From d21c9872f0dee0c64691fd73ad68c38a6166b8ab Mon Sep 17 00:00:00 2001 From: LeonardoGonzales Date: Wed, 5 Jun 2024 12:53:03 +0100 Subject: [PATCH 1/3] 2024_04 changes (TRM-31122,TRM-31125,TRM-31265,TRM-31263,TRM-31390) --- .../META-INF/drlineconfiguration.json | 25 ------------------- .../cv/xdb/UniProtKBDatabaseTypesTest.java | 17 +++---------- .../src/test/resources/xdb/dr_ord | 3 --- .../evidence/EvidenceDatabaseTypes.java | 15 +---------- .../evidence/EvidenceDatabaseTypesTest.java | 2 +- .../UniProtKBEntryValueMapperTest.java | 10 ++------ .../src/test/resources/uniprot/Q15758.dat | 2 -- .../test/resources/uniprotkb/entry/Q8NDV7.dat | 2 -- .../src/test/resources/entryIT/A0A0A0MSM0.dat | 4 +-- .../src/test/resources/entryIT/P05067.dat | 2 -- .../src/test/resources/entryIT/P09470.dat | 3 --- .../src/test/resources/entryIT/P35626.dat | 2 -- .../src/test/resources/entryIT/Q00731.txl | 1 - .../src/test/resources/entryIT/Q03112.dat | 1 - .../src/test/resources/entryIT/Q13362.dat | 1 - .../src/test/resources/entryIT/Q15758.dat | 2 -- .../src/test/resources/entryIT/Q15758.txl | 2 -- .../src/test/resources/entryIT/Q63HN8.dat | 2 -- .../src/test/resources/entryIT/Q64524.dat | 1 - .../src/test/resources/entryIT/Q6P2Q9.dat | 2 -- .../src/test/resources/entryIT/Q96SD1.dat | 2 -- .../src/test/resources/entryIT/Q9NYP9.dat | 2 -- .../src/test/resources/entryIT/Q9U299.txl | 1 - .../scorer/uniprotkb/Q04756ScoredTest.java | 1 - .../UniProtKBCrossReferenceConverterTest.java | 6 ++--- 25 files changed, 11 insertions(+), 100 deletions(-) diff --git a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json index 5be948594..ed428ff50 100644 --- a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json +++ b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json @@ -379,13 +379,6 @@ "category": "PFAM", "uriLink": "http://www.moonlightingproteins.org/proteins/?q=%id" }, - { - "name": "CLAE", - "displayName": "CLAE", - "category": "PFAM", - "uriLink": "https://clae.fungalgenomics.ca/enzyme/%id", - "idMappingName": "CLAE_ID" - }, { "name": "PeroxiBase", "displayName": "PeroxiBase", @@ -545,12 +538,6 @@ "category": "2DG", "uriLink": "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=%id" }, - { - "name": "DOSAC-COBS-2DPAGE", - "displayName": "DOSAC-COBS-2DPAGE", - "category": "2DG", - "uriLink": "http://www.dosac.unipa.it/cgi-bin/2d/2d.cgi?ac=%id" - }, { "name": "OGP", "displayName": "OGP", @@ -570,18 +557,6 @@ "uriLink": "https://assays.cancer.gov/%id", "idMappingName": "CPTAC_ID" }, - { - "name": "EPD", - "displayName": "EPD", - "category": "PROTEOMIC", - "uriLink": "https://www.peptracker.com/epd/analytics/?protein_id=%id" - }, - { - "name": "MaxQB", - "displayName": "MaxQB", - "category": "PROTEOMIC", - "uriLink": "http://maxqb.biochem.mpg.de/mxdb/protein/show/%id" - }, { "name": "PaxDb", "displayName": "PaxDb", 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 2e8b9b8fe..0baf8d6cf 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 @@ -129,17 +129,6 @@ void testSwiss2dpageType() { assertThrows(IllegalArgumentException.class,()->UniProtDatabaseTypes.INSTANCE.getDbTypeByName("SWISS-2DPAGE")); } - @Test - void testMaxQBType() { - UniProtDatabaseDetail opType = UniProtDatabaseTypes.INSTANCE.getDbTypeByName("MaxQB"); - assertEquals("MaxQB", opType.getName()); - assertEquals("MaxQB", opType.getDisplayName()); - assertEquals(PROTEOMIC_DATABASES, opType.getCategory()); - assertEquals("http://maxqb.biochem.mpg.de/mxdb/protein/show/%id", opType.getUriLink()); - assertEquals(1, opType.getAttributes().size()); - verifyAttribute(opType.getAttributes().get(0), "Description", "description", null); - } - @Test void testDNASUType() { UniProtDatabaseDetail opType = UniProtDatabaseTypes.INSTANCE.getDbTypeByName("DNASU"); @@ -288,13 +277,13 @@ void testDatabaseFieldSize() { verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(CHEMISTRY), 6); verifyGroupSize( UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PROTEIN_FAMILY_GROUP_DATABASES), - 13); + 12); verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PTM_DATABASES), 10); verifyGroupSize( UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(GENERIC_VARIATION_DATABASES), 6); - verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(D2_GEL_DATABASES), 4); + verifyGroupSize(UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(D2_GEL_DATABASES), 3); verifyGroupSize( - UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PROTEOMIC_DATABASES), 12); + UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory(PROTEOMIC_DATABASES), 10); verifyGroupSize( UniProtDatabaseTypes.INSTANCE.getDBTypesByCategory( PROTOCOLS_AND_MATERIALS_DATABASES), diff --git a/controlled-vocabulary/src/test/resources/xdb/dr_ord b/controlled-vocabulary/src/test/resources/xdb/dr_ord index 682c455dd..264d6048c 100644 --- a/controlled-vocabulary/src/test/resources/xdb/dr_ord +++ b/controlled-vocabulary/src/test/resources/xdb/dr_ord @@ -47,17 +47,14 @@ BioMuta 1 dbSNP 1 DMDM 1 COMPLUYEAST-2DPAGE 1 -DOSAC-COBS-2DPAGE 1 OGP 1 REPRODUCTION-2DPAGE 1 SWISS-2DPAGE 1 UCD-2DPAGE 1 World-2DPAGE 1 CPTAC 1 -EPD 1 jPOST 1 MassIVE 1 -MaxQB 1 PaxDb 1 PeptideAtlas 1 PRIDE 1 diff --git a/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java b/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java index 0ced716ec..b934927f0 100644 --- a/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java +++ b/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java @@ -44,13 +44,6 @@ private void init() { "I", "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=%value")); typeMap.put("EMBL", evd("EMBL", "EMBL", "I", "https://www.ebi.ac.uk/ena/data/view/%value")); - typeMap.put( - "EPD", - evd( - "EPD", - "EPD", - "C", - "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomics_mapping/README")); typeMap.put("Ensembl", evd("Ensembl", "Ensembl", "I", "https://www.ensembl.org/id/%value")); typeMap.put( "EnsemblBacteria", @@ -106,13 +99,7 @@ private void