Add note on tooltip to indicate this is v4 data

cBioPortal · Oct 3, 2024 · f8c2e98 · f8c2e98
1 parent 8ab1fcb
commit f8c2e98
Show file tree

Hide file tree

Showing 3 changed files with 43 additions and 19 deletions.
diff --git a/packages/react-variant-view/src/component/functionalPrediction/MutationAssessor.tsx b/packages/react-variant-view/src/component/functionalPrediction/MutationAssessor.tsx
@@ -27,20 +27,32 @@ export default class MutationAssessor extends React.Component<
     IMutationAssessorProps,
     {}
 > {
-    // Change to new url when available
+    // Change to new url when manuscript available
     // New url will need to be added in tooltip, discrption, "Please refer to the score range here." and "Go to Mutation Assessor"
     // private static MUTATION_ASSESSOR_URL: string = 'http://mutationassessor.org/r3/';
 
     private static mutationAssessorText() {
         return (
-            <div style={{ width: 450, height: 110 }}>
+            <div style={{ width: 450, height: 130 }}>
                 Mutation Assessor predicts the functional impact of amino-acid
                 substitutions in proteins, such as mutations discovered in
                 cancer or missense polymorphisms. The functional impact is
                 assessed based on evolutionary conservation of the affected
                 amino acid in protein homologs. The method has been validated on
-                a large set of disease associated and polymorphic variants
-                (ClinVar).
+                a large set of disease associated and polymorphic variants (
+                <a href="https://www.ncbi.nlm.nih.gov/clinvar/" target="_blank">
+                    ClinVar
+                </a>
+                ).
+                <br />
+                <b>
+                    Mutation Assessor V4 data is now available in the portal!
+                </b>{' '}
+                New manuscript is in preparation. Click{` `}
+                <a href="http://mutationassessor.org/r3/" target="_blank">
+                    here
+                </a>
+                {` `} to see information about V3 data.
             </div>
         );
     }
@@ -146,14 +158,6 @@ export default class MutationAssessor extends React.Component<
 
     public render() {
         let maContent: JSX.Element = <span />;
-        const dataSource = (
-            <>
-                Mutation Assessor&nbsp;
-                <i className="fas fa-external-link-alt" />
-                {!this.props.isCanonicalTranscriptSelected && <span> *</span>}
-            </>
-        );
-
         if (
             this.props.mutationAssessor &&
             this.props.mutationAssessor.functionalImpactPrediction != null &&
@@ -168,7 +172,15 @@ export default class MutationAssessor extends React.Component<
         return (
             <div className={featureTableStyle['feature-table-layout']}>
                 <div className={featureTableStyle['data-source']}>
-                    {this.mutationAssessorTooltip(<>{dataSource}</>)}
+                    {this.mutationAssessorTooltip(
+                        <>
+                            Mutation Assessor&nbsp;
+                            <i className="fas fa-external-link-alt" />
+                            {!this.props.isCanonicalTranscriptSelected && (
+                                <span> *</span>
+                            )}
+                        </>
+                    )}
                 </div>
                 <div>
                     {this.mutationAssessorTooltip(

diff --git a/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx b/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx
@@ -19,7 +19,7 @@ export default class MutationAssessor extends React.Component<
     IMutationAssessorProps,
     {}
 > {
-    // Replace to new url when publication available
+    // Replace to new url when manuscript available
     // static MUTATION_ASSESSOR_URL: string = 'http://mutationassessor.org/r3/';
 
     constructor(props: IMutationAssessorProps) {
@@ -87,8 +87,8 @@ export default class MutationAssessor extends React.Component<
                         <tr>
                             <td>Source</td>
                             <td>
-                                {/* Add link when pubilcation is available */}
-                                MutationAssessor
+                                {/* Add link when manuscript is available */}
+                                Mutation Assessor
                             </td>
                         </tr>
                         <tr>

diff --git a/src/shared/components/mutationTable/column/FunctionalImpactColumnFormatter.tsx b/src/shared/components/mutationTable/column/FunctionalImpactColumnFormatter.tsx
@@ -305,14 +305,26 @@ class FunctionalImpactColumnTooltip extends React.Component<
 
     public static mutationAssessorText() {
         return (
-            <div style={{ width: 450, height: 100 }}>
+            <div style={{ width: 450, height: 130 }}>
                 Mutation Assessor predicts the functional impact of amino-acid
                 substitutions in proteins, such as mutations discovered in
                 cancer or missense polymorphisms. The functional impact is
                 assessed based on evolutionary conservation of the affected
                 amino acid in protein homologs. The method has been validated on
-                a large set of disease associated and polymorphic variants
-                (ClinVar).
+                a large set of disease associated and polymorphic variants (
+                <a href="https://www.ncbi.nlm.nih.gov/clinvar/" target="_blank">
+                    ClinVar
+                </a>
+                ).
+                <br />
+                <b>
+                    Mutation Assessor V4 data is now available in the portal!
+                </b>{' '}
+                New manuscript is in preparation. Click{` `}
+                <a href="http://mutationassessor.org/r3/" target="_blank">
+                    here
+                </a>
+                {` `} to see information about V3 data.
             </div>
         );
     }