Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Deprecate DisGeNET (release 114) #670

Merged
merged 1 commit into from
Dec 12, 2024
Merged

Deprecate DisGeNET (release 114) #670

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 0 additions & 25 deletions lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm
View file
Open in desktop
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
View file
Open in desktop
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