Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

2024 04 changes #233

Merged
merged 5 commits into from
Jul 15, 2024
Merged

2024 04 changes #233

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
d21c987
2024_04 changes (TRM-31122,TRM-31125,TRM-31265,TRM-31263,TRM-31390)
LeonardoGonzales Jun 5, 2024
fa063aa
version bump
supun-ebi Jun 5, 2024
3c02341
Update NCBIfam details
LeonardoGonzales Jun 5, 2024
dbe68bb
Merge remote-tracking branch 'origin/2024_04_changes' into 2024_04_ch…
LeonardoGonzales Jun 5, 2024
4432ddc
Merge branch 'main' into 2024_04_changes
supun-ebi Jul 15, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 0 additions & 25 deletions controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand Down
17 changes: 3 additions & 14 deletions controlled-vocabulary/src/test/java/org/uniprot/cv/xdb/UniProtKBDatabaseTypesTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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");
Expand Down Expand Up @@ -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),
Expand Down
3 changes: 0 additions & 3 deletions controlled-vocabulary/src/test/resources/xdb/dr_ord
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
15 changes: 1 addition & 14 deletions core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypes.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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("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(
Expand Down
2 changes: 1 addition & 1 deletion core-domain/src/test/java/org/uniprot/core/uniprotkb/evidence/EvidenceDatabaseTypesTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ void testGetAllEvidenceDatabases() {
List<EvidenceDatabaseDetail> evidenceDatabases =
EvidenceDatabaseTypes.INSTANCE.getAllEvidenceDatabases();
assertNotNull(evidenceDatabases);
assertEquals(53, evidenceDatabases.size());
assertEquals(52, evidenceDatabases.size());
}

@Test
Expand Down
10 changes: 2 additions & 8 deletions ...rser/src/test/java/org/uniprot/core/parser/tsv/uniprot/UniProtKBEntryValueMapperTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -659,21 +659,18 @@ void testXRefs3() {
"xref_drugbank",
"xref_guidetopharmacology",
"xref_tcdb",
"xref_dmdm",
"xref_maxqb");
"xref_dmdm");
Map<String, String> result = new UniProtKBEntryValueMapper().mapEntity(entryQ15758, fields);

verify("Q15758", "accession", result);
String drugbank = "DB00174;DB13146;DB00130;";
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
Expand All @@ -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<String, String> result = new UniProtKBEntryValueMapper().mapEntity(entryQ15758, fields);

verify("Q15758", "accession", result);
Expand All @@ -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
Expand Down
2 changes: 0 additions & 2 deletions core-parser/src/test/resources/uniprot/Q15758.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
2 changes: 0 additions & 2 deletions core-parser/src/test/resources/uniprotkb/entry/Q8NDV7.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
4 changes: 1 addition & 3 deletions ff-parser/src/test/resources/entryIT/A0A0A0MSM0.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down Expand Up @@ -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"
Expand Down
2 changes: 0 additions & 2 deletions ff-parser/src/test/resources/entryIT/P05067.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
3 changes: 0 additions & 3 deletions ff-parser/src/test/resources/entryIT/P09470.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down Expand Up @@ -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; -.
Expand Down
2 changes: 0 additions & 2 deletions ff-parser/src/test/resources/entryIT/P35626.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
1 change: 0 additions & 1 deletion ff-parser/src/test/resources/entryIT/Q00731.txl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand Down
1 change: 0 additions & 1 deletion ff-parser/src/test/resources/entryIT/Q03112.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
1 change: 0 additions & 1 deletion ff-parser/src/test/resources/entryIT/Q13362.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
2 changes: 0 additions & 2 deletions ff-parser/src/test/resources/entryIT/Q15758.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
2 changes: 0 additions & 2 deletions ff-parser/src/test/resources/entryIT/Q15758.txl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
2 changes: 0 additions & 2 deletions ff-parser/src/test/resources/entryIT/Q63HN8.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
1 change: 0 additions & 1 deletion ff-parser/src/test/resources/entryIT/Q64524.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
2 changes: 0 additions & 2 deletions ff-parser/src/test/resources/entryIT/Q6P2Q9.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
2 changes: 0 additions & 2 deletions ff-parser/src/test/resources/entryIT/Q96SD1.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
2 changes: 0 additions & 2 deletions ff-parser/src/test/resources/entryIT/Q9NYP9.dat
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
1 change: 0 additions & 1 deletion ff-parser/src/test/resources/entryIT/Q9U299.txl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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; -.
Expand Down
1 change: 0 additions & 1 deletion tools-entry-scorer/src/test/java/org/uniprot/core/scorer/uniprotkb/Q04756ScoredTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down
6 changes: 3 additions & 3 deletions ...rser/src/test/java/org/uniprot/core/xml/uniprot/UniProtKBCrossReferenceConverterTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down
Loading