Enable searching genes by Ensembl ID

src/js/kit/related-genes.js

@@ -473,36 +473,48 @@ function fetchGenesFromCache(names, type, ideo) {
   const locusMap = isSymbol ? cache.lociByName : cache.lociById;
   const nameMap = isSymbol ? cache.idsByName : cache.namesById;
 
+  const ensemblGeneIdRegex = /ENS[A-Z]{0,3}G\d{11}/;
+
   const hits = names.map(name => {
 
-    const nameLc = name.toLowerCase();
+    let isSynonym = false;
+    let synonym = null;
 
-    if (
-      !locusMap[name] &&
-      !cache.nameCaseMap[nameLc] &&
-      !getGeneBySynonym(name, ideo)
-    ) {
-      if (isSymbol) {
-        throwGeneNotFound(name, ideo);
-      } else {
-        return;
-      }
+    if (ensemblGeneIdRegex.test(name)) {
+      // Omit version if given Ensembl gene ID + version, e.g.
+      // ENSG00000010404.11 -> ENSG00000010404
+      name = name.split('.')[0];
     }
+    const isIdentifier = name in cache.namesById;
+    if (isIdentifier && isSymbol) {
+      name = cache.namesById[name];
+    } else {
+      const nameLc = name.toLowerCase();
 
-    let isSynonym = false;
-    let synonym = null;
+      if (
+        !locusMap[name] &&
+        !cache.nameCaseMap[nameLc] &&
+        !getGeneBySynonym(name, ideo)
+      ) {
+        if (isSymbol) {
+          throwGeneNotFound(name, ideo);
+        } else {
+          return;
+        }
+      }
 
-    // Canonicalize name if it is mistaken in upstream data source.
-    // This can sometimes happen in WikiPathways, e.g. when searching
-    // interactions for rat Pten, it includes a result for "PIK3CA".
-    // In that case, this would correct PIK3CA to be Pik3ca.
-    if (isSymbol && !locusMap[name]) {
-      if (cache.nameCaseMap[nameLc]) {
-        name = cache.nameCaseMap[nameLc];
-      } else {
-        synonym = name;
-        name = getGeneBySynonym(synonym, ideo);
-        isSynonym = true;
+      // Canonicalize name if it is mistaken in upstream data source.
+      // This can sometimes happen in WikiPathways, e.g. when searching
+      // interactions for rat Pten, it includes a result for "PIK3CA".
+      // In that case, this would correct PIK3CA to be Pik3ca.
+      if (isSymbol && !locusMap[name]) {
+        if (cache.nameCaseMap[nameLc]) {
+          name = cache.nameCaseMap[nameLc];
+        } else {
+          synonym = name;
+          name = getGeneBySynonym(synonym, ideo);
+          isSynonym = true;
+        }
       }
     }
 
@@ -522,6 +534,7 @@ function fetchGenesFromCache(names, type, ideo) {
         ensemblgene: ensemblId
       },
       isSynonym,
+      isIdentifier,
       synonym
     };
 

test/online/related-genes.test.js

@@ -269,20 +269,16 @@ describe('Ideogram related genes kit', function() {
     const ideogram = Ideogram.initRelatedGenes(config);
   });
 
-  it('handles gene with no interacting genes and no paralogs', done => {
+  it('handles search by Ensembl ID', done => {
 
     async function callback() {
       const ideo = this;
 
-      await ideogram.plotRelatedGenes('BRCA1');
+      // Ensembl ID for gene "LPL"
+      await ideo.plotRelatedGenes('ENSG00000175445');
 
-      const related = ideo.getRelatedGenesByType();
-
-      const numParalogs = related.paralogous.length;
-      const numInteractingGenes = related.interacting.length;
-
-      assert.equal(numInteractingGenes, 0);
-      assert.equal(numParalogs, 0);
+      const chr10ParalogNeighborhoods = ideo.annotsOther['9'].annots;
+      assert.equal(chr10ParalogNeighborhoods.length, 1);
 
       done();
     }
@@ -292,7 +288,7 @@ describe('Ideogram related genes kit', function() {
     }
 
     var config = {
-      organism: 'Macaca mulatta', // Also tests standard, non-slugged name
+      organism: 'Homo sapiens', // Also tests standard, non-slugged name
       onLoad: callback,
       dataDir: '/dist/data/bands/native/',
       cacheDir: '/dist/data/cache/',
@@ -303,6 +299,7 @@ describe('Ideogram related genes kit', function() {
   });
 
   it('handles gene with no interacting genes and no paralogs', done => {
+
     async function callback() {
       const ideo = this;
 
@@ -324,16 +321,16 @@ describe('Ideogram related genes kit', function() {
     }
 
     var config = {
-      organism: 'Macaca mulatta',
+      organism: 'Macaca mulatta', // Also tests standard, non-slugged name
       onLoad: callback,
       dataDir: '/dist/data/bands/native/',
+      cacheDir: '/dist/data/cache/',
       onClickAnnot
     };
 
     const ideogram = Ideogram.initRelatedGenes(config);
   });
 
-
   it('handles gene that is unknown', done => {
 
     async function callback() {