init() { "JaponicusDB", evd("JaponicusDB", "JaponicusDB", "I", "https://www.japonicusdb.org/gene/%value")); typeMap.put("MGI", evd("MGI", "MGI", "I", "http://www.informatics.jax.org/marker/%value")); - typeMap.put( - "MaxQB", - evd( - "MaxQB", - "MaxQB", - "C", - "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/proteomics_mapping/README")); + typeMap.put("NCIfam", evd("NCIfam", "NCIfam", "A", "https://www.uniprot.org/arba/%value")); typeMap.put( "PDB", evd("PDB", "PDB", "I", "https://www.ebi.ac.uk/pdbe-srv/view/entry/%value")); typeMap.put( diff --git a/core-domain/src/test/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java b/core-domain/src/test/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java index ecf370efe..1b21a6eb0 100644 --- a/core-domain/src/test/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java +++ b/core-domain/src/test/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java @@ -24,7 +24,7 @@ void testGetAllEvidenceDatabases() { List evidenceDatabases = EvidenceDatabaseTypes.INSTANCE.getAllEvidenceDatabases(); assertNotNull(evidenceDatabases); - assertEquals(53, evidenceDatabases.size()); + assertEquals(52, evidenceDatabases.size()); } @Test diff --git a/core-parser/src/test/java/org/uniprot/core/parser/tsv/uniprot/UniProtKBEntryValueMapperTest.java b/core-parser/src/test/java/org/uniprot/core/parser/tsv/uniprot/UniProtKBEntryValueMapperTest.java index e4dc63d5e..074c734ec 100644 --- a/core-parser/src/test/java/org/uniprot/core/parser/tsv/uniprot/UniProtKBEntryValueMapperTest.java +++ b/core-parser/src/test/java/org/uniprot/core/parser/tsv/uniprot/UniProtKBEntryValueMapperTest.java @@ -659,8 +659,7 @@ void testXRefs3() { "xref_drugbank", "xref_guidetopharmacology", "xref_tcdb", - "xref_dmdm", - "xref_maxqb"); + "xref_dmdm"); Map result = new UniProtKBEntryValueMapper().mapEntity(entryQ15758, fields); verify("Q15758", "accession", result); @@ -668,12 +667,10 @@ void testXRefs3() { String guidetopharmacology = "874;"; String tcdb = "2.A.23.3.3;"; String dmdm = "21542389;"; - String maxqb = "Q15758;"; verify(drugbank, "xref_drugbank", result); verify(guidetopharmacology, "xref_guidetopharmacology", result); verify(tcdb, "xref_tcdb", result); verify(dmdm, "xref_dmdm", result); - verify(maxqb, "xref_maxqb", result); } @Test @@ -684,8 +681,7 @@ void testXRefs3Full() { "xref_drugbank_full", "xref_guidetopharmacology_full", "xref_tcdb_full", - "xref_dmdm_full", - "xref_maxqb_full"); + "xref_dmdm_full"); Map result = new UniProtKBEntryValueMapper().mapEntity(entryQ15758, fields); verify("Q15758", "accession", result); @@ -694,12 +690,10 @@ void testXRefs3Full() { String tcdb = "\"2.A.23.3.3; the dicarboxylate/amino acid:cation (na(+) or h(+)) symporter (daacs) family.