diff --git a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json index 90971d77a..99371f031 100644 --- a/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json +++ b/controlled-vocabulary/src/main/resources/META-INF/drlineconfiguration.json @@ -1742,8 +1742,8 @@ ] }, { - "name": "TIGRFAMs", - "displayName": "TIGRFAMs", + "name": "NCBIfam", + "displayName": "NCBIfam", "category": "FMD", "uriLink": "https://www.ncbi.nlm.nih.gov/genome/annotation_prok/evidence/%id/", "attributes": [ diff --git a/controlled-vocabulary/src/test/resources/xdb/dr_ord b/controlled-vocabulary/src/test/resources/xdb/dr_ord index b1b4f4863..682c455dd 100644 --- a/controlled-vocabulary/src/test/resources/xdb/dr_ord +++ b/controlled-vocabulary/src/test/resources/xdb/dr_ord @@ -160,5 +160,5 @@ PRINTS 2 SFLD 1 SMART 2 SUPFAM 2 -TIGRFAMs 2 +NCBIfam 2 PROSITE 2 diff --git a/core-domain/src/main/java/org/uniprot/core/uniparc/SignatureDbType.java b/core-domain/src/main/java/org/uniprot/core/uniparc/SignatureDbType.java index c31670a1a..191f0906d 100644 --- a/core-domain/src/main/java/org/uniprot/core/uniparc/SignatureDbType.java +++ b/core-domain/src/main/java/org/uniprot/core/uniparc/SignatureDbType.java @@ -17,7 +17,7 @@ public enum SignatureDbType implements EnumDisplay { SFLD("SFLD"), SMART("SMART"), SUPFAM("SUPFAM"), - TIGRFAMS("TIGRFAMs"); + NCBIFAM("NCBIfam"); private final String name; diff --git a/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceCode.java b/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceCode.java index 5701bc572..a7c158923 100644 --- a/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceCode.java +++ b/core-domain/src/main/java/org/uniprot/core/uniprotkb/evidence/EvidenceCode.java @@ -255,8 +255,13 @@ public enum EvidenceCode implements EnumDisplay { "Combinatorial", "combinatorial computational and experimental evidence used in automatic assertion", Collections.singletonList("Combined sources"), - EnumSet.of(Category.AUTOMATIC)); // replacing ECO_0000213 - // from 2021.2 release + EnumSet.of(Category.AUTOMATIC)), // replacing ECO_0000213 + + ECO_0008006("ECO:0008006", + "Deep learning", + "deep learning method evidence used in automatic assertion", + Collections.singletonList("Automatic Annotation"), + EnumSet.of(Category.AUTOMATIC)); private final String code; private final String name; diff --git a/core-parser/src/main/java/org/uniprot/core/parser/tsv/uniparc/UniParcSequenceFeatureMap.java b/core-parser/src/main/java/org/uniprot/core/parser/tsv/uniparc/UniParcSequenceFeatureMap.java index 709e7e8e6..d61da4cd9 100644 --- a/core-parser/src/main/java/org/uniprot/core/parser/tsv/uniparc/UniParcSequenceFeatureMap.java +++ b/core-parser/src/main/java/org/uniprot/core/parser/tsv/uniparc/UniParcSequenceFeatureMap.java @@ -30,7 +30,7 @@ public class UniParcSequenceFeatureMap implements NamedValueMap { "SFLD", "SMART", "SUPFAM", - "TIGRFAMs")); + "NCBIfam")); private final List features; @@ -56,7 +56,7 @@ public Map attributeValues() { map.put(FIELDS.get(10), getData(SignatureDbType.SFLD)); map.put(FIELDS.get(11), getData(SignatureDbType.SMART)); map.put(FIELDS.get(12), getData(SignatureDbType.SUPFAM)); - map.put(FIELDS.get(13), getData(SignatureDbType.TIGRFAMS)); + map.put(FIELDS.get(13), getData(SignatureDbType.NCBIFAM)); return map; } diff --git a/core-parser/src/test/java/org/uniprot/core/parser/tsv/uniparc/UniParcSequenceFeatureMapTest.java b/core-parser/src/test/java/org/uniprot/core/parser/tsv/uniparc/UniParcSequenceFeatureMapTest.java index 561826e80..6671c9d13 100644 --- a/core-parser/src/test/java/org/uniprot/core/parser/tsv/uniparc/UniParcSequenceFeatureMapTest.java +++ b/core-parser/src/test/java/org/uniprot/core/parser/tsv/uniparc/UniParcSequenceFeatureMapTest.java @@ -59,7 +59,7 @@ void testFields() { "SFLD", "SMART", "SUPFAM", - "TIGRFAMs"); + "NCBIfam"); assertEquals(UniParcSequenceFeatureMap.FIELDS, fields); } diff --git a/ff-parser/src/test/resources/entryIT/A0A176EY13.txl b/ff-parser/src/test/resources/entryIT/A0A176EY13.txl index 951ebfeff..4bd5188b3 100644 --- a/ff-parser/src/test/resources/entryIT/A0A176EY13.txl +++ b/ff-parser/src/test/resources/entryIT/A0A176EY13.txl @@ -39,8 +39,8 @@ DR Pfam; PF00590; TP_methylase; 1. DR PIRSF; PIRSF036428; CobL; 1. DR SUPFAM; SSF53335; SSF53335; 1. DR SUPFAM; SSF53790; SSF53790; 1. -DR TIGRFAMs; TIGR02467; CbiE; 1. -DR TIGRFAMs; TIGR02469; CbiT; 1. +DR NCBIfam; NF02467; CbiE; 1. +DR NCBIfam; NF02469; CbiT; 1. PE 4: Predicted; KW Complete proteome {ECO:0000313|Proteomes:UP000077043}; KW Methyltransferase {ECO:0000313|EMBL:KZY30980.1}; diff --git a/ff-parser/src/test/resources/entryIT/A0A2D8TK40.txl b/ff-parser/src/test/resources/entryIT/A0A2D8TK40.txl index e657c71fd..2c612f617 100644 --- a/ff-parser/src/test/resources/entryIT/A0A2D8TK40.txl +++ b/ff-parser/src/test/resources/entryIT/A0A2D8TK40.txl @@ -35,7 +35,7 @@ DR Pfam; PF00394; Cu-oxidase; 1. DR Pfam; PF07731; Cu-oxidase_2; 1. DR Pfam; PF07732; Cu-oxidase_3; 1. DR SUPFAM; SSF49503; SSF49503; 3. -DR TIGRFAMs; TIGR01409; TAT_signal_seq; 1. +DR NCBIfam; NF01409; TAT_signal_seq; 1. DR PROSITE; PS00080; MULTICOPPER_OXIDASE2; 1. DR PROSITE; PS51318; TAT; 1. PE 4: Predicted; diff --git a/ff-parser/src/test/resources/entryIT/A8EZU1.dat b/ff-parser/src/test/resources/entryIT/A8EZU1.dat index f0df0b47e..2c978746a 100644 --- a/ff-parser/src/test/resources/entryIT/A8EZU1.dat +++ b/ff-parser/src/test/resources/entryIT/A8EZU1.dat @@ -56,7 +56,7 @@ DR InterPro; IPR023091; MetalPrtase_cat_dom_sf_prd. DR InterPro; IPR002036; YbeY. DR InterPro; IPR020549; YbeY_CS. DR