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Deprecate DisGeNET
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@dglemos @nwillhoft
dglemos authored and nwillhoft committed Dec 12, 2024
1 parent 7f165f7 commit 8cba57b
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25 changes: 0 additions & 25 deletions lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -768,7 +768,6 @@ sub configure_vep {
'Mastermind' => '0,0,1',
'GO' => '1',
'Phenotypes' => '1',
'DisGeNET' => 'disease=1',
'CADD' => '1',
'EVE' => '1',
'SpliceAI' => '1'
Expand Down Expand Up @@ -928,7 +927,6 @@ sub get_dataset_allele_response {
my @clinical; # clinicalInterpretations (part of variantLevelData)
my %unique_phenotypes;
my $var;
my $disgenet = [];
my $frequency = [];
my $cadd = [];

Expand Down Expand Up @@ -984,7 +982,6 @@ sub get_dataset_allele_response {

$molecular_interactions = $vep_consequence_results->{molecular_interactions};
$gene_ontology = $vep_consequence_results->{gene_ontology};
$disgenet = $vep_consequence_results->{disgenet};
$cadd = $vep_consequence_results->{cadd};

# Frequency data from gnomAD
Expand Down Expand Up @@ -1049,7 +1046,6 @@ sub get_dataset_allele_response {

$result_details->{variantLevelData}->{clinicalInterpretations} = \@clinical if (scalar @clinical > 0);

$result_details->{variantLevelData}->{phenotypicEffects} = $disgenet if (scalar @{$disgenet} > 0);
$result_details->{variantLevelData}->{pathogenicityPredictions} = $cadd if (scalar @{$cadd} > 0);

$result_details->{FrequencyInPopulations}->{frequencies} = $frequency if (scalar @{$frequency} > 0);
Expand Down Expand Up @@ -1114,8 +1110,6 @@ sub get_vep_molecular_attribs {
my %molecular_interactions;
my @intact_data;
my @phenotypes;
my %unique_disgenet;
my @disgenet_data;
my @cadd_scores;
my %cadd_unique;

Expand All @@ -1139,24 +1133,6 @@ sub get_vep_molecular_attribs {
}
}

# DisGeNET
if($transcript_consequences->{'disgenet'}) {
foreach my $disgenet (@{$transcript_consequences->{'disgenet'}}) {
my $key = $disgenet->{score} . '-' . $disgenet->{pmid} . '-' . $disgenet->{diseaseName};
if(!$unique_disgenet{$key}) {
my $disgenet_obj;
$disgenet_obj->{annotatedWith}->{toolName} = 'DisGeNET';
$disgenet_obj->{annotatedWith}->{version} = 'v7';
$disgenet_obj->{conditionId} = $disgenet->{diseaseName};
$disgenet_obj->{evidenceType}->{id} = "isDefinedBy";
$disgenet_obj->{evidenceType}->{label} = 'PMID:' . $disgenet->{pmid};
$disgenet_obj->{score} = $disgenet->{score};
push @disgenet_data, $disgenet_obj;
$unique_disgenet{$key} = 1;
}
}
}

# CADD
if($transcript_consequences->{'cadd_phred'} || $transcript_consequences->{'cadd_raw'}) {
my $cadd;
Expand All @@ -1183,7 +1159,6 @@ sub get_vep_molecular_attribs {

$results{molecular_interactions} = \%molecular_interactions;
$results{gene_ontology} = \@gene_ontology_list;
$results{disgenet} = \@disgenet_data;
$results{cadd} = \@cadd_scores;

return (\%results);
Expand Down
30 changes: 0 additions & 30 deletions root/documentation/vep.conf
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Original file line number Diff line number Diff line change
Expand Up @@ -300,11 +300,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<DisGeNET>
type=Boolean
description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/DisGeNET.pm">plugin details</a>)
default=0
</DisGeNET>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
Expand Down Expand Up @@ -670,11 +665,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<DisGeNET>
type=Boolean
description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/DisGeNET.pm">plugin details</a>)
default=0
</DisGeNET>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
Expand Down Expand Up @@ -1028,11 +1018,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<DisGeNET>
type=Boolean
description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/DisGeNET.pm">plugin details</a>)
default=0
</DisGeNET>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
Expand Down Expand Up @@ -1380,11 +1365,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<DisGeNET>
type=Boolean
description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/DisGeNET.pm">plugin details</a>)
default=0
</DisGeNET>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
Expand Down Expand Up @@ -1743,11 +1723,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<DisGeNET>
type=Boolean
description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/DisGeNET.pm">plugin details</a>)
default=0
</DisGeNET>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
Expand Down Expand Up @@ -2114,11 +2089,6 @@
description=Retrieves overlapping phenotype information (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Phenotypes.pm">plugin details</a>)
default=0
</Phenotypes>
<DisGeNET>
type=Boolean
description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/DisGeNET.pm">plugin details</a>)
default=0
</DisGeNET>
<Mastermind>
type=Boolean
description= Variants that have clinical evidence cited in the medical literature reported by <a target="_blank" href="https://www.genomenon.com/mastermind">Mastermind Genomic Search Engine</a> (<a target="_blank" href="https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/Mastermind.pm">plugin details</a>)
Expand Down

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