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Deprecate disgenet plugin (release 114) #846

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Dec 17, 2024
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Deprecate disgenet plugin (release 114) #846

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4 changes: 0 additions & 4 deletions covid19/conf/vep_plugins_web_config.txt
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Expand Up @@ -39,10 +39,6 @@
"available" => 0
},

DisGeNET => {
"available" => 0
},

SpliceAI => {
"available" => 0
},
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9 changes: 0 additions & 9 deletions docs/htdocs/info/docs/tools/vep/online/input.html
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Expand Up @@ -486,14 +486,6 @@ <h2 id="annotation">Additional annotations</h2>
</p>
</li>

<li><b>DisGeNET</b>
<p>
Report Variant-Disease-PMID associations from the <a href="https://www.disgenet.org/" rel="external">DisGeNET</a> database. This functionality is provided by the
<a href="https://github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/DisGeNET.pm">DisGeNET</a> plugin.<br />
<b>Note:</b> A <a href="https://www.disgenet.org/legal">license</a> is needed for commercial use.
</p>
</li>

<li><b>Mastermind</b>
<p>
Uses the <a href="https://www.genomenon.com/mastermind" rel="external">Mastermind Genomic Search Engine</a> to report variants that have clinical evidence cited in the medical literature. This functionality is provided by the
Expand Down Expand Up @@ -557,7 +549,6 @@ <h2>Regulatory impact</h2>
<h2>Phenotype data and citations</h2>
<div class="form-field"><label class="ff-label"><span class="_ht ht">Phenotypes</span>:</label><div class="ff-right"><p class="ff-checklist"><input class="plugin_enable _stt" type="checkbox"></p></div></div>
<div class="form-field"><label class="ff-label"><span class="_ht ht">Gene Ontology</span>:</label><div class="ff-right"><p class="ff-checklist"><input class="_stt plugin_enable" type="checkbox"></p></div></div>
<div class="form-field"><label class="ff-label"><span class="_ht ht">DisGeNET</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox" class="plugin_enable _stt"></p></div></div>
<div class="form-field"><label class="ff-label"><span class="ht _ht">Mastermind</span>:</label><div class="ff-right"><p class="ff-checklist"><input type="checkbox" class="plugin_enable _stt"></p></div></div></fieldset>
</div>
</div>
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3 changes: 0 additions & 3 deletions docs/htdocs/info/docs/tools/vep/script/vep_download.html
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Expand Up @@ -356,7 +356,6 @@ <h4>New in version 104 <i>(May 2021)</i></h4>
<ul>
<li><a href="//github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/dbNSFP.pm" rel="external">dbNSFP</a> - now supports matching by peptides</li>
<li><a href="//github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/SpliceAI.pm" rel="external">SpliceAI</a> - now compares gene symbols to improve score accuracy</li>
<li><a href="//github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/DisGeNET.pm" rel="external">DisGeNET</a> - improvements have been made to output structure</li>
</ul>
</ul>
</div>
Expand Down Expand Up @@ -397,7 +396,6 @@ <h4>New in version 102 <i>(November 2020)</i></h4>
<li> Web VEP options:
<ul>
<li>Shifting variants in the 3' direction with <a href="vep_options.html#opt_shift_3prime">--shift_3prime</a> and <a href="vep_options.html#opt_shift_genomic">--shift_genomic</a> is now supported through the web interface.</li>
<li><a href="//github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/DisGeNET.pm" rel="external">DisGeNET</a> - <b>new</b>: DisGeNET results are available through the web interface.</li>
<li><a href="//github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/SpliceAI.pm" rel="external">SpliceAI</a> - <b>new</b>: SpliceAI pre-calculated scores are available through the web interface.</li>
</ul>
</li>
Expand Down Expand Up @@ -447,7 +445,6 @@ <h4>New in version 100 <i>(April 2020)</i></h4>
<li>VEP plugins:
<ul>
<li><a href="//github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/SpliceAI.pm" rel="external">SpliceAI</a> - <b>new</b>: SpliceAI is a deep neural network, developed by Illumina, Inc that predicts splice junctions from an arbitrary pre-mRNA transcript sequence.</li>
<li><a href="//github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/DisGeNET.pm" rel="external">DisGeNET</a> - <b>new</b>: DisGeNET is a database containing human variant-disease associations</li>
</ul>
</li>
</ul>
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32 changes: 0 additions & 32 deletions docs/htdocs/info/docs/tools/vep/script/vep_plugins.html
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Expand Up @@ -400,38 +400,6 @@ <h2 id="plugins_existing">Existing plugins</h2>
mv DeNovo.pm ~/.vep/Plugins
./vep -i variations.vcf --plugin DeNovo,ped=samples.ped
./vep -i variations.vcf --plugin DeNovo,ped=samples.ped,full_report=1