Pfam; PF02130; YbeY; 1. -DR TIGRFAMs; TIGR00043; TIGR00043; 1. +DR NCBIfam; NF00043; NF00043; 1. DR PROSITE; PS01306; UPF0054; 1. PE 3: Inferred from homology; KW Cytoplasm; Endonuclease; Hydrolase; Metal-binding; Nuclease; diff --git a/ff-parser/src/test/resources/entryIT/A8EZU1_D6RDV7.dat b/ff-parser/src/test/resources/entryIT/A8EZU1_D6RDV7.dat index 7688909f2..394e883bf 100644 --- a/ff-parser/src/test/resources/entryIT/A8EZU1_D6RDV7.dat +++ b/ff-parser/src/test/resources/entryIT/A8EZU1_D6RDV7.dat @@ -56,7 +56,7 @@ DR InterPro; IPR023091; MetalPrtase_cat_dom_sf_prd. DR InterPro; IPR002036; YbeY. DR InterPro; IPR020549; YbeY_CS. DR Pfam; PF02130; YbeY; 1. -DR TIGRFAMs; TIGR00043; TIGR00043; 1. +DR NCBIfam; NF00043; NF00043; 1. DR PROSITE; PS01306; UPF0054; 1. PE 3: Inferred from homology; KW Cytoplasm; Endonuclease; Hydrolase; Metal-binding; Nuclease; diff --git a/ff-parser/src/test/resources/entryIT/A8EZU1_D6RDV7.dat.gz b/ff-parser/src/test/resources/entryIT/A8EZU1_D6RDV7.dat.gz index 535f9ecc6..de31d89ae 100644 Binary files a/ff-parser/src/test/resources/entryIT/A8EZU1_D6RDV7.dat.gz and b/ff-parser/src/test/resources/entryIT/A8EZU1_D6RDV7.dat.gz differ diff --git a/ff-parser/src/test/resources/entryIT/A8EZU1_ERROR_D6RDV7.dat b/ff-parser/src/test/resources/entryIT/A8EZU1_ERROR_D6RDV7.dat index f8d39f1eb..84cfafe4d 100644 --- a/ff-parser/src/test/resources/entryIT/A8EZU1_ERROR_D6RDV7.dat +++ b/ff-parser/src/test/resources/entryIT/A8EZU1_ERROR_D6RDV7.dat @@ -56,7 +56,7 @@ DR InterPro; IPR023091; MetalPrtase_cat_dom_sf_prd. DR InterPro; IPR002036; YbeY. DR InterPro; IPR020549; YbeY_CS. DR Pfam; PF02130; YbeY; 1. -DR TIGRFAMs; TIGR00043; TIGR00043; 1. +DR NCBIfam; NF00043; NF00043; 1. DR PROSITE; PS01306; UPF0054; 1. PE 3: Inferred from homology; KW Cytoplasm; Endonuclease; Hydrolase; Metal-binding; Nuclease; @@ -142,7 +142,7 @@ DR InterPro; IPR023091; MetalPrtase_cat_dom_sf_prd. DR InterPro; IPR002036; YbeY. DR InterPro; IPR020549; YbeY_CS. DR Pfam; PF02130; UPF0054; 1. -DR TIGRFAMs; TIGR00043; TIGR00043; 1. +DR NCBIfam; NF00043; NF00043; 1. DR PROSITE; PS01306; UPF0054; 1. PE 3: Inferred from homology; KW Complete proteome; Cytoplasm; Endonuclease; Hydrolase; Metal-binding; diff --git a/ff-parser/src/test/resources/entryIT/A9N0W4.txl b/ff-parser/src/test/resources/entryIT/A9N0W4.txl index 8045ea5e9..0e6de76dc 100644 --- a/ff-parser/src/test/resources/entryIT/A9N0W4.txl +++ b/ff-parser/src/test/resources/entryIT/A9N0W4.txl @@ -36,7 +36,7 @@ DR InterPro; IPR001150; Gly_radical. DR InterPro; IPR011140; Glycyl_radical_cofactor_GrcA. DR Pfam; PF01228; Gly_radical; 1. DR PIRSF; PIRSF000378; Gly_radicl_yfiD; 1. -DR TIGRFAMs; TIGR04365; spare_glycyl; 1. +DR NCBIfam; NF04365; spare_glycyl; 1. DR PROSITE; PS00850; GLY_RADICAL_1; 1. DR PROSITE; PS51149; GLY_RADICAL_2; 