Added the gaf download link, fiz some typos geneontology/go-site#2432 …

…and geneontology/go-site#2430

site-react/src/@pango.core/data/config.ts

@@ -34,23 +34,23 @@ export const ASPECT_MAP: { [key: string]: AspectMapType } = {
     shorthand: 'MF',
     label: 'Molecular Function',
     description: 'What a protein encoded by the gene does at the molecular level',
-    color: getColor('green', 500) || '#000000'
+    color: getColor('green', 400) || '#000000'
   },
   'biological process': {
     id: 'biological process',
     icon: 'coverage-2',
     shorthand: 'BP',
     label: 'Biological Process',
     description: '“System” functions, at the level of the cell or whole organism, that the gene helps to carry out, usually together with other genes',
-    color: getColor('brown', 500) || '#000000'
+    color: getColor('brown', 400) || '#000000'
   },
   'cellular component': {
     id: 'cellular component',
     icon: 'coverage-1',
     shorthand: 'CC',
     label: 'Cellular Component',
     description: 'The part of a cell where a protein encoded by the gene performs its molecular function',
-    color: getColor('purple', 500) || '#000000'
+    color: getColor('purple', 400) || '#000000'
   }
 }
 

site-react/src/@pango.core/data/constants.ts

@@ -1,4 +1,5 @@
 export const ENVIRONMENT = {
+  contactUrl: "https://docs.google.com/forms/d/e/1FAIpQLScX_caoY-mqsyK5Y6M2bof7EXVG0UY5DhOQ67zBMoAKKlRF4Q/viewform?usp=sharing",
   amigoTermUrl: "http://amigo.geneontology.org/amigo/term/",
   amigoGPUrl: "http://amigo.geneontology.org/amigo/gene_product/",
   pubmedUrl: "https://www.ncbi.nlm.nih.gov/pubmed/",
@@ -18,7 +19,7 @@ export const ENVIRONMENT = {
   // 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/",
+  downloadAnnotationsGAFUrl: "http://data.pantherdb.org/ftp/downloads/paint/pango/functionome_release.gaf.gz",
   downloadEvolutionaryModelsGAFUrl: "http://data.pantherdb.org/ftp/downloads/paint/pango/IBD.gaf"
 
 };

site-react/src/app/Home.tsx

@@ -12,6 +12,7 @@ import { useGetGenesStatsQuery } from '@/features/genes/slices/genesApiSlice';
 import { transformCategoryTerms } from '@/features/terms/services/termsService';
 import { setFunctionCategories } from '@/features/terms/slices/termsSlice';
 import { Link } from 'react-router-dom';
+import { ENVIRONMENT } from '@/@pango.core/data/constants';
 
 const Home: React.FC = () => {
   const dispatch = useAppDispatch();
@@ -52,8 +53,7 @@ const Home: React.FC = () => {
               that have been assigned based on expert review and integration of available experimental evidence
               in 6,333 families of protein-coding genes.
               ( <Link to="/about" className="text-accent-500 hover:text-accent-200"> Read More</Link> ).
-
-              Each characteristic is linked to the experimental evidence supporting
+              Each characteristic is linked to the experimental evidence supporting it.
             </h2>
             <div className='flex items-center'>
               <div className='w-[300px] mr-4'>
@@ -62,7 +62,7 @@ const Home: React.FC = () => {
 
               <h3 className="text-white">
                 See any missing or incorrect functions?
-                <a href="https://help.geneontology.org/"
+                <a href={ENVIRONMENT.contactUrl}
                   target="_blank"
                   rel="noopener noreferrer"
                   className="text-accent-500 hover:text-accent-200 px-1">

site-react/src/app/layout/Footer.tsx

@@ -1,16 +1,18 @@
+import { ENVIRONMENT } from '@/@pango.core/data/constants';
 import type React from 'react';
+import { Link } from 'react-router-dom';
 
 const Footer: React.FC = () => {
   const currentYear = new Date().getFullYear();
 
   return (
-    <div className="footer flex flex-row items-start p-5 bg-gradient-to-r from-[#0e2a3b] to-[#34306b] text-white">
+    <div className="footer flex flex-row items-start p-5 py-10 bg-gradient-to-r from-[#0e2a3b] to-[#34306b] text-white">
       <div className="flex flex-row items-start flex-1">
         <div className="mr-4">
-          <a href="/" className="text-white">Home</a>
+          <Link to="/" className="text-white">Home</Link>
         </div>
         <div className="mr-4">
-          <a href="http://help.geneontology.org" className="text-white" target="_blank" rel="noopener noreferrer">Contact us</a>
+          <a href={ENVIRONMENT.contactUrl} className="text-white" target="_blank" rel="noopener noreferrer">Contact us</a>
         </div>
       </div>
       <span className="flex-grow"></span>

site-react/src/features/annotations/components/AnnotationTable.tsx

@@ -86,7 +86,7 @@ const AnnotationTable: React.FC<AnnotationTableProps> = ({
         <tbody className="divide-y divide-gray-200">
           {annotations.map((row, idx) => (
             <tr key={idx} onClick={() => handleRowClick(row)} className="hover:bg-gray-50 cursor-pointer">
-              <td className="px-3 py-2 min-w-[250px]">
+              <td className="px-3 py-4 min-w-[250px]">
                 <div className="flex items-center">
                   <span
                     className="inline-flex items-center justify-center !h-8 !w-8 rounded-full text-xs font-bold border"
@@ -104,7 +104,7 @@ const AnnotationTable: React.FC<AnnotationTableProps> = ({
                   </div>
                 </div>
               </td>
-              <td className="px-3 py-2  min-w-[220px]">
+              <td className="px-3 py-4 min-w-[220px]">
                 {row.slimTerms.map((term, termIdx) => (
                   <div key={termIdx} className="mb-1 last:mb-0 flex items-center">
                     <span
@@ -122,7 +122,7 @@ const AnnotationTable: React.FC<AnnotationTableProps> = ({
                   </div>
                 ))}
               </td>
-              <td className="px-3 py-2">
+              <td className="px-3 py-5">
                 {row.evidence.slice(0, maxEvidences).map((evidence, evidenceIdx) => (
                   <div key={evidenceIdx} className="mb-2 last:mb-0 pb-2 last:pb-0 border-b last:border-0 border-gray-200">
                     {evidence.withGeneId && (
@@ -160,7 +160,7 @@ const AnnotationTable: React.FC<AnnotationTableProps> = ({
                   </button>
                 )}
               </td>
-              <td className="px-3 py-2">
+              <td className="px-3 py-5">
                 {row.detailedGroups.map((group, groupIdx) => (
                   group && (
                     <a key={groupIdx} href={group.id} target="_blank" rel="noopener noreferrer"

site-react/src/index.css

@@ -30,7 +30,7 @@ code {
   }
 
   td {
-    @apply align-top;
+    @apply align-top  border-r border-gray-300;
   }
 
 

site-react/src/shared/components/CategoryStats.tsx

@@ -110,7 +110,7 @@ const CategoryStats: React.FC = () => {
                   <div className="line-clamp-2">{item.label}</div>
                 </div>
               </Tooltip>
-              <div className="flex-1 relative h-12">
+              <div className="flex-1 relative h-9">
                 <div
                   className="h-full absolute"
                   style={{
@@ -121,7 +121,7 @@ const CategoryStats: React.FC = () => {
 
 
                 <div
-                  className="absolute  transform -translate-y-1/2 "
+                  className="absolute h-7 transform -translate-y-1/2 "
                   style={{
                     left: item.countPos,
                     top: '50%'