Template:UBERON: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
mNo edit summary |
||
| (56 intermediate revisions by 4 users not shown) | |||
| Line 1: | Line 1: | ||
{{Loading|loadingimage=sprites.gif}} | |||
<html> | |||
<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; | |||
} | |||
div.b { | |||
width: 20%; | |||
float: right; | |||
padding:5px; | |||
margin:5px; | |||
} | |||
div.description | |||
{ | |||
width:auto; | |||
height:auto; | |||
overflow:auto; | |||
} | |||
</style> | |||
</html> | |||
<div class="description"> | |||
<table> | <table> | ||
<tr><th scope="row" align="right" valign="top"> [[Property: | {{#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:{{{ | {{#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"> | ||
{{#if:{{{ | <!-- | ||
{{#if:{{{ | <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"> | ||
{{#if:{{{ | --> | ||
{{ | <span style="background:gainsboro;"> from <a href="http://lifesciencedb.jp/bp3d/">BodyParts3D</a></span> | ||
{{#if:{{{ | </html> | ||
{{#if:{{{ | {{#set:bp3d_img_id={{#replace:{{{bp3d_img_id}}}|:|}}}} | ||
|{{#set:bp3d_img_id=}} | |||
{{#if:{{{subset}}}|<tr><th scope="row" align="right" valign="top"> | }} | ||
{{ | <html> | ||
{{#if:{{{ | <script type="text/javascript" language="javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script> | ||
{{#if:{{{ | <script type="text/javascript" language="javascript" src="/resource_browser/rb_js/datatables/media/js/jquery.dataTables.js"></script> | ||
{{#if:{{{ | <script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.min.js"></script> | ||
{{#if:{{{ | <script type="text/javascript" language="javascript" > | ||
</ | |||
{{# | |||
== | |||
< | |||
== | |||
$(document).ready(function() { | |||
{{ | if( $('.ont_enrich_ffcp').length ) { | ||
var oTable= $('.ont_enrich_ffcp').DataTable({ | |||
dom: 'Blfrti', | |||
scrollY: "300px", | |||
scrollCollapse: true, | |||
paging: false, | |||
order: [[0,'asc']], | |||
buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |||
columnDefs: [{ width: "100px", targets: [0], type: "html-num"}], | |||
columns: [null, | |||
{ render: function ( data, type, row, meta ) { | |||
var title = data.split("#")[0]; | |||
return "<a href=\"/resource_browser/index.php/"+title+"\">"+title+"</a>"; | |||
}, | |||
}, | |||
null | |||
] | |||
}); | |||
} | |||
else | |||
{ | |||
} | |||
} ); | |||
</script> | |||
</html> | |||
{{#ask:[[ancestors_in_anatomy_facet::{{FULLPAGENAME}}]]|[[sample_species::Chicken (Gallus gallus)]]|?name=|limit=10|format=ul|headers=hide|intro= | {{Fontsize|3|Ontology association}}{{#info:<br>Each term has an is_a parent in the Uberon Ontology, which has a linkage to an another entity and FANTOM5 samples.Libraries were grouped into mutually exclusive facets according to the FANTOM5 sample ontology mapping to UBERON ontologies. | ||
<br> | |||
<br>link to ontology dataset | |||
<br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ff-phase1-prerelease-20130717.obo data] | |||
}} | |||
---- | |||
{{Fontsize|3|Parents}} | |||
{{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{is_a}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{disjoint_from}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{union_of}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{derives_from}}}|:|0}}|1|0}} +{{#if:{{#pos:{{{has_quality}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{located_in}}}|:|0}}|1|0}}+{{#if:{{#pos:{{{part_of}}}|:|0}}|1|0}} }} |NA|<table> | |||
{{#if:{{{is_a}}}|<tr><th width=100 align="right">is_a:</th><td>{{#arraymap:{{{is_a}}}|;;|$|[[$]]({{#show:$|?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=$}}}} | ||
| Line 54: | Line 133: | ||
{{#arraymap:{{{part_of}}}|;;|$|{{#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]] | ||
Latest revision as of 15:45, 13 February 2020
| Name: | {{{name}}} | ||
|---|---|---|---|
| Namespace: | {{{namespace}}} | ||
| Definition: | {{{def}}} | ||
| Xrefs: |
| ||
| 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.