\";"; - String maxqb = "Q15758;"; verify(drugbank, "xref_drugbank_full", result); assertNull(result.get("xref_guidetopharmacology_full")); verify(tcdb, "xref_tcdb_full", result); assertNull(result.get("xref_dmdm_full")); - assertNull(result.get("xref_maxqb_full")); } @Test diff --git a/core-parser/src/test/resources/uniprot/Q15758.dat b/core-parser/src/test/resources/uniprot/Q15758.dat index 5c1c930b6..da73d6918 100644 --- a/core-parser/src/test/resources/uniprot/Q15758.dat +++ b/core-parser/src/test/resources/uniprot/Q15758.dat @@ -386,10 +386,8 @@ DR PhosphoSitePlus; Q15758; -. DR SwissPalm; Q15758; -. DR BioMuta; SLC1A5; -. DR DMDM; 21542389; -. -DR EPD; Q15758; -. DR jPOST; Q15758; -. DR MassIVE; Q15758; -. -DR MaxQB; Q15758; -. DR PaxDb; Q15758; -. DR PeptideAtlas; Q15758; -. DR PRIDE; Q15758; -. diff --git a/core-parser/src/test/resources/uniprotkb/entry/Q8NDV7.dat b/core-parser/src/test/resources/uniprotkb/entry/Q8NDV7.dat index bd4d38dd0..51625abe3 100644 --- a/core-parser/src/test/resources/uniprotkb/entry/Q8NDV7.dat +++ b/core-parser/src/test/resources/uniprotkb/entry/Q8NDV7.dat @@ -465,10 +465,8 @@ DR iPTMnet; Q8NDV7; -. DR PhosphoSitePlus; Q8NDV7; -. DR BioMuta; TNRC6A; -. DR DMDM; 296452846; -. -DR EPD; Q8NDV7; -. DR jPOST; Q8NDV7; -. DR MassIVE; Q8NDV7; -. -DR MaxQB; Q8NDV7; -. DR PaxDb; Q8NDV7; -. DR PeptideAtlas; Q8NDV7; -. DR PRIDE; Q8NDV7; -. diff --git a/ff-parser/src/test/resources/entryIT/A0A0A0MSM0.dat b/ff-parser/src/test/resources/entryIT/A0A0A0MSM0.dat index e50100618..c4f1aae23 100644 --- a/ff-parser/src/test/resources/entryIT/A0A0A0MSM0.dat +++ b/ff-parser/src/test/resources/entryIT/A0A0A0MSM0.dat @@ -115,7 +115,6 @@ CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AL137142; -; NOT_ANNOTATED_CDS; Genomic_DNA. DR RefSeq; NP_001273434.1; NM_001286505.1. -DR EPD; A0A0A0MSM0; -. DR jPOST; A0A0A0MSM0; -. DR PeptideAtlas; A0A0A0MSM0; -. DR PRIDE; A0A0A0MSM0; -. @@ -151,8 +150,7 @@ DR PROSITE; PS01036; HSP70_3; 1. PE 1: Evidence at protein level; KW Coiled coil {ECO:0000256|SAM:Coils}; KW Complete proteome {ECO:0000313|Proteomes:UP000005640}; -KW Proteomics identification {ECO:0000213|EPD:A0A0A0MSM0, -KW ECO:0000213|MaxQB:A0A0A0MSM0, ECO:0000213|PeptideAtlas:A0A0A0MSM0}; +KW Proteomics identification {ECO:0000213|PeptideAtlas:A0A0A0MSM0}; KW Reference proteome {ECO:0000313|Proteomes:UP000005640}. FT COILED 544..568 FT /evidence="ECO:0000256|SAM:Coils" diff --git a/ff-parser/src/test/resources/entryIT/P05067.dat b/ff-parser/src/test/resources/entryIT/P05067.dat index d173f6cc0..a8d1a8abe 100644 --- a/ff-parser/src/test/resources/entryIT/P05067.dat +++ b/ff-parser/src/test/resources/entryIT/P05067.dat @@ -2416,10 +2416,8 @@ DR UniCarbKB; P05067; -. DR BioMuta; APP; -. DR DMDM; 112927; -. DR SWISS-2DPAGE; P05067; -. -DR EPD; P05067; -. DR jPOST; P05067; -. DR MassIVE; P05067; -. -DR MaxQB; P05067; -. DR PaxDb; P05067; -. DR PeptideAtlas; P05067; -. DR PRIDE; P05067; -. diff --git a/ff-parser/src/test/resources/entryIT/P09470.dat b/ff-parser/src/test/resources/entryIT/P09470.dat index 4c5131ae4..cb8812e70 100644 --- a/ff-parser/src/test/resources/entryIT/P09470.dat +++ b/ff-parser/src/test/resources/entryIT/P09470.dat @@ -534,7 +534,6 @@ DR GlyGen; P09470; 