From 002883b0764e7efcfc91706b88d54710c8251abd Mon Sep 17 00:00:00 2001
From: Diana Lemos <44366649+dglemos@users.noreply.github.com>
Date: Mon, 16 Dec 2024 10:41:47 +0000
Subject: [PATCH] Deprecate plugin 114 (#671)
* Update docs pointer to latest version (#668)
* Deprecate DisGeNET
* Fix conflict
---------
Co-authored-by: Natalie Willhoft <70575561+nwillhoft@users.noreply.github.com>
---
lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm | 25 ---------------------
root/documentation/vep.conf | 30 --------------------------
2 files changed, 55 deletions(-)
diff --git a/lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm b/lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm
index 9a3e1042..8ac8b918 100644
--- a/lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm
+++ b/lib/EnsEMBL/REST/Model/ga4gh/Beacon.pm
@@ -768,7 +768,6 @@ sub configure_vep {
'Mastermind' => '0,0,1',
'GO' => '1',
'Phenotypes' => '1',
- 'DisGeNET' => 'disease=1',
'CADD' => '1',
'EVE' => '1',
'SpliceAI' => '1'
@@ -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 = [];
@@ -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
@@ -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);
@@ -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;
@@ -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;
@@ -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);
diff --git a/root/documentation/vep.conf b/root/documentation/vep.conf
index 4bebbfc6..8e09b648 100644
--- a/root/documentation/vep.conf
+++ b/root/documentation/vep.conf
@@ -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>)
@@ -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>)
@@ -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>)
@@ -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>)
@@ -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>)
@@ -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>)
--
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