fixed the download links and geneontology/go-site#2430

pantherdb · Feb 4, 2025 · b37df26 · b37df26
1 parent ee47ea9
commit b37df26
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Showing 6 changed files with 42 additions and 18 deletions.
diff --git a/site-react/src/@pango.core/data/constants.ts b/site-react/src/@pango.core/data/constants.ts
@@ -10,5 +10,15 @@ export const ENVIRONMENT = {
 
   uniprotUrl: 'https://www.uniprot.org/uniprotkb/',
   agrPrefixUrl: 'https://www.alliancegenome.org/gene/',
-  hgncPrefixUrl: 'https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/'
+  hgncPrefixUrl: 'https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/',
+  ncbiGeneUrl: 'https://www.ncbi.nlm.nih.gov/gene/?term=',
+  pantreeUrl: 'https://pantree.org/tree/family.jsp?accession=',
+
+
+  // Downloads
+  downloadAllDataCSVUrl: "https://functionome.org/download/export_annotations.zip",
+  downloadAllDataJSONUrl: "https://functionome.org/download/export_annotations.json.gz",
+  downloadAnnotationsGAFUrl: "http://data.pantherdb.org/ftp/downloads/paint/pango/",
+  downloadEvolutionaryModelsGAFUrl: "http://data.pantherdb.org/ftp/downloads/paint/pango/IBD.gaf"
+
 };
diff --git a/site-react/src/@pango.core/services/linksService.ts b/site-react/src/@pango.core/services/linksService.ts
@@ -19,7 +19,7 @@ export const getUniprotLink = (gene: string) => {
   if (!gene) return ENVIRONMENT.uniprotUrl;
 
   const geneId = gene.split(':');
-  return geneId.length > 1 ? `${ENVIRONMENT.uniprotUrl}${geneId[1]}` : ENVIRONMENT.uniprotUrl;
+  return geneId.length > 1 ? ENVIRONMENT.uniprotUrl + geneId[1] : ENVIRONMENT.uniprotUrl;
 };
 
 export const getFamilyLink = (element: Annotation) => {

diff --git a/site-react/src/app/Gene.tsx b/site-react/src/app/Gene.tsx
@@ -86,10 +86,7 @@ const Gene: React.FC = () => {
 
   const knownTermTypes = annotations.filter(a => a.termType === TermType.KNOWN).length;
   const unknownTermTypes = annotations.filter(a => a.termType === TermType.UNKNOWN).length;
-
-  const groupedTerms = transformTerms(annotations, 100);
-
-
+  const groupedTerms = transformTerms(annotations, 150);
 
   return (
     <div className="w-full bg-slate-200">
@@ -110,10 +107,8 @@ const Gene: React.FC = () => {
                 <InfoRow
                   label="GO annotations from all sources"
                   value={annotation.gene}
-                  href={`${ENVIRONMENT.amigoGPUrl}${annotation.gene}`}
+                  href={ENVIRONMENT.amigoGPUrl + annotation.gene}
                 />
-
-
               </div>
             </div>
 
@@ -154,6 +149,11 @@ const Gene: React.FC = () => {
                     />
                   </>
                 )}
+                <InfoRow
+                  label="NCBI Gene"
+                  value={annotation.geneSymbol}
+                  href={ENVIRONMENT.ncbiGeneUrl + annotation.geneSymbol}
+                />
               </div>
             </div>
           </div>
@@ -184,7 +184,13 @@ const Gene: React.FC = () => {
           </div>
         )}
         <div className="py-6 px-4 bg-gradient-to-r from-slate-100 to-white">
-          <h2 className="text-2xl font-semibold tracking-tight m-0">Function Details</h2>
+          <h2 className="text-2xl font-semibold tracking-tight m-0">Function Details (
+            <a href={ENVIRONMENT.pantreeUrl + annotation.pantherFamily}
+              target="_blank" rel="noopener noreferrer"
+              className="text-lg font-normal">
+              PAN-GO evolutionary model for this family
+            </a>)
+          </h2>
         </div>
         {annotations.length > 0 && (
           <div className="w-full bg-white py-4">

