From 9e2e8674afeed27b0007e9f26f1f85649a8f5d13 Mon Sep 17 00:00:00 2001 From: supun Date: Tue, 14 May 2024 16:46:46 +0100 Subject: [PATCH] readd kegg and remove ko --- .../resources/META-INF/drlineconfiguration.json | 13 +++++++------ .../uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java | 4 ++-- .../core/flatfile/writer/line/DRLineBuildTest.java | 2 ++ .../scorer/uniprotkb/UniProtKBEntryScorerTest.java | 5 +++-- 4 files changed, 14 insertions(+), 10 deletions(-) diff --git a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json index 0cb6c1c37..5be948594 100644 --- 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 index 9e62f5ae2..2e8b9b8fe 100644 --- 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 index 1b83a7c77..918c52ac2 100644 --- 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/tools-entry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/UniProtKBEntryScorerTest.java b/tools-entry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/UniProtKBEntryScorerTest.java index 2f423d4e1..c7b0664e3 100644 --- a/tools-entry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/UniProtKBEntryScorerTest.java +++ b/tools-entry-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); } }