</pre></p></p></div></td><td><div class="vdoc_dtype_count" style="white-space:normal;float:left;padding:2px 6px;cursor:default;background-color:#B22222">Variant data</div></td><td><ul style="padding-left:1em"><li><a href="https://metacpan.org/pod/List::MoreUtils" rel="external">List::MoreUtils</a> qw(uniq)</li><li><a href="https://metacpan.org/pod/Cwd" rel="external">Cwd</a></li></ul></td><td>Ensembl</td></tr>
<tr id="DisGeNET" class="bg1 plugin_row" data-category="phenotype_data_and_citations"><td><div style="font-weight:bold"><a rel="external" href="https://github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/DisGeNET.pm">DisGeNET</a></div></td><td><p> This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
adds Variant-Disease-PMID associations from the DisGeNET database.
It is available for GRCh38. <a class="button" href="#disgenet" style="padding:3px 8px 0px 8px !important;height:18px" onclick="show_hide('disgenet');" id="a_disgenet">more</a></p><div id="div_disgenet" style="display:none;word-wrap:break-word;"><p> Please cite the DisGeNET publication alongside the VEP if you use this resource:
<a href="https://academic.oup.com/nar/article/48/D1/D845/5611674">https://academic.oup.com/nar/article/48/D1/D845/5611674</a></p><p> Options are passed to the plugin as key=value pairs:<table class="ss"><thead><tr><th>Argument</th><th>Description</th></tr></thead><tbody>
<tr class="bg1"><td><pre>file</pre></td><td>Path to DisGeNET data file (mandatory).
<tr class="bg2"><td><pre>disease</pre></td><td>Set value to 1 to include the diseases/phenotype names reporting the Variant-PMID association (optional).</p><p><tr class="bg1"><td><pre>rsid</pre></td><td>Set value to 1 to include the dbSNP variant Identifier (optional).
<tr class="bg2"><td><pre>filter_score</pre></td><td>Only reports citations with score greater or equal than input value (optional).
<tr class="bg1"><td><pre>filter_source</pre></td><td>Only reports citations from input sources (optional). Accepted sources are: UNIPROT, CLINVAR, GWASDB, GWASCAT, BEFREE
Separate multiple values with <kbd>&</kbd>.</p><p></td></tr></tbody></table><p>
Output:
Each element of the output includes:
<ul><li>PMID of the publication reporting the Variant-Disease association (default)</li><li>DisGeNET score for the Variant-Disease association (default)</li><li>diseases/phenotype names (optional)</li><li>dbSNP variant Identifier (optional)
</li></ul><p> This plugin uses file <kbd>all_variant_disease_pmid_associations.tsv.gz</kbd>.
File can be downloaded from: <a href="https://www.disgenet.org/downloads">https://www.disgenet.org/downloads</a>.
The following steps are necessary before running this plugin (tested with DisGeNET export date 2020-05-26):</p><p><pre class="code sh_sh">gunzip all_variant_disease_pmid_associations.tsv.gz
awk '($1 ~ /^snpId/ || $2 ~ /NA/) {next} {print $0}' all_variant_disease_pmid_associations.tsv &gt all_variant_disease_pmid_associations_clean.tsv
sort -t $'\t' -k2,2 -k3,3n all_variant_disease_pmid_associations_clean.tsv &gt all_variant_disease_pmid_associations_sorted.tsv
awk '{ gsub (/\t +/, "\t", $0); print}' all_variant_disease_pmid_associations_sorted.tsv &gt all_variant_disease_pmid_associations_final.tsv
bgzip all_variant_disease_pmid_associations_final.tsv
tabix -s 2 -b 3 -e 3 all_variant_disease_pmid_associations_final.tsv.gz
</pre><p> The plugin can then be run as default:
<pre class="code sh_sh">./vep -i variations.vcf --plugin DisGeNET,file=all_variant_disease_pmid_associations_final.tsv.gz
</pre><p> or with an option to include optional data or/and filters:
<pre class="code sh_sh">./vep -i variations.vcf --plugin DisGeNET,file=all_variant_disease_pmid_associations_final.tsv.gz,disease=1
./vep -i variations.vcf --plugin DisGeNET,file=all_variant_disease_pmid_associations_final.tsv.gz,disease=1,filter_source=<kbd>GWASDB&GWASCAT</kbd>
</pre><p> Of notice: this plugin only matches the chromosome and the position in the
chromosome, the alleles are not taken into account to append the DisGeNET data.
The rsid is provided (optional) in the output in order to help to filter the relevant data.</p><p></ul><p><p><h2>Usage examples:</h2> <pre class="code sh_sh">
mv DisGeNET.pm ~/.vep/Plugins
./vep -i variations.vcf --plugin DisGeNET,file=/path/to/disgenet/data.tsv.gz
./vep -i variations.vcf --plugin DisGeNET,file=/path/to/disgenet/data.tsv.gz,disease=1
</pre></p></p></div></td><td><div class="vdoc_dtype_count" style="white-space:normal;float:left;padding:2px 6px;cursor:default;background-color:#009911">Phenotype data and citations</div></td><td><a href="https://metacpan.org/pod/List::MoreUtils" rel="external">List::MoreUtils</a> qw(uniq)</td><td>Ensembl</td></tr>
<tr id="DosageSensitivity" class="bg2 plugin_row" data-category="gene_tolerance_to_change"><td><div style="font-weight:bold"><a rel="external" href="https://github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/DosageSensitivity.pm">DosageSensitivity</a></div></td><td><p> A VEP plugin that retrieves haploinsufficiency and triplosensitivity probability scores
for affected genes from a dosage sensitivity catalogue published in paper -
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4 changes: 0 additions & 4 deletions tools/conf/vep_plugins_web_config.txt
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Expand Up @@ -43,10 +43,6 @@
"available" => 1
},

