feat/graphql: add dbNSFP

server/graphql/graphqlHandler.js

@@ -10,6 +10,7 @@ const dioptResolvers = require('./resolvers/diopt.resolvers');
 const phenotypeOntologyResolvers = require('./resolvers/phenotype-ontology.resolvers');
 const pharosResolvers = require('./resolvers/pharos.resolver');
 const stringResolvers = require('./resolvers/string.resolvers');
+const dbnsfpResolvers = require('./resolvers/dbnsfp.resolvers');
 
 // Read schema files
 const clinvarTypeDefs = readFileSync(path.join(__dirname, 'schemas/clinvar.schema.graphql'), 'utf8');
@@ -18,6 +19,7 @@ const dioptTypeDefs = readFileSync(path.join(__dirname, 'schemas/diopt.schema.gr
 const phenotypeOntologyTypeDefs = readFileSync(path.join(__dirname, 'schemas/phenotype-ontology.schema.graphql'), 'utf8');
 const pharosTypeDefs = readFileSync(path.join(__dirname, 'schemas/pharos.schema.graphql'), 'utf8');
 const stringTypeDefs = readFileSync(path.join(__dirname, 'schemas/string.schema.graphql'), 'utf8');
+const dbnsfpTypeDefs = readFileSync(path.join(__dirname, 'schemas/dbnsfp.schema.graphql'), 'utf8');
 
 // Combine all schemas
 const typeDefs = `
@@ -27,6 +29,7 @@ const typeDefs = `
   ${phenotypeOntologyTypeDefs}
   ${pharosTypeDefs}
   ${stringTypeDefs}
+  ${dbnsfpTypeDefs}
 
   type Query {
     clinvarByGeneSymbol(symbol: String!): [Clinvar!]!
@@ -58,6 +61,9 @@ const typeDefs = `
 
     stringInteractionsByEnsemblId(ensemblId: String!, limit: Int = 100, start: Int = 0): [StringInteraction!]!
     stringInteractionBetweenProteins(ensemblId1: String!, ensemblId2: String!): StringInteraction
+
+    dbnsfpByVariant(chr: String!, pos: Int!, ref: String!, alt: String!, build: String!): DbNSFP
+    dbnsfpByPosition(chr: String!, pos: Int!, build: String!, limit: Int = 100, start: Int = 0): [DbNSFP!]!
   }
 `;
 
@@ -95,6 +101,9 @@ const rootValue = {
   stringInteractionsByEnsemblProteinId: stringResolvers.stringInteractionsByEnsemblProteinId,
   stringInteractionBetweenProteins: stringResolvers.stringInteractionBetweenProteins,
 
+  dbnsfpByVariant: dbnsfpResolvers.dbnsfpByVariant,
+  dbnsfpByPosition: dbnsfpResolvers.dbnsfpByPosition,
+
   // Type resolvers
   PharosTarget: pharosResolvers.PharosTarget,
 };

server/graphql/resolvers/dbnsfp.resolvers.js

@@ -0,0 +1,51 @@
+const DbNSFP = require('../../models/dbNSFP.model');
+
+/**
+ * dbNSFP GraphQL resolvers
+ */
+const dbnsfpResolvers = {
+  // Root query resolvers
+  dbnsfpByVariant: async (args) => {
+    try {
+      const { chr, pos, ref, alt, build } = args;
+      let query = {};
+      if (build === 'hg19') {
+        query = { hg19Chr: chr, hg19Pos: pos, ref, alt };
+      } else if (build === 'hg38') {
+        query = { hg38Chr: chr, hg38Pos: pos, ref, alt };
+      } else {
+        throw new Error(`Unsupported build: ${build}. Use 'hg19' or 'hg38'`);
+      }
+
+      const variant = await DbNSFP.findOne(query);
+      return variant;
+    } catch (error) {
+      console.error('Error in dbnsfpByVariant resolver:', error);
+      throw error;
+    }
+  },
+
+  dbnsfpByPosition: async (args) => {
+    try {
+      const { chr, pos, build, limit = 100, start = 0 } = args;
+      let query = {};
+      if (build === 'hg19') {
+        query = { hg19Chr: chr, hg19Pos: pos };
+      } else if (build === 'hg38') {
+        query = { hg38Chr: chr, hg38Pos: pos };
+      } else {
+        throw new Error(`Unsupported build: ${build}. Use 'hg19' or 'hg38'`);
+      }
+      const variants = await DbNSFP
+        .find(query)
+        .skip(start)
+        .limit(limit);
+      return variants;
+    } catch (error) {
+      console.error('Error in dbnsfpByPosition resolver:', error);
+      throw error;
+    }
+  }
+};
+
+module.exports = dbnsfpResolvers;

server/graphql/schemas/dbnsfp.schema.graphql

@@ -0,0 +1,85 @@
+"""
+A variant annotation score from a prediction tool
+"""
+type PredictionScore {
+  scores: [Float]
+  predictions: [String]
+  rankscore: Float
+}
+
+"""
+A single prediction score (for tools that don't have multiple transcripts)
+"""
+type SinglePredictionScore {
+  score: Float
+  prediction: String
+  rankscore: Float
+}
+
+"""
+CADD scores (different structure)
+"""
+type CADDScore {
+  rawScore: Float
+  phred: Float
+  rankscore: Float
+}
+
+"""
+REVEL scores (scores only, no predictions)
+"""
+type REVELScore {
+  scores: [Float]
+  rankscore: Float
+}
+
+"""
+Conservation scores (score only)
+"""
+type ConservationScore {
+  score: Float
+  rankscore: Float
+}
+
+"""
+All prediction scores for a variant
+"""
+type DbNSFPScores {
+  SIFT: PredictionScore
+  SIFT4G: PredictionScore
+  Polyphen2HDIV: PredictionScore
+  Polyphen2HVAR: PredictionScore
+  MutationTaster: PredictionScore
+  MutationAssessor: PredictionScore
+  CADD: CADDScore
+  REVEL: REVELScore
+  AlphaMissense: PredictionScore
+  PrimateAI: SinglePredictionScore
+  MCAP: SinglePredictionScore
+  GERPppRS: ConservationScore
+  phyloP100way_vertebrate: ConservationScore
+  phyloP470way_mammalian: ConservationScore
+}
+
+"""
+A dbNSFP variant annotation entry
+"""
+type DbNSFP {
+  hg38Chr: String!
+  hg38Pos: Int!
+  ref: String!
+  alt: String!
+  hg19Chr: String
+  hg19Pos: Int
+  hg18Chr: String
+  hg18Pos: Int
+  aaPos: Int
+  aaRef: String
+  aaAlt: String
+  rsid: String
+  ensemblId: String
+  transcriptEnsemblId: String
+  proteinEnsemblId: String
+  symbol: String
+  scores: DbNSFPScores!
+}