id::{{{id}}}]]
$(document).ready(function() {
*name: [[name::{{{name}}}]]
{{#if: {{{namespace}}} | *namespace: {{#show:{{FULLPAGENAME}}|?namespace}}|}}{{#if: {{{def}}} | *def: {{#show:{{FULLPAGENAME}}|?def}}|}}{{#if: {{{xref}}} | *xref: {{#show:{{FULLPAGENAME}}|?xref}}|}}{{#if: {{{is_a}}} | *is_a: {{#show:{{FULLPAGENAME}}|?is_a}}|}}{{#if: {{{synonym}}} | *synonym: {{#show:{{FULLPAGENAME}}|?synonym}}|}}{{#if: {{{comment}}} | *comment: {{#show:{{FULLPAGENAME}}|?comment}}|}}{{#if: {{{alt_id}}} | *alt_id: {{#show:{{FULLPAGENAME}}|?alt_id}}|}}{{#if: {{{disjoint_from}}} | *disjoint_from: {{#show:{{FULLPAGENAME}}|?disjoint_from}}|}}{{#if: {{{union_of}}} | *union_of: {{#show:{{FULLPAGENAME}}|?union_of}}|}}{{#if: {{{created_by}}} | *created_by: {{#show:{{FULLPAGENAME}}|?created_by}}|}}{{#if: {{{subset}}} | *subset: {{#show:{{FULLPAGENAME}}|?subset}}|}}{{#if: {{{obo_creation_date}}} | *creation_date: {{#show:{{FULLPAGENAME}}|?obo_creation_date}}|}}{{#if: {{{adjacent_to}}} | *adjacent_to: {{#show:{{FULLPAGENAME}}|?adjacent_to}}|}}{{#if: {{{derives_from}}} | *derives_from: {{#show:{{FULLPAGENAME}}|?derives_from}}|}}{{#if: {{{develops_from}}} | *develops_from: {{#show:{{FULLPAGENAME}}|?develops_from}}|}}{{#if: {{{has_quality}}} | *has_quality: {{#show:{{FULLPAGENAME}}|?has_quality}}|}}{{#if: {{{located_in}}} | *located_in: {{#show:{{FULLPAGENAME}}|?located_in}}|}}{{#if: {{{part_of}}} | *part_of: {{#show:{{FULLPAGENAME}}|?part_of}}|}}
== Children ==
{{#ask:[[is_a::{{FULLPAGENAME}}]]|format=list|intro=*|outro= is_a: {{FULLPAGENAME}}}}{{#ask:[[disjoint_from::{{FULLPAGENAME}}]]|format=list|intro=*|outro= disjoint_from: {{FULLPAGENAME}}}}{{#ask:[[adjacent_to::{{FULLPAGENAME}}]]|format=list|intro=*|outro= adjacent_to: {{FULLPAGENAME}}}}{{#ask:[[derives_from::{{FULLPAGENAME}}]]|format=list|intro=*|outro= derives_from: {{FULLPAGENAME}}}}{{#ask:[[develops_from::{{FULLPAGENAME}}]]|format=list|intro=*|outro= develops_from: {{FULLPAGENAME}}}}{{#ask:[[has_quality::{{FULLPAGENAME}}]]|format=list|intro=*|outro= has_quality: {{FULLPAGENAME}}}}{{#ask:[[located_in::{{FULLPAGENAME}}]]|format=list|intro=*|outro= located_in: {{FULLPAGENAME}}}}{{#ask:[[part_of::{{FULLPAGENAME}}]]|format=list|intro=*|outro= part_of: {{FULLPAGENAME}}}}
== Ontology Tree ==
<onttree nodeid={{{id}}} />
== FF samples ==
{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Human (Homo sapiens)]]|?name=|limit=10|format=ul|headers=hide|intro='''Human (Homo sapiens)'''}}
 
{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Mouse (Mus musculus)]]|?name=|limit=10|format=ul|headers=hide|intro='''Mouse (Mus musculus)'''}}


{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Rat (Rattus rattus)]]|?name=|limit=10|format=ul|headers=hide|intro='''Rat (Rattus rattus)'''}}
if( $('.ont_enrich_ffcp').length ) {
var oTable= $('.ont_enrich_ffcp').DataTable({
        dom: 'Blfrti',
scrollY: "300px",
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
{
}
 


{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Dog (Canis lupus familaris)]]|?name=|limit=10|format=ul|headers=hide|intro='''Dog (Canis lupus familaris)'''}}
} );
</script>
</html>


{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Chicken (Gallus gallus)]]|?name=|limit=10|format=ul|headers=hide|intro='''Chicken (Gallus gallus)'''}}
{{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] ==
{{#ncbo_onttree2:{{#explode:{{{id}}}|:|0}}|{{#explode:{{{id}}}|:|1}}}}
<!--
<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:{{{namespace}}}|;;|$|{{#set:namespace=$}}}}
Line 43: Line 133:
{{#arraymap:{{{part_of}}}|;;|$|{{#set:part_of=$}}}}
{{#arraymap:{{{part_of}}}|;;|$|{{#set:part_of=$}}}}
{{#arraymap:{{{property_value}}}|;;|$|{{#set:property_value=$}}}}
{{#arraymap:{{{property_value}}}|;;|$|{{#set:property_value=$}}}}
{{#set:id={{{id}}}}}


[[Category:Uber_Anatomy_Ontology]]
[[Category:Uber_Anatomy_Ontology]]
__NOTOC__

Latest revision as of 15:45, 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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Template:UBERON&oldid=4575720"