From 8cba57b8003aee74ff958819ec1e228a525a88ce Mon Sep 17 00:00:00 2001 From: dglemos Date: Wed, 11 Dec 2024 10:22:09 +0000 Subject: [PATCH] Deprecate DisGeNET --- 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 (plugin details) default=0 - - type=Boolean - description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (plugin details) - default=0 - type=Boolean description= Variants that have clinical evidence cited in the medical literature reported by Mastermind Genomic Search Engine (plugin details) @@ -670,11 +665,6 @@ description=Retrieves overlapping phenotype information (plugin details) default=0 - - type=Boolean - description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (plugin details) - default=0 - type=Boolean description= Variants that have clinical evidence cited in the medical literature reported by Mastermind Genomic Search Engine (plugin details) @@ -1028,11 +1018,6 @@ description=Retrieves overlapping phenotype information (plugin details) default=0 - - type=Boolean - description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (plugin details) - default=0 - type=Boolean description= Variants that have clinical evidence cited in the medical literature reported by Mastermind Genomic Search Engine (plugin details) @@ -1380,11 +1365,6 @@ description=Retrieves overlapping phenotype information (plugin details) default=0 - - type=Boolean - description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (plugin details) - default=0 - type=Boolean description= Variants that have clinical evidence cited in the medical literature reported by Mastermind Genomic Search Engine (plugin details) @@ -1743,11 +1723,6 @@ description=Retrieves overlapping phenotype information (plugin details) default=0 - - type=Boolean - description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (plugin details) - default=0 - type=Boolean description= Variants that have clinical evidence cited in the medical literature reported by Mastermind Genomic Search Engine (plugin details) @@ -2114,11 +2089,6 @@ description=Retrieves overlapping phenotype information (plugin details) default=0 - - type=Boolean - description=Retrieves Variant-Disease-PMID associations from the DisGeNET database (plugin details) - default=0 - type=Boolean description= Variants that have clinical evidence cited in the medical literature reported by Mastermind Genomic Search Engine (plugin details)