14 sites, 9 N-linked glycans (5 sites). DR iPTMnet; P09470; -. DR PhosphoSitePlus; P09470; -. DR jPOST; P09470; -. -DR MaxQB; P09470; -. DR PaxDb; P09470; -. DR PeptideAtlas; P09470; -. DR PRIDE; P09470; -. @@ -1020,10 +1019,8 @@ DR iPTMnet; P35626; -. DR PhosphoSitePlus; P35626; -. DR BioMuta; GRK3; -. DR DMDM; 116241253; -. -DR EPD; P35626; -. DR jPOST; P35626; -. DR MassIVE; P35626; -. -DR MaxQB; P35626; -. DR PaxDb; P35626; -. DR PeptideAtlas; P35626; -. DR PRIDE; P35626; -. diff --git a/ff-parser/src/test/resources/entryIT/P35626.dat b/ff-parser/src/test/resources/entryIT/P35626.dat index 06c0c2035..29a937313 100644 --- a/ff-parser/src/test/resources/entryIT/P35626.dat +++ b/ff-parser/src/test/resources/entryIT/P35626.dat @@ -122,9 +122,7 @@ DR iPTMnet; P35626; -. DR PhosphoSitePlus; P35626; -. DR BioMuta; GRK3; -. DR DMDM; 116241253; -. -DR EPD; P35626; -. DR jPOST; P35626; -. -DR MaxQB; P35626; -. DR PaxDb; P35626; -. DR PeptideAtlas; P35626; -. DR PRIDE; P35626; -. diff --git a/ff-parser/src/test/resources/entryIT/Q00731.txl b/ff-parser/src/test/resources/entryIT/Q00731.txl index e6f0bac46..5b217b418 100644 --- a/ff-parser/src/test/resources/entryIT/Q00731.txl +++ b/ff-parser/src/test/resources/entryIT/Q00731.txl @@ -217,7 +217,6 @@ DR DIP; DIP-31909N; -. DR IntAct; Q00731; 3. DR STRING; 10090.ENSMUSP00000115883; -. DR PhosphoSitePlus; Q00731; -. -DR MaxQB; Q00731; -. DR PaxDb; Q00731; -. DR PRIDE; Q00731; -. DR Ensembl; ENSMUST00000024747; ENSMUSP00000024747; ENSMUSG00000023951. [Q00731-3] diff --git a/ff-parser/src/test/resources/entryIT/Q03112.dat b/ff-parser/src/test/resources/entryIT/Q03112.dat index 6359c7a84..a38bd15ea 100644 --- a/ff-parser/src/test/resources/entryIT/Q03112.dat +++ b/ff-parser/src/test/resources/entryIT/Q03112.dat @@ -469,7 +469,6 @@ DR BioMuta; MECOM; -. DR DMDM; 145559472; -. DR jPOST; Q03112; -. DR MassIVE; Q03112; -. -DR MaxQB; Q03112; -. DR PaxDb; Q03112; -. DR PeptideAtlas; Q03112; -. DR PRIDE; Q03112; -. diff --git a/ff-parser/src/test/resources/entryIT/Q13362.dat b/ff-parser/src/test/resources/entryIT/Q13362.dat index 810f6295f..53d5ab077 100644 --- a/ff-parser/src/test/resources/entryIT/Q13362.dat +++ b/ff-parser/src/test/resources/entryIT/Q13362.dat @@ -364,7 +364,6 @@ DR BioMuta; PPP2R5C; -. DR DMDM; 116241235; -. DR jPOST; Q13362; -. DR MassIVE; Q13362; -. -DR MaxQB; Q13362; -. DR PaxDb; Q13362; -. DR PeptideAtlas; Q13362; -. DR PRIDE; Q13362; -. diff --git a/ff-parser/src/test/resources/entryIT/Q15758.dat b/ff-parser/src/test/resources/entryIT/Q15758.dat index 5aea10d65..da3c2d118 100644 --- a/ff-parser/src/test/resources/entryIT/Q15758.dat +++ b/ff-parser/src/test/resources/entryIT/Q15758.dat @@ -394,10 +394,8 @@ DR PhosphoSitePlus; Q15758; -. DR SwissPalm; Q15758; -. DR BioMuta; SLC1A5; -. DR DMDM; 21542389; -. -DR EPD; Q15758; -. DR jPOST; Q15758; -. DR MassIVE; Q15758; -. -DR MaxQB; Q15758; -. DR PaxDb; Q15758; -. DR PeptideAtlas; Q15758; -. DR PRIDE; Q15758; -. diff --git