feat: store score components in DB

server/app/graphql/types/interaction_type.rb

@@ -12,6 +12,9 @@ class InteractionType < Types::BaseObject
     field :publications, [Types::PublicationType], null: false
     field :sources, [Types::SourceType], null: false
     field :interaction_score, Float, null: false
+    field :drug_specificity, Float, null: false
+    field :gene_specificity, Float, null: false
+    field :evidence_score, Integer, null: false
 
     def interaction_claims
       Loaders::AssociationLoader.for(Interaction, :interaction_claims).load(object)

server/app/models/interaction.rb

@@ -51,15 +51,29 @@ def interaction_score(known_drug_partners_per_gene = nil, known_gene_partners_pe
     end
   end
 
-  def calculate_interaction_score(known_drug_partners_per_gene = nil, known_gene_partners_per_drug = nil)
-    known_drug_partners_per_gene = Interaction.group(:gene_id).count if known_drug_partners_per_gene.nil?
-    average_known_drug_partners_per_gene = known_drug_partners_per_gene.values.sum / known_drug_partners_per_gene.values.size.to_f
-    known_gene_partners_per_drug = Interaction.group(:drug_id).count if known_gene_partners_per_drug.nil?
-    average_known_gene_partners_per_drug = known_gene_partners_per_drug.values.sum / known_gene_partners_per_drug.values.size.to_f
-    known_drug_partners_for_interaction_gene = known_drug_partners_per_gene[self.gene_id]
-    known_gene_partners_for_interaction_drug = known_gene_partners_per_drug[self.drug_id]
+  def calculate_interaction_score(drug_partners_per_gene = nil, gene_partners_per_drug = nil, update = false)
+    drug_partners_per_gene = Interaction.group(:gene_id).count if drug_partners_per_gene.nil?
+    avg_drug_partners_per_gene = drug_partners_per_gene.values.sum / drug_partners_per_gene.values.size.to_f
+    drug_partners_for_this_gene = drug_partners_per_gene[gene_id]
 
-    (self.publications.count + self.sources.count) * average_known_gene_partners_per_drug/known_gene_partners_for_interaction_drug * average_known_drug_partners_per_gene/known_drug_partners_for_interaction_gene
+    gene_partners_per_drug = Interaction.group(:drug_id).count if gene_partners_per_drug.nil?
+    avg_gene_partners_per_drug = gene_partners_per_drug.values.sum / gene_partners_per_drug.values.size.to_f
+    gene_partners_for_this_drug = gene_partners_per_drug[drug_id]
+
+    drug_specificity = avg_gene_partners_per_drug / gene_partners_for_this_drug
+    gene_specificity = avg_drug_partners_per_gene / drug_partners_for_this_gene
+    evidence_score = publications.count + sources.count
+    interaction_score = evidence_score * drug_specificity * gene_specificity
+
+    if update
+      self.score = interaction_score
+      self.drug_specificity = drug_specificity
+      self.gene_specificity = gene_specificity
+      self.evidence_score = evidence_score
+      save!
+    end
+
+    interaction_score
   end
 
 end

server/db/migrate/20240826185158_add_score_components.rb

@@ -0,0 +1,7 @@
+class AddScoreComponents < ActiveRecord::Migration[6.1]
+  def change
+    add_column :interactions, :drug_specificity, :float
+    add_column :interactions, :gene_specificity, :float
+    add_column :interactions, :evidence_score, :integer
+  end
+end

server/db/structure.sql

@@ -458,7 +458,10 @@ CREATE TABLE public.interactions (
     id text NOT NULL,
     drug_id text NOT NULL,
     gene_id text NOT NULL,
-    score numeric
+    score numeric,
+    drug_specificity double precision,
+    gene_specificity double precision,
+    evidence_score integer
 );
 
 
@@ -1878,6 +1881,7 @@ INSERT INTO "schema_migrations" (version) VALUES
 ('20220523183117'),
 ('20230104221712'),
 ('20230110183235'),
-('20230214150515');
+('20230214150515'),
+('20240826185158');
 
 

server/lib/genome/groupers/interaction_grouper.rb

@@ -89,12 +89,11 @@ def self.add_member(interaction_claim)
       def self.cache_interaction_scores
         count = Interaction.count
 
-        known_drug_partners_per_gene = Interaction.group(:gene_id).count
-        known_gene_partners_per_drug = Interaction.group(:drug_id).count
+        drug_partners_per_gene = Interaction.group(:gene_id).count
+        gene_partners_per_drug = Interaction.group(:drug_id).count
         pbar = ProgressBar.create(title: 'Calculating interaction scores', total: count, format: "%t: %p%% %a |%B|")
         Interaction.find_each do |interaction|
-          interaction.score = interaction.calculate_interaction_score(known_drug_partners_per_gene, known_gene_partners_per_drug)
-          interaction.save!
+          interaction.calculate_interaction_score(drug_partners_per_gene, gene_partners_per_drug, true)
           pbar.progress += 1
         end
       end