[Platform]: pharmgkb allele column (#335)

opentargets · Feb 27, 2024 · 81d6a96 · 81d6a96
1 parent b383f9b
commit 81d6a96
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Showing 6 changed files with 33 additions and 2 deletions.
diff --git a/apps/platform/src/components/AssociationsToolkit/static_datasets/prioritisationColumns.ts b/apps/platform/src/components/AssociationsToolkit/static_datasets/prioritisationColumns.ts
@@ -130,7 +130,7 @@ const geneEssentiality: Column = {
 
 const hasSafetyEvent: Column = {
   id: "hasSafetyEvent",
-  label: "Known adverse events",
+  label: "Known safety events",
   aggregation: aggregations.safety,
   sectionId: "safety",
   description: "Target associated with a curated adverse event",

diff --git a/packages/sections/src/drug/Pharmacogenomics/Body.jsx b/packages/sections/src/drug/Pharmacogenomics/Body.jsx
@@ -99,6 +99,20 @@ function Body({ id: chemblId, label: name, entity }) {
           naLabel
         ),
     },
+    {
+      id: "starAllele",
+      label: "Star Allele",
+      renderCell: ({ haplotypeId, haplotypeFromSourceId }) => {
+        const displayId = haplotypeId || haplotypeFromSourceId || naLabel;
+        const LinkComponent = haplotypeFromSourceId && (
+          <Link external to={`https://www.pharmgkb.org/haplotype/${haplotypeFromSourceId}`}>
+            {displayId}
+          </Link>
+        );
+
+        return LinkComponent || displayId || naLabel;
+      },
+    },
     {
       id: "genotypeId",
       label: "Genotype ID",

diff --git a/packages/sections/src/drug/Pharmacogenomics/Pharmacogenomics.gql b/packages/sections/src/drug/Pharmacogenomics/Pharmacogenomics.gql
@@ -12,6 +12,8 @@ query PharmacogenomicsQuery($chemblId: String!) {
         id
         approvedSymbol
       }
+      haplotypeId
+      haplotypeFromSourceId
       isDirectTarget
       phenotypeFromSourceId
       genotypeAnnotationText

diff --git a/packages/sections/src/evidence/Chembl/Body.jsx b/packages/sections/src/evidence/Chembl/Body.jsx
@@ -395,7 +395,6 @@ function Body({ id, label, entity }) {
             variables={{
               ensemblId,
               efoId,
-              cursor,
               size,
             }}
           />

diff --git a/packages/sections/src/target/Pharmacogenomics/Pharmacogenomics.gql b/packages/sections/src/target/Pharmacogenomics/Pharmacogenomics.gql
@@ -8,6 +8,8 @@ query PharmacogenomicsQuery($ensemblId: String!) {
         id
         label
       }
+      haplotypeId
+      haplotypeFromSourceId
       isDirectTarget
       drugFromSource
       drugId

diff --git a/packages/sections/src/target/Pharmacogenomics/PharmacogenomicsTable.jsx b/packages/sections/src/target/Pharmacogenomics/PharmacogenomicsTable.jsx
@@ -78,6 +78,20 @@ function OverviewTab({ pharmacogenomics, query, variables }) {
           naLabel
         ),
     },
+    {
+      id: "starAllele",
+      label: "Star Allele",
+      renderCell: ({ haplotypeId, haplotypeFromSourceId }) => {
+        const displayId = haplotypeId || haplotypeFromSourceId || naLabel;
+        const LinkComponent = haplotypeFromSourceId && (
+          <Link external to={`https://www.pharmgkb.org/haplotype/${haplotypeFromSourceId}`}>
+            {displayId}
+          </Link>
+        );
+
+        return LinkComponent || displayId || naLabel;
+      },
+    },
     {
       id: "genotypeId",
       label: "Genotype ID",