feat: exposing transcripts in the target index

Author: DSuveges

app/models/entities/Target.scala

@@ -124,6 +124,17 @@ case class Constraint(
 
 case class ReactomePathway(pathway: String, pathwayId: String, topLevelTerm: String)
 
+case class Transcript(
+    transcriptId: String,
+    biotype: String,
+    isEnsemblCanonical: Boolean,
+    uniprotId: Option[String],
+    isUniprotReviewed: Option[Boolean],
+    translationId: Option[String],
+    alphafoldId: Option[String],
+    uniprotIsoformId: Option[String]
+)
+
 case class Target(
     id: String,
     alternativeGenes: Seq[String] = Seq.empty,
@@ -152,7 +163,8 @@ case class Target(
     targetClass: Seq[TargetClass] = Seq.empty,
     tep: Option[Tep],
     tractability: Seq[Tractability] = Seq.empty,
-    transcriptIds: Seq[String] = Seq.empty
+    transcriptIds: Seq[String] = Seq.empty,
+    transcripts: Seq[Transcript] = Seq.empty
 )
 
 object Target extends OTLogging {
@@ -202,6 +214,7 @@ object Target extends OTLogging {
   implicit val hallmarkAttributeImpF: OFormat[HallmarkAttribute] =
     Json.format[models.entities.HallmarkAttribute]
   implicit val hallmarksImpF: OFormat[Hallmarks] = Json.format[models.entities.Hallmarks]
+  implicit val transcriptImpF: OFormat[Transcript] = Json.format[models.entities.Transcript]
   implicit val targetImpF: OFormat[Target] =
     Json.format[Target]
 }

app/models/gql/Objects.scala

@@ -137,6 +137,19 @@ object Objects extends OTLogging {
     )
   )
 
+  implicit val transcriptImp: ObjectType[Backend, Transcript] =
+    deriveObjectType[Backend, Transcript](
+      ObjectTypeDescription("Transcript annotation for a target gene"),
+      DocumentField("transcriptId", "Ensembl transcript identifier"),
+      DocumentField("biotype", "Biotype classification of the transcript"),
+      DocumentField("isEnsemblCanonical", "Whether this is the Ensembl canonical transcript"),
+      DocumentField("uniprotId", "UniProt accession mapped to the transcript"),
+      DocumentField("isUniprotReviewed", "Whether the UniProt entry is reviewed (Swiss-Prot)"),
+      DocumentField("translationId", "Ensembl translation identifier"),
+      DocumentField("alphafoldId", "AlphaFold structure prediction identifier"),
+      DocumentField("uniprotIsoformId", "UniProt isoform identifier")
+    )
+
   implicit lazy val targetImp: ObjectType[Backend, Target] = deriveObjectType(
     ObjectTypeDescription(
       "Core annotation for drug targets (gene/proteins). Targets are defined based on EMBL-EBI Ensembl database and uses the Ensembl gene ID as the  primary identifier. An Ensembl gene ID is considered potential drug target if included in the canonical assembly or if present alternative assemblies but encoding for a reviewed protein product according to the UniProt database."
@@ -191,6 +204,9 @@ object Objects extends OTLogging {
     DocumentField("transcriptIds",
                   "List of Ensembl transcript identifiers associated with the target"
     ),
+    DocumentField("transcripts",
+                  "List of transcripts associated with the target including protein and structure annotations"
+    ),
     DocumentField("pathways", "Pathway annotations for the target"),
     RenameField("go", "geneOntology"),
     RenameField("constraint", "geneticConstraint"),

test/controllers/GqlTest.scala

@@ -555,6 +555,9 @@ class GqlTest
     "return valid response for subcellular location fragment" taggedAs IntegrationTestTag in {
       testQueryAgainstGqlEndpoint(TargetFragment("SubcellularLocation_SubcellularLocationFragment"))
     }
+    "return valid response for target transcripts query" taggedAs IntegrationTestTag in {
+      testQueryAgainstGqlEndpoint(Target("TargetPage_Transcripts"))(ensgTransform)
+    }
     "return a valid response for genetic contraint query" taggedAs IntegrationTestTag in {
       testQueryAgainstGqlEndpoint(Target("GeneticConstraint_GeneticConstraint"))(ensgTransform)
     }

test/resources/gqlQueries/TargetPage_Transcripts.gql

@@ -0,0 +1,14 @@
+query TargetTranscriptsQuery($ensgId: String!) {
+  target(ensemblId: $ensgId) {
+    transcripts {
+      transcriptId
+      biotype
+      isEnsemblCanonical
+      uniprotId
+      isUniprotReviewed
+      translationId
+      alphafoldId
+      uniprotIsoformId
+    }
+  }
+}