feat(graphql): add Gene-GOs

server/graphql/graphqlHandler.js

@@ -8,6 +8,7 @@ const clinvarResolvers = require('./resolvers/clinvar.resolvers');
 const geneResolvers = require('./resolvers/gene.resolvers');
 const dioptResolvers = require('./resolvers/diopt.resolvers');
 const phenotypeOntologyResolvers = require('./resolvers/phenotype-ontology.resolvers');
+const goResolvers = require('./resolvers/go.resolvers');
 const pharosResolvers = require('./resolvers/pharos.resolver');
 const stringResolvers = require('./resolvers/string.resolvers');
 const dbnsfpResolvers = require('./resolvers/dbnsfp.resolvers');
@@ -17,6 +18,7 @@ const clinvarTypeDefs = readFileSync(path.join(__dirname, 'schemas/clinvar.schem
 const geneTypeDefs = readFileSync(path.join(__dirname, 'schemas/gene.schema.graphql'), 'utf8');
 const dioptTypeDefs = readFileSync(path.join(__dirname, 'schemas/diopt.schema.graphql'), 'utf8');
 const phenotypeOntologyTypeDefs = readFileSync(path.join(__dirname, 'schemas/phenotype-ontology.schema.graphql'), 'utf8');
+const goTypeDefs = readFileSync(path.join(__dirname, 'schemas/go.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');
@@ -26,6 +28,7 @@ const typeDefs = `
   ${clinvarTypeDefs}
   ${geneTypeDefs}
   ${dioptTypeDefs}
+  ${goTypeDefs}
   ${phenotypeOntologyTypeDefs}
   ${pharosTypeDefs}
   ${stringTypeDefs}
@@ -55,6 +58,8 @@ const typeDefs = `
     phenotypeOntologyByNamespace(namespace: String!, limit: Int = 100, start: Int = 0): [PhenotypeOntology!]!
     phenotypeOntologyByCategory(categoryId: Int!, limit: Int = 100, start: Int = 0): [PhenotypeOntology!]!
     phenotypeOntologyByEntrezId(entrezId: Int!): [PhenotypeOntology!]!
+    goByEntrezId(entrezId: Int!): [GeneGO!]!
+
     phenotypeOntologyByGeneSymbol(symbol: String!): [PhenotypeOntology!]!
 
     pharosTargetById(id: Int!): PharosTarget
@@ -90,6 +95,8 @@ const rootValue = {
   dioptOrthologsByEntrezId: dioptResolvers.findOrthologsByEntrezId,
 
   phenotypeOntologyByPoId: phenotypeOntologyResolvers.findByPoId,
+  goByEntrezId: goResolvers.findByEntrezId,
+
   phenotypeOntologyByName: phenotypeOntologyResolvers.findByName,
   phenotypeOntologyByTaxonId: phenotypeOntologyResolvers.findByTaxonId,
   phenotypeOntologyByNamespace: phenotypeOntologyResolvers.findByNamespace,

server/graphql/index.js

@@ -2,7 +2,7 @@
  * GraphQL API module for MARRVEL
  *
  * This module provides GraphQL API endpoints for various data sources
- * including Clinvar, genes, DIOPT, phenotype ontology, and other genomic databases.
+ * including Clinvar, genes, DIOPT, phenotype ontology, gene ontology, and other genomic databases.
  *
  * Usage:
  * - Access GraphQL playground at /graphql (in development)
@@ -16,6 +16,7 @@
  *          findOrthologsByTaxonIds
  * - PhenotypeOntology: findByPoId, findByName, findByTaxonId, findByNamespace,
  *                      findByCategory
+ * - GeneOntology: findByEntrezId
  */
 
 module.exports = {

server/graphql/resolvers/go.resolvers.js

@@ -0,0 +1,29 @@
+const Genes = require('../../models/genes.model');
+
+/**
+ * Find Gene Ontology terms by gene Entrez ID
+ */
+const findByEntrezId = async ({ entrezId }) => {
+  try {
+    const gene = await Genes.findOne({ entrezId }, '-_id gos')
+      .populate('gos.ontology');
+    if (!gene || !gene.gos) {
+      return [];
+    }
+
+    return gene.gos.map((go) => ({
+      goId: go.goId,
+      eviCode: go.eviCode,
+      date: go.date,
+      assignedBy: go.assignedBy,
+      ontology: go.ontology
+    }));
+  } catch (error) {
+    console.error('Error fetching GOs by Entrez ID:', error);
+    throw new Error('Failed to fetch GOs by Entrez ID');
+  }
+};
+
+module.exports = {
+  findByEntrezId
+};

server/graphql/schemas/go.schema.graphql

@@ -0,0 +1,23 @@
+"""
+A Gene Ontology term
+"""
+type GO {
+  id: String!
+  name: String
+  synonyms: [String]
+  is_a: [String]
+  namespace: String
+  def: String
+  agrSlimGoId: String
+}
+
+"""
+Gene Ontology with evidence information
+"""
+type GeneGO {
+  goId: String!
+  eviCode: String
+  date: String
+  assignedBy: String
+  ontology: GO
+}