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Public docs update (e113) - Variation docs (#815)
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nakib103 authored Aug 13, 2024
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36 changes: 18 additions & 18 deletions ensembl/htdocs/info/genome/variation/phenotype/phenotype_annotation.html
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Expand Up @@ -26,10 +26,10 @@ <h2 id="clin_significance">Clinical significance</h2>
<tr><td style="text-align:center"><img src="/i/val/clinsig_pathogenic.png" title="pathogenic"/></td><td>pathogenic</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs5051">rs5051</a></td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/StructuralVariation/Evidence?sv=esv2830397">esv2830397</a></td></tr>
<tr class="bg2"><td style="text-align:center"><img src="/i/val/clinsig_pathogenic-low-penetrance.png" title="pathogenic low penetrance"/></td><td>pathogenic low penetrance</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs6025">rs6025</a></td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/StructuralVariation/Evidence?sv=nsv7093359">nsv7093359</a></td></tr>
<tr><td style="text-align:center"><img src="/i/val/clinsig_likely-pathogenic.png" title="likely pathogenic"/></td><td>likely pathogenic</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs381418">rs381418</a></td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/StructuralVariation/Evidence?sv=esv1791726">esv1791726</a></td></tr>
<tr class="bg2"><td style="text-align:center"><img src="/i/val/clinsig_likely-pathogenic-low-penetrance.png" title="likely pathogenic low penetrance"/></td><td>likely pathogenic low penetrance</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs202173660">rs202173660</a></td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/StructuralVariation/Evidence?sv=nsv6314862">nsv6314862</a></td></tr>
<tr class="bg2"><td style="text-align:center"><img src="/i/val/clinsig_likely-pathogenic-low-penetrance.png" title="likely pathogenic low penetrance"/></td><td>likely pathogenic low penetrance</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs563816801">rs563816801</a></td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/StructuralVariation/Evidence?sv=nsv6314862">nsv6314862</a></td></tr>
<tr><td style="text-align:center"><img src="/i/val/clinsig_protective.png" title="protective"/></td><td>protective</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs1050501">rs1050501</a></td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/StructuralVariation/Evidence?sv=nsv1398576">nsv1398576</a></td></tr>
<tr class="bg2"><td style="text-align:center"><img src="/i/val/clinsig_established-risk-allele.png" title="established risk allele"/></td><td>established risk allele</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs1801581">rs1801581</a></td><td style="border-left:1px solid #BBB">-</td></tr>
<tr><td style="text-align:center"><img src="/i/val/clinsig_likely-risk-allele.png" title="likely risk allele"/></td><td>likely risk allele</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs374351038">rs374351038</a></td><td style="border-left:1px solid #BBB">-</td></tr>
<tr class="bg2"><td style="text-align:center"><img src="/i/val/clinsig_established-risk-allele.png" title="established risk allele"/></td><td>established risk allele</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs1801466">rs1801466</a></td><td style="border-left:1px solid #BBB">-</td></tr>
<tr><td style="text-align:center"><img src="/i/val/clinsig_likely-risk-allele.png" title="likely risk allele"/></td><td>likely risk allele</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs10754555">rs10754555</a></td><td style="border-left:1px solid #BBB">-</td></tr>
<tr class="bg2"><td style="text-align:center"><img src="/i/val/clinsig_risk-factor.png" title="risk factor"/></td><td>risk factor</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs699">rs699</a></td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/StructuralVariation/Evidence?sv=nsv3871638">nsv3871638</a></td></tr>
<tr><td style="text-align:center"><img src="/i/val/clinsig_not-provided.png" title="not provided"/></td><td>not provided</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs1921">rs1921</a></td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/StructuralVariation/Evidence?sv=nsv984836">nsv984836</a></td></tr>
<tr class="bg2"><td style="text-align:center"><img src="/i/val/clinsig_other.png" title="other"/></td><td>other</td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Explore?v=rs5275">rs5275</a></td><td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/StructuralVariation/Evidence?sv=nsv4769276">nsv4769276</a></td></tr>
Expand All @@ -39,25 +39,25 @@ <h2 id="clin_significance">Clinical significance</h2>
</table>
<p>Further explanations about the clinical significance terms are available on the <a href="http://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/">ClinVar website</a>.</p>
<h3>ClinVar rating</h3>
<p>We use the <a href="http://www.ncbi.nlm.nih.gov/clinvar/docs/details/#interpretation">ClinVar "four-star" rating</a> system to indicate the quality of classification/validation of the variant:</p>
<p>We use the <a href="https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status">ClinVar "four-star" rating</a> system to indicate the quality of classification/validation of the variant:</p>
<table class="ss" style="width:auto">
<tr><th>Rating</th><th>Description</th><th style="border-left:1px solid #BBB">Example</th></tr>
<tr>
<td><span class="_ht" title="not classified by submitter"><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/></span></td>
<td>not classified by submitter</td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs1772975334">rs1772975334</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs1561693779">rs1561693779</a></td>
</tr> <tr class="bg2">
<td><span class="_ht" title="classified by single submitter"><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/></span></td>
<td>classified by single submitter</td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs886038205">rs886038205</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs761189368">rs761189368</a></td>
</tr> <tr>
<td><span class="_ht" title="classified by multiple submitters"><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/></span></td>
<td>classified by multiple submitters</td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs115070660">rs115070660</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs368765062">rs368765062</a></td>
</tr> <tr class="bg2">
<td><span class="_ht" title="reviewed by expert panel"><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/><img style="vertical-align:top" src="/i/val/grey_star.png" alt="grey"/></span></td>
<td>reviewed by expert panel</td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs118192163">rs118192163</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs1554080082">rs1554080082</a></td>
</tr> <tr>
<td><span class="_ht" title="practice guideline"><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/><img style="vertical-align:top" src="/i/val/gold_star.png" alt="gold"/></span></td>
<td>practice guideline</td>
Expand All @@ -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">'Tuberous sclerosis syndrome' 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=rs1800725">rs1800725</a></td>
<td style="border-left:1px solid #BBB">'Malignant tumor of urinary bladder' 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=rs786202457">rs786202457</a></td>
</tr> <tr class="bg2">
<td><b>tumour</b></td>
<td style="border-left:1px solid #BBB">'Prostate 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=COSV65031212">COSV65031212</a></td>
<td style="border-left:1px solid #BBB">'Breast 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=COSV59161128">COSV59161128</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=rs148386572">rs148386572</a></td>
<td style="border-left:1px solid #BBB"><a href="/Homo_sapiens/Variation/Phenotype?v=rs587778020">rs587778020</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">2019-02-19</span></td>
<td style="border-left:1px solid #BBB"><span id="cmo_version"></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">3.49.0</span></td>
<td style="border-left:1px solid #BBB"><span id="efo_version">3.66.0</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">2022-06-11</span></td>
<td style="border-left:1px solid #BBB"><span id="hp_version">2024-04-26</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"></span></td>
<td style="border-left:1px solid #BBB"><span id="mp_version">2024-04-23</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></td>
<td style="border-left:1px solid #BBB"><span id="vt_version"></span>2024-05-15</td>
</tr>

</tbody>
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