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20 changes: 10 additions & 10 deletions ensembl/htdocs/info/genome/variation/phenotype/phenotype_annotation.html
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Expand Up @@ -76,16 +76,16 @@ <h2 id="phenotype_classes">Phenotype classes</h2>
<table class="ss" style="width:auto">
<tr> <th>Classes</th> <th style="border-left:1px solid #BBB"> Example phenotypes</th> <th style="border-left:1px solid #BBB">Example variants</th></tr> <tr>
<td><b>trait</b></td>
<td style="border-left:1px solid #BBB">'Inborn genetic diseases' from <a href="https://www.ncbi.nlm.nih.gov/clinvar/">ClinVar</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs376574181">rs376574181</a></td>
<td style="border-left:1px solid #BBB">'OSTEOGENESIS IMPERFECTA' from <a href="https://www.ncbi.nlm.nih.gov/clinvar/">ClinVar</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs193922173">rs193922173</a></td>
</tr> <tr class="bg2">
<td><b>tumour</b></td>
<td style="border-left:1px solid #BBB">'Lung tumour' from <a href="https://cancer.sanger.ac.uk/cosmic">COSMIC</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=COSV67207411">COSV67207411</a></td>
<td style="border-left:1px solid #BBB">'Central nervous system tumour' from <a href="https://cancer.sanger.ac.uk/cosmic">COSMIC</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=COSV99527653">COSV99527653</a></td>
</tr> <tr>
<td><b>non_specified</b></td>
<td style="border-left:1px solid #BBB">'not specified' from <a href="https://www.ncbi.nlm.nih.gov/clinvar/">ClinVar</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs751840065">rs751840065</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs1414372233">rs1414372233</a></td>
</tr>
</table>
<!-- Data pheno_class - end -->
Expand All @@ -107,27 +107,27 @@ <h2 id="phenotype_ontologies">Phenotype/disease ontologies</h2>
<tr>
<td><b>CMO</b></td>
<td><a href="https://www.ebi.ac.uk/ols/ontologies/cmo">Clinical Measurement Ontology</a></td>
<td style="border-left:1px solid #BBB"><span id="cmo_version"></span></td>
<td style="border-left:1px solid #BBB"><span id="cmo_version">2.252</span></td>
</tr>
<tr class="bg2">
<td><b>EFO</b></a></td>
<td><a href="https://www.ebi.ac.uk/efo">Experimental Factor Ontology</a></td>
<td style="border-left:1px solid #BBB"><span id="efo_version">3.76.0</span></td>
<td style="border-left:1px solid #BBB"><span id="efo_version">3.80.0</span></td>
</tr>
<tr>
<td><b>HPO</b></td>
<td><a href="http://www.human-phenotype-ontology.org">Human Phenotype Ontology</a></td>
<td style="border-left:1px solid #BBB"><span id="hp_version">2025-01-16</span></td>
<td style="border-left:1px solid #BBB"><span id="hp_version">2025-05-06</span></td>
</tr>
<tr class="bg2">
<td><b>MP</b></td>
<td><a href="http://www.informatics.jax.org/vocab/mp_ontology/">Mammalian Phenotype Ontology</a></td>
<td style="border-left:1px solid #BBB"><span id="mp_version">2025-01-30</span></td>
<td style="border-left:1px solid #BBB"><span id="mp_version">2025-07-29</span></td>
</tr>
<tr>
<td><b>VT</b></td>
<td><a href="https://www.ebi.ac.uk/ols/ontologies/vt">Vertebrate Trait Ontology</a></td>
<td style="border-left:1px solid #BBB"><span id="vt_version"></span>2024-05-15</td>
<td style="border-left:1px solid #BBB"><span id="vt_version"></span>2025-07-15</td>
</tr>

</tbody>
Expand Down
179 changes: 179 additions & 0 deletions ensembl/htdocs/info/genome/variation/species/populations.html
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Expand Up @@ -1966,7 +1966,186 @@ <h3>Populations from the <a href="https://www.ebi.ac.uk/eva/?eva-study=PRJEB342
<td>Population from EVA study PRJEB34225</td>
</tr>
</table>
<div style="padding-left:0px;padding-bottom:3px;margin-top:50px;margin-bottom:20px">
<a href="/Sus_scrofa/Info/Index" title="Sus scrofa Ensembl Home page" style="vertical-align:middle" target="_blank"><img src="/i/species/Sus_scrofa.png" alt="Sus_scrofa" class="badge-48" style="float:none;margin-right:4px;vertical-align:middle" /></a>
<h2 id="Sus_scrofa" style="display:inline;color:#333">Sus scrofa<span class="small vdoc_species_sci_name"> (Pig)</span></h2>
</div>
<div style="margin-left:10px">

<h3>Populations from the <a href="https://www.ebi.ac.uk/eva/?eva-study=PRJEB93975" target="_blank" style="text-decoration:none">EVA study PRJEB93975</a></h3>
<table id="eva_study_prjeb93975" class="ss" style="margin-bottom:5px">

