Template:EFO: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
mNo edit summary |
||
| (8 intermediate revisions by the same user not shown) | |||
| Line 67: | Line 67: | ||
<br> | <br> | ||
<br>link to ontology dataset | <br>link to ontology dataset | ||
<br>[ | <br>[//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ff-phase1-prerelease-20130717.obo data] | ||
}} | }} | ||
---- | ---- | ||
| Line 77: | Line 77: | ||
{{#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: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}} | {{#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/CL BioPortal] == | == Ontology Tree: Loaded from [http://purl.bioontology.org/ontology/CL 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=46604&nodeid=</html>{{{id}}}<html>&server=http://rest.bioontology.org/bioportal" pluginspage="http://www.adobe.com/go/getflashplayer"></embed></object></html> | <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=46604&nodeid=</html>{{{id}}}<html>&server=http://rest.bioontology.org/bioportal" pluginspage="http://www.adobe.com/go/getflashplayer"></embed></object></html> | ||
| Line 87: | Line 86: | ||
{{Fontsize|3|FF samples}}{{#info:<br>It includes FANTOM5 samples that overlay the [http://cellontology.org/ Cell] ontology.}} | {{Fontsize|3|FF samples}}{{#info:<br>It includes FANTOM5 samples that overlay the [http://cellontology.org/ Cell] ontology.}} | ||
---- | ---- | ||
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Human (Homo sapiens)]][[name::+]][[datafreeze_phase:: | {{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Human (Homo sapiens)]][[name::+]][[datafreeze_phase::2]]|?name=|limit=10|format=ul|headers=hide|intro=<b>Human (Homo sapiens)</b>}} | ||
{{#ask:[[ancestors_in_cell_lineage_facet::{{FULLPAGENAME}}]]|[[sample_species::Mouse (Mus musculus)]][[name::+]][[datafreeze_phase:: | {{#ask:[[ancestors_in_cell_lineage_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_cell_lineage_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_cell_lineage_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_cell_lineage_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_cell_lineage_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>}} | ||
| Line 97: | Line 96: | ||
<br><br> | <br><br> | ||
link to source dataset <br> | link to source dataset <br> | ||
human : [ | human : [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/hg19exp_cell_types_general_term_excluded.txt.gz data] <br> | ||
mouse : [ | mouse : [//fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/mm9exp_cell_types_general_term_excluded.txt.gz data] | ||
}} | }} | ||
---- | ---- | ||
| Line 121: | Line 120: | ||
{{#arraymap:{{{obo_creation_date}}}|;;|$|{{#set:obo_creation_date=$}}}} | {{#arraymap:{{{obo_creation_date}}}|;;|$|{{#set:obo_creation_date=$}}}} | ||
{{#if: {{#pos:{{{adjacent_to}}}|:}} |{{#arraymap:{{{adjacent_to}}}|;;|$|{{#set:adjacent_to=$}}}}}} | {{#if: {{#pos:{{{adjacent_to}}}|:}} |{{#arraymap:{{{adjacent_to}}}|;;|$|{{#set:adjacent_to=$}}}}}} | ||
{{#arraymap:{{{derives_from}}}|;;|$|{{#set:derives_from=$}}}} | {{#arraymap:{{{derives_from|}}}|;;|$|{{#set:derives_from=$}}}} | ||
{{#arraymap:{{{develops_from}}}|;;|$|{{#set:develops_from=$}}}} | {{#arraymap:{{{develops_from|}}}|;;|$|{{#set:develops_from=$}}}} | ||
{{#arraymap:{{{has_quality}}}|;;|$|{{#set:has_quality=$}}}} | {{#arraymap:{{{has_quality}}}|;;|$|{{#set:has_quality=$}}}} | ||
{{#arraymap:{{{located_in}}}|;;|$|{{#set:located_in=$}}}} | {{#arraymap:{{{located_in}}}|;;|$|{{#set:located_in=$}}}} | ||
Latest revision as of 15:18, 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 Cell 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 Cell 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 Cell ontology.
Enrichment analysis: top 100 FFCP enriched with this ontology termTOP 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 for this cluster
"{{{obo_creation_date}}}" contains an extrinsic dash or other characters that are invalid for a date interpretation.