a/ff-parser/src/test/resources/entryIT/Q15758.txl b/ff-parser/src/test/resources/entryIT/Q15758.txl index cc1f16811..f080e977a 100644 --- a/ff-parser/src/test/resources/entryIT/Q15758.txl +++ b/ff-parser/src/test/resources/entryIT/Q15758.txl @@ -390,10 +390,8 @@ DR PhosphoSitePlus; Q15758; -. DR SwissPalm; Q15758; -. DR BioMuta; SLC1A5; -. DR DMDM; 21542389; -. -DR EPD; Q15758; -. DR jPOST; Q15758; -. DR MassIVE; Q15758; -. -DR MaxQB; Q15758; -. DR PaxDb; Q15758; -. DR PeptideAtlas; Q15758; -. DR PRIDE; Q15758; -. diff --git a/ff-parser/src/test/resources/entryIT/Q63HN8.dat b/ff-parser/src/test/resources/entryIT/Q63HN8.dat index d84a7c1e9..2c956f9ec 100644 --- a/ff-parser/src/test/resources/entryIT/Q63HN8.dat +++ b/ff-parser/src/test/resources/entryIT/Q63HN8.dat @@ -500,10 +500,8 @@ DR PhosphoSitePlus; Q63HN8; -. DR SwissPalm; Q63HN8; -. DR BioMuta; RNF213; -. DR DMDM; 380865458; -. -DR EPD; Q63HN8; -. DR jPOST; Q63HN8; -. DR MassIVE; Q63HN8; -. -DR MaxQB; Q63HN8; -. DR PaxDb; Q63HN8; -. DR PeptideAtlas; Q63HN8; -. DR PRIDE; Q63HN8; -. diff --git a/ff-parser/src/test/resources/entryIT/Q64524.dat b/ff-parser/src/test/resources/entryIT/Q64524.dat index e8d688579..35ad18df9 100644 --- a/ff-parser/src/test/resources/entryIT/Q64524.dat +++ b/ff-parser/src/test/resources/entryIT/Q64524.dat @@ -214,7 +214,6 @@ DR iPTMnet; Q64524; -. DR PhosphoSitePlus; Q64524; -. DR SwissPalm; Q64524; -. DR jPOST; Q64524; -. -DR MaxQB; Q64524; -. DR PaxDb; Q64524; -. DR PeptideAtlas; Q64524; -. DR PRIDE; Q64524; -. diff --git a/ff-parser/src/test/resources/entryIT/Q6P2Q9.dat b/ff-parser/src/test/resources/entryIT/Q6P2Q9.dat index 47965f833..789b74b7c 100644 --- a/ff-parser/src/test/resources/entryIT/Q6P2Q9.dat +++ b/ff-parser/src/test/resources/entryIT/Q6P2Q9.dat @@ -649,10 +649,8 @@ DR PhosphoSitePlus; Q6P2Q9; -. DR SwissPalm; Q6P2Q9; -. DR BioMuta; PRPF8; -. DR DMDM; 67460824; -. -DR EPD; Q6P2Q9; -. DR jPOST; Q6P2Q9; -. DR MassIVE; Q6P2Q9; -. -DR MaxQB; Q6P2Q9; -. DR PaxDb; Q6P2Q9; -. DR PeptideAtlas; Q6P2Q9; -. DR PRIDE; Q6P2Q9; -. diff --git a/ff-parser/src/test/resources/entryIT/Q96SD1.dat b/ff-parser/src/test/resources/entryIT/Q96SD1.dat index 37cdfb9e3..c52d188c9 100644 --- a/ff-parser/src/test/resources/entryIT/Q96SD1.dat +++ b/ff-parser/src/test/resources/entryIT/Q96SD1.dat @@ -445,10 +445,8 @@ DR iPTMnet; Q96SD1; -. DR PhosphoSitePlus; Q96SD1; -. DR BioMuta; DCLRE1C; -. DR DMDM; 71153325; -. -DR EPD; Q96SD1; -. DR jPOST; Q96SD1; -. DR MassIVE; Q96SD1; -. -DR MaxQB; Q96SD1; -. DR PaxDb; Q96SD1; -. DR PeptideAtlas; Q96SD1; -. DR PRIDE; Q96SD1; -. diff --git a/ff-parser/src/test/resources/entryIT/Q9NYP9.dat b/ff-parser/src/test/resources/entryIT/Q9NYP9.dat index 7ec22e866..f5729554e 100644 --- a/ff-parser/src/test/resources/entryIT/Q9NYP9.dat +++ b/ff-parser/src/test/resources/entryIT/Q9NYP9.dat @@ -241,10 +241,8 @@ DR PhosphoSitePlus; Q9NYP9; -. DR SwissPalm; Q9NYP9; -. DR BioMuta; MIS18A; -. DR DMDM; 12229716; -. -DR EPD; Q9NYP9; -. DR jPOST; Q9NYP9; -. DR