<tr>
<th style="width:200px">Name</th>
<th style="width:36px">Size</th>
<th>Description</th>
</tr>

<tr class="supergroup">
<td><b>PRJEB93975:ALL</b></td>
<td style="text-align:right">127</td>
<td>ALL populations from EVA study PRJEB93975</td>
</tr>
<tr class="subgroup">
<td><ul style="margin:0px"><li style="margin:0px"><b>PRJEB93975:SWC</b></li></ul></td>
<td style="text-align:right">57</td>
<td>South Western China super-population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Tibetan</b></li></ul></td>
<td style="text-align:right">29</td>
<td>Tibetan population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Wujin</b></li></ul></td>
<td style="text-align:right">3</td>
<td>Wujin population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Yanan</b></li></ul></td>
<td style="text-align:right">3</td>
<td>Yanan population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Neijiang</b></li></ul></td>
<td style="text-align:right">3</td>
<td>Neijiang population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Xiaoer</b></li></ul></td>
<td style="text-align:right">7</td>
<td>Xiaoer population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Hechuan</b></li></ul></td>
<td style="text-align:right">7</td>
<td>Hechuan population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:cwb1</b></li></ul></td>
<td style="text-align:right">3</td>
<td>cwb1 population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Bamei</b></li></ul></td>
<td style="text-align:right">1</td>
<td>Bamei population from EVA study PRJEB93975</td>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Rongchang</b></li></ul></td>
<td style="text-align:right">1</td>
<td>Rongchang population from EVA study PRJEB93975</td>
</tr>
<tr class="subgroup">
<td><ul style="margin:0px"><li style="margin:0px"><b>PRJEB93975:SCC</b></li></ul></td>
<td style="text-align:right">57</td>
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<td style="text-align:right">57</td>
<td style="text-align:right">48</td>

<td>South Central China super-population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Penzhou</b></li></ul></td>
<td style="text-align:right">2</td>
<td>Penzhou population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Ningxiang</b></li></ul></td>
<td style="text-align:right">17</td>
<td>Ningxiang population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Debao</b></li></ul></td>
<td style="text-align:right">7</td>
<td>Debao population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Qinshaohua</b></li></ul></td>
<td style="text-align:right">7</td>
<td>Qinshaohua population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Daweizi</b></li></ul></td>
<td style="text-align:right">7</td>
<td>Daweizi population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Shaziling</b></li></ul></td>
<td style="text-align:right">7</td>
<td>Shaziling population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Bama-miniature</b></li></ul></td>
<td style="text-align:right">1</td>
<td>Bama-miniature population from EVA study PRJEB93975</td>
</tr>
<tr class="subgroup">
<td><ul style="margin:0px"><li style="margin:0px"><b>PRJEB93975:EC</b></li></ul></td>
<td style="text-align:right">12</td>
<td>Eastern China super-population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Jinhua</b></li></ul></td>
<td style="text-align:right">4</td>
<td>Jinhua population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Tiegu</b></li></ul></td>
<td style="text-align:right">7</td>
<td>Tiegu population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Meishan</b></li></ul></td>
<td style="text-align:right">1</td>
<td>Meishan population from EVA study PRJEB93975</td>
</tr>
<tr class="subgroup">
<td><ul style="margin:0px"><li style="margin:0px"><b>PRJEB93975:WE</b></li></ul></td>
<td style="text-align:right">12</td>
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<td style="text-align:right">12</td>
<td style="text-align:right">5</td>

<td>Western Europe super-population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Hampshire</b></li></ul></td>
<td style="text-align:right">1</td>
<td>Hampshire population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Berkshire</b></li></ul></td>
<td style="text-align:right">1</td>
<td>Berkshire population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Landrace</b></li></ul></td>
<td style="text-align:right">1</td>
<td>Landrace population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Pietrain</b></li></ul></td>
<td style="text-align:right">1</td>
<td>Pietrain population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:LargeWhite</b></li></ul></td>
<td style="text-align:right">1</td>
<td>LargeWhite population from EVA study PRJEB93975</td>
</tr>
<tr class="subgroup">
<td><ul style="margin:0px"><li style="margin:0px"><b>PRJEB93975:Others</b></li></ul></td>
<td style="text-align:right">5</td>
<td>Others super-population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:USMARC</b></li></ul></td>
<td style="text-align:right">1</td>
<td>USMARC population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:Duroc</b></li></ul></td>
<td style="text-align:right">1</td>
<td>Duroc population from EVA study PRJEB93975</td>
</tr>
<tr class="bg2">
<td><ul style="margin:0px; padding-left:60px"><li style="margin:0px"><b>PRJEB93975:PK-15_cell_line</b></li></ul></td>
<td style="text-align:right">3</td>
<td>PK-15_cell_line population from EVA study PRJEB93975</td>
</tr>
</table>

<div style="margin-bottom:35px"></div>
</div><!-- Data populations - end -->
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