1. PE 3: Inferred from homology; diff --git a/ff-parser/src/test/resources/entryIT/ERROR_ERROR.dat b/ff-parser/src/test/resources/entryIT/ERROR_ERROR.dat index 816b8bc92..c85ced23b 100644 --- a/ff-parser/src/test/resources/entryIT/ERROR_ERROR.dat +++ b/ff-parser/src/test/resources/entryIT/ERROR_ERROR.dat @@ -56,7 +56,7 @@ DR InterPro; IPR023091; MetalPrtase_cat_dom_sf_prd. DR InterPro; IPR002036; YbeY. DR InterPro; IPR020549; YbeY_CS. DR Pfam; PF02130; UPF0054; 1. -DR TIGRFAMs; TIGR00043; TIGR00043; 1. +DR NCBIfam; NF00043; NF00043; 1. DR PROSITE; PS01306; UPF0054; 1. PE 3: Inferred from homology; KW Complete proteome; Cytoplasm; Endonuclease; Hydrolase; Metal-binding; @@ -136,7 +136,7 @@ DR InterPro; IPR023091; MetalPrtase_cat_dom_sf_prd. DR InterPro; IPR002036; YbeY. DR InterPro; IPR020549; YbeY_CS. DR Pfam; PF02130; UPF0054; 1. -DR TIGRFAMs; TIGR00043; TIGR00043; 1. +DR NCBIfam; NF00043; NF00043; 1. DR PROSITE; PS01306; UPF0054; 1. PE 3: Inferred from homology; KW Complete proteome; Cytoplasm; Endonuclease; Hydrolase; Metal-binding; diff --git a/ff-parser/src/test/resources/entryIT/O05204.dat b/ff-parser/src/test/resources/entryIT/O05204.dat index b6bd42ecf..b8189dff6 100644 --- a/ff-parser/src/test/resources/entryIT/O05204.dat +++ b/ff-parser/src/test/resources/entryIT/O05204.dat @@ -76,7 +76,7 @@ DR Pfam; PF13192; Thioredoxin_3; 1. DR PIRSF; PIRSF000238; AhpF; 1. DR SUPFAM; SSF51905; SSF51905; 1. DR SUPFAM; SSF52833; SSF52833; 2. -DR TIGRFAMs; TIGR03140; AhpF; 1. +DR NCBIfam; NF03140; AhpF; 1. DR PROSITE; PS51354; GLUTAREDOXIN_2; 1. DR PROSITE; PS00573; PYRIDINE_REDOX_2; 1. PE 3: Inferred from homology; diff --git a/ff-parser/src/test/resources/entryIT/P55301.dat b/ff-parser/src/test/resources/entryIT/P55301.dat index 179465cde..af72d9f69 100644 --- a/ff-parser/src/test/resources/entryIT/P55301.dat +++ b/ff-parser/src/test/resources/entryIT/P55301.dat @@ -97,7 +97,7 @@ DR Pfam; PF01913; FTR; 1. DR Pfam; PF02741; FTR_C; 1. DR PIRSF; PIRSF006414; Ftr_formyl_trnsf; 1. DR SUPFAM; SSF55112; SSF55112; 2. -DR TIGRFAMs; TIGR03119; one_C_fhcD; 1. +DR NCBIfam; NF03119; one_C_fhcD; 1. PE 1: Evidence at protein level; KW 3D-structure; Acyltransferase; Complete proteome; Cytoplasm; KW Direct protein sequencing; Methanogenesis; One-carbon metabolism; diff --git a/ff-parser/src/test/resources/entryIT/Q04664.dat b/ff-parser/src/test/resources/entryIT/Q04664.dat index c5e5d0cf9..b111679ee 100644 --- a/ff-parser/src/test/resources/entryIT/Q04664.dat +++ b/ff-parser/src/test/resources/entryIT/Q04664.dat @@ -101,7 +101,7 @@ DR GO; GO:0000271; P:polysaccharide biosynthetic process; IEA:UniProtKB-KW. DR InterPro; IPR003362; Bact_transf. DR InterPro; IPR017475; EPS_sugar_tfrase. DR Pfam; PF02397; Bac_transf; 1. -DR TIGRFAMs; TIGR03025; EPS_sugtrans