MassIVE; Q9NYP9; -. -DR MaxQB; Q9NYP9; -. DR PaxDb; Q9NYP9; -. DR PeptideAtlas; Q9NYP9; -. DR PRIDE; Q9NYP9; -. diff --git a/ff-parser/src/test/resources/entryIT/Q9U299.txl b/ff-parser/src/test/resources/entryIT/Q9U299.txl index efa89e1da..21fa36fb5 100644 --- a/ff-parser/src/test/resources/entryIT/Q9U299.txl +++ b/ff-parser/src/test/resources/entryIT/Q9U299.txl @@ -120,7 +120,6 @@ DR ComplexPortal; CPX-420; xtbd-paxt-1 complex. DR DIP; DIP-24636N; -. DR IntAct; Q9U299; 3. DR STRING; 6239.Y48B6A.3; -. -DR EPD; Q9U299; -. DR PaxDb; Q9U299; -. DR PeptideAtlas; Q9U299; -. DR PRIDE; Q9U299; -. diff --git a/tools-entry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/Q04756ScoredTest.java b/tools-entry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/Q04756ScoredTest.java index efea0efd6..331717e09 100644 --- a/tools-entry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/Q04756ScoredTest.java +++ b/tools-entry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/Q04756ScoredTest.java @@ -248,7 +248,6 @@ class Q04756ScoredTest { + "DR DMDM; 547643; -.\n" + "DR jPOST; Q04756; -.\n" + "DR MassIVE; Q04756; -.\n" - + "DR MaxQB; Q04756; -.\n" + "DR PaxDb; Q04756; -.\n" + "DR PeptideAtlas; Q04756; -.\n" + "DR PRIDE; Q04756; -.\n" diff --git a/xml-parser/src/test/java/org/uniprot/core/xml/uniprot/UniProtKBCrossReferenceConverterTest.java b/xml-parser/src/test/java/org/uniprot/core/xml/uniprot/UniProtKBCrossReferenceConverterTest.java index 1a6dd9cd4..ef897872a 100644 --- a/xml-parser/src/test/java/org/uniprot/core/xml/uniprot/UniProtKBCrossReferenceConverterTest.java +++ b/xml-parser/src/test/java/org/uniprot/core/xml/uniprot/UniProtKBCrossReferenceConverterTest.java @@ -48,9 +48,9 @@ void testEmbl3Attributes() { } @Test - void testEPDNoAttributes() { - // DR EPD; Q9U3D6; -. - String dbName = "EPD"; + void testPRIDENoAttributes() { + // DR PRIDE; Q9U3D6; -. + String dbName = "PRIDE"; String id = "Q9U3D6"; String description = "-"; String thirdAttribute = null; From fa063aad276d09c0f9bbf31c70b8fa7739f66243 Mon Sep 17 00:00:00 2001 From: supun Date: Wed, 5 Jun 2024 13:54:01 +0100 Subject: [PATCH 2/3] version bump --- controlled-vocabulary/pom.xml | 2 +- core-common/pom.xml | 2 +- core-domain-utils/pom.xml | 2 +- core-domain/pom.xml | 2 +- core-parser/pom.xml | 2 +- ff-parser/pom.xml | 2 +- jacoco-aggregate-report/pom.xml | 2 +- json-parser/pom.xml | 2 +- pom.xml | 2 +- tools-entry-scorer/pom.xml | 2 +- xml-parser/pom.xml | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/controlled-vocabulary/pom.xml b/controlled-vocabulary/pom.xml index e4383a600..496fe2b17 100644 --- a/controlled-vocabulary/pom.xml +++ b/controlled-vocabulary/pom.xml @@ -6,7 +6,7 @@ org.uniprot core-parent - 1.0.32-SNAPSHOT + 2024.4 ../ diff --git a/core-common/pom.xml b/core-common/pom.xml index e1ca4c6ee..26e551982 100644 --- a/core-common/pom.xml +++ b/core-common/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.32-SNAPSHOT + 2024.4 ../ diff --git