DisGeNET => {
"available" => 1
},

SpliceAI => {
"available" => 1
},
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23 changes: 0 additions & 23 deletions tools/modules/EnsEMBL/Web/Component/Tools/VEP/Results.pm
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Expand Up @@ -164,15 +164,6 @@ sub content {
}
}

# Overwrite DisGeNET header description
# Description example: "Variant-Disease-PMID associations from the DisGeNET database. The output includes
# the PMID of the publication reporting the Variant-Disease association, DisGeNET score for the Variant-Disease association,
# name of associated disease. Each value is separated by ':'"
# In Web VEP, the values are not separated by ':' and therefore remove it from the description.
if(exists $header_extra_descriptions->{'DisGeNET'}) {
$header_extra_descriptions->{'DisGeNET'} =~ s/ Each value is separated.*//;
}

# Overwrite header description
for (keys %{$header_extra_descriptions}) {
# remove filename from specific plugins
Expand Down Expand Up @@ -241,7 +232,6 @@ sub content {
'REFSEQ_MATCH' => 'RefSeq match',
'HGVS_OFFSET' => 'HGVS offset',
'PHENOTYPES' => 'Associated phenotypes',
'DisGeNET' => 'DisGeNET',
'Mastermind_MMID3' => 'Mastermind URL',
'VAR_SYNONYMS' => 'Variant synonyms',
'IntAct_ap_ac' => 'IntAct affected protein AC',
Expand Down Expand Up @@ -291,9 +281,6 @@ sub content {
elsif ($header eq 'PHENOTYPES'){
$row->{$header} = $self->get_items_in_list($row_id, 'phenotype', 'Phenotype associations', $row->{$header}, $species, 3);
}
elsif ($header eq 'DisGeNET'){
$row->{$header} = $self->get_items_in_list($row_id, 'disgenet', 'DisGeNET', $row->{$header}, $species);
}
elsif ($header eq 'Mastermind_MMID3'){
$row->{$header} = $self->get_items_in_list($row_id, 'mastermind_mmid3', 'Mastermind URL', $row->{$header}, $species);
}
Expand Down Expand Up @@ -1303,16 +1290,6 @@ sub get_items_in_list {
@items_list = $self->prettify_phenotypes(\@items_list, $species);
@items_with_url = @items_list;
}
elsif ($type eq 'disgenet') {
foreach my $entry (@items_list) {
# entry example '18630525:0.02:Malignant_Neoplasms'
$entry =~ s/_/&nbsp;/g;
my @disgenet_value = split /:/, $entry;
my $pmid_url = $hub->get_ExtURL_link($disgenet_value[0], 'EPMC_MED', $disgenet_value[0]);
my $new_entry = $pmid_url . ' <b>Score:</b>&nbsp;' . $disgenet_value[1] . ' <b>Disease:</b>&nbsp;' . $disgenet_value[2];
push (@items_with_url, $new_entry);
}
}
elsif ($type eq 'variant_synonyms') {
my %synonyms;
foreach my $entry (@items_list) {
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7 changes: 0 additions & 7 deletions tools_hive/conf/vep_plugins_hive_config.txt
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Expand Up @@ -75,13 +75,6 @@
]
},

DisGeNET => {
"params" => [
"file=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/all_variant_disease_pmid_associations_final.tsv.gz",
"disease=1"
]
},

SpliceAI => {
"params" => [
"snv=[[ENSEMBL_VEP_PLUGIN_DATA_DIR]]/spliceai_scores.masked.snv.hg38.vcf.gz",
Expand Down