readd kegg and remove ko

ebi-uniprot · May 14, 2024 · 9e2e867 · 9e2e867
1 parent 33ff438
commit 9e2e867
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Showing 4 changed files with 14 additions and 10 deletions.
diff --git a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json
@@ -781,6 +781,13 @@
 			}
 		]
 	},
+	{
+		"name": "KEGG",
+		"displayName": "KEGG",
+		"category": "GMA",
+		"uriLink": "https://www.genome.jp/dbget-bin/www_bget?%id",
+		"idMappingName": "KEGG_ID"
+	},
 	{
 		"name": "MANE-Select",
 		"displayName": "MANE-Select",
@@ -1311,12 +1318,6 @@
 		"category": "PLG",
 		"uriLink": "https://inparanoidb.sbc.su.se/orthologs/%id&1/"
 	},
-	{
-		"name": "KO",
-		"displayName": "KO",
-		"category": "PLG",
-		"uriLink": "https://www.genome.jp/dbget-bin/www_bget?ko:%id"
-	},
 	{
 		"name": "OMA",
 		"displayName": "OMA",

diff --git a/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java b/controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java
@@ -301,12 +301,12 @@ void testDatabaseFieldSize() {
                 4);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENOME_ANNOTATION_DATABASES),
-                13);
+                14);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(ORGANISM_SPECIFIC_DATABASES),
                 42);
         verifyGroupSize(
-                UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PHYLOGENOMIC_DATABASES), 9);
+                UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PHYLOGENOMIC_DATABASES), 8);
         verifyGroupSize(
                 UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(ENZYME_AND_PATHWAY_DATABASES),
                 10);

diff --git a/ff-parser/src/test/java/org/uniprot/core/flatfile/writer/line/DRLineBuildTest.java b/ff-parser/src/test/java/org/uniprot/core/flatfile/writer/line/DRLineBuildTest.java
@@ -52,6 +52,7 @@ void test1() {
                         + "DR   CAZy; GT4; Glycosyltransferase Family 4.\n"
                         + "DR   EnsemblFungi; YNL048W; YNL048W; YNL048W.\n"
                         + "DR   GeneID; 855679; -.\n"
+                        + "DR   KEGG; sce:YNL048W; -.\n"
                         + "DR   SGD; S000004993; ALG11.\n"
                         + "DR   eggNOG; fuNOG07615; -.\n"
                         + "DR   GeneTree; EFGT00050000003720; -.\n"
@@ -97,6 +98,7 @@ void test1() {
         xrefs.add(createUniProtDBCrossReference("CAZy", "GT4", "Glycosyltransferase Family 4"));
         xrefs.add(createUniProtDBCrossReference("EnsemblFungi", "YNL048W", "YNL048W", "YNL048W"));
         xrefs.add(createUniProtDBCrossReference("GeneID", "855679", "-"));
+        xrefs.add(createUniProtDBCrossReference("KEGG", "sce:YNL048W", "-"));
         xrefs.add(createUniProtDBCrossReference("SGD", "S000004993", "ALG11"));
         xrefs.add(createUniProtDBCrossReference("eggNOG", "fuNOG07615", "-"));
         xrefs.add(createUniProtDBCrossReference("GeneTree", "EFGT00050000003720", "-"));

diff --git a/...ntry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/UniProtKBEntryScorerTest.java b/...ntry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/UniProtKBEntryScorerTest.java
@@ -53,6 +53,7 @@ class UniProtKBEntryScorerTest {
                     + "DR   RefSeq; YP_654585.1; NC_008187.1.\n"
                     + "DR   SMR; Q197E7; -.\n"
                     + "DR   GeneID; 4156262; -.\n"
+                    + "DR   KEGG; vg:4156262; -.\n"
                     + "DR   OrthoDB; 14281at10239; -.\n"
                     + "DR   Proteomes; UP000001358; Genome.\n"
                     + "DR   GO; GO:0033644; C:host cell membrane; IEA:UniProtKB-SubCell.\n"
@@ -81,7 +82,7 @@ void test1() throws IOException {
         scored.scoreEntry(entry);
         scored.shutDown();
         assertEquals(1, scored.getTotalScore().getCount());
-        assertEquals(14.6, scored.getTotalScore().getSum(), 0.0001);
-        assertEquals(14.6, scored.getTotalScore().getMax(), 0.0001);
+        assertEquals(14.7, scored.getTotalScore().getSum(), 0.0001);
+        assertEquals(14.7, scored.getTotalScore().getMax(), 0.0001);
     }
 }