a/core-domain-utils/pom.xml b/core-domain-utils/pom.xml index 0706060f4..6c65b8482 100644 --- a/core-domain-utils/pom.xml +++ b/core-domain-utils/pom.xml @@ -5,7 +5,7 @@ core-parent org.uniprot - 1.0.32-SNAPSHOT + 2024.4 4.0.0 diff --git a/core-domain/pom.xml b/core-domain/pom.xml index ca761bd8f..df5473aaa 100644 --- a/core-domain/pom.xml +++ b/core-domain/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.32-SNAPSHOT + 2024.4 ../ diff --git a/core-parser/pom.xml b/core-parser/pom.xml index 86f846c2f..a75d2288b 100644 --- a/core-parser/pom.xml +++ b/core-parser/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.32-SNAPSHOT + 2024.4 ../ diff --git a/ff-parser/pom.xml b/ff-parser/pom.xml index 2226b7e6c..1fb2f9cd3 100644 --- a/ff-parser/pom.xml +++ b/ff-parser/pom.xml @@ -6,7 +6,7 @@ org.uniprot core-parent - 1.0.32-SNAPSHOT + 2024.4 ../ diff --git a/jacoco-aggregate-report/pom.xml b/jacoco-aggregate-report/pom.xml index 2f49b57a1..5b6263be4 100644 --- a/jacoco-aggregate-report/pom.xml +++ b/jacoco-aggregate-report/pom.xml @@ -5,7 +5,7 @@ core-parent org.uniprot - 1.0.32-SNAPSHOT + 2024.4 4.0.0 diff --git a/json-parser/pom.xml b/json-parser/pom.xml index 921ea9cd2..d19ad3149 100644 --- a/json-parser/pom.xml +++ b/json-parser/pom.xml @@ -5,7 +5,7 @@ org.uniprot core-parent - 1.0.32-SNAPSHOT + 2024.4 ../ 4.0.0 diff --git a/pom.xml b/pom.xml index 6f9758380..37769e382 100644 --- a/pom.xml +++ b/pom.xml @@ -7,7 +7,7 @@ org.uniprot core-parent pom - 1.0.32-SNAPSHOT + 2024.4 UniProt Core Aggregator diff --git a/tools-entry-scorer/pom.xml b/tools-entry-scorer/pom.xml index 0be56c820..f4da7f16b 100644 --- a/tools-entry-scorer/pom.xml +++ b/tools-entry-scorer/pom.xml @@ -5,7 +5,7 @@ core-parent org.uniprot - 1.0.32-SNAPSHOT + 2024.4 ../ 4.0.0 diff --git a/xml-parser/pom.xml b/xml-parser/pom.xml index 719b5520d..f0ab6e095 100644 --- a/xml-parser/pom.xml +++ b/xml-parser/pom.xml @@ -6,7 +6,7 @@ org.uniprot core-parent - 1.0.32-SNAPSHOT + 2024.4 ../ From 3c023413b363d6a88ca9816c0c39c3e49c5cc898 Mon Sep 17 00:00:00 2001 From: LeonardoGonzales Date: Wed, 5 Jun 2024 14:16:05 +0100 Subject: [PATCH 3/3] Update NCBIfam details --- .../uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java b/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java index b934927f0..1210f3a16 100644 --- a/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java +++ b/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java @@ -99,7 +99,7 @@ private void init() { "JaponicusDB", evd("JaponicusDB", "JaponicusDB", "I", "https://www.japonicusdb.org/gene/%value")); typeMap.put("MGI", evd("MGI", "MGI", "I", "http://www.informatics.jax.org/marker/%value")); - typeMap.put("NCIfam", evd("NCIfam", "NCIfam", "A", "https://www.uniprot.org/arba/%value")); + typeMap.put("NCBIfam", evd("NCBIfam", "NCBIfam", "A", "https://www.ebi.ac.uk/interpro/entry/ncbifam/%value")); typeMap.put( "PDB", evd("PDB", "PDB", "I", "https://www.ebi.ac.uk/pdbe-srv/view/entry/%value")); typeMap.put(