diff --git a/site-react/src/app/layout/Toolbar.tsx b/site-react/src/app/layout/Toolbar.tsx
@@ -6,6 +6,7 @@ import { Link } from 'react-router-dom';
 import { useAppDispatch } from '../hooks';
 import { toggleLeftDrawer } from '@/@pango.core/components/drawer/drawerSlice';
 import { VersionedLink } from '@/shared/components/VersionedLink';
+import { ENVIRONMENT } from '@/@pango.core/data/constants';
 
 interface ToolbarProps {
   showLoadingBar?: boolean;
@@ -75,14 +76,19 @@ const Toolbar: React.FC<ToolbarProps> = ({ showLoadingBar }) => {
               open={Boolean(exportMenuAnchor)}
               onClose={handleCloseExportMenu}
             >
-              <MenuItem component="a" href="https://functionome.org/download/export_annotations.zip">
-                As CSV
+              <MenuItem component="a" href={ENVIRONMENT.downloadAllDataCSVUrl}>
+                All data as CSV
               </MenuItem>
-              <MenuItem component="a" href="https://functionome.org/download/export_annotations.json.gz">
-                As JSON
+              <MenuItem component="a" href={ENVIRONMENT.downloadAllDataJSONUrl}>
+                All data as JSON
+              </MenuItem>
+              <MenuItem component="a" href={ENVIRONMENT.downloadAnnotationsGAFUrl}>
+                Annotations as GAF
+              </MenuItem>
+              <MenuItem component="a" href={ENVIRONMENT.downloadEvolutionaryModelsGAFUrl} target='_blank' rel='noopener noreferrer'>
+                Evolutionary models as GAF
               </MenuItem>
             </Menu>
-
             <Button
               color="inherit"
               component={Link}

diff --git a/site-react/src/features/annotations/components/AnnotationTable.tsx b/site-react/src/features/annotations/components/AnnotationTable.tsx
@@ -31,7 +31,7 @@ const AnnotationTable: React.FC<AnnotationTableProps> = ({
   const getPubmedArticleUrl = (pmid: string): string => {
     if (!pmid) return '';
     const id = pmid?.split(':');
-    return id.length > 0 ? `${ENVIRONMENT.pubmedUrl}${id[1]}` : '';
+    return id.length > 0 ? ENVIRONMENT.pubmedUrl + id[1] : '';
   };
 
   return (
@@ -122,7 +122,7 @@ const AnnotationTable: React.FC<AnnotationTableProps> = ({
                     {evidence.withGeneId && (
                       <div className="text-sm mb-1">
                         {evidence.withGeneId.gene} ({evidence.withGeneId.geneSymbol})
-                        (<a href={`${ENVIRONMENT.taxonApiUrl}${evidence.withGeneId.taxonId}`} target="_blank" rel="noopener noreferrer"
+                        (<a href={ENVIRONMENT.taxonApiUrl + evidence.withGeneId.taxonId} target="_blank" rel="noopener noreferrer"
                           className="">
                           {evidence.withGeneId.taxonAbbr}
                         </a>)

diff --git a/site-react/src/features/terms/components/TermLink.tsx b/site-react/src/features/terms/components/TermLink.tsx
@@ -8,7 +8,9 @@ interface TermLinkProps {
 
 const TermLink: React.FC<TermLinkProps> = ({ term }) => {
   return term.displayId ? (
-    <a href={`${ENVIRONMENT.amigoTermUrl}${term.id}`} target="_blank" rel="noopener noreferrer" className="no-underline">
+    <a href={ENVIRONMENT.amigoTermUrl + term.id}
+      target="_blank"
+      rel="noopener noreferrer" className="no-underline">
       {term.label}
     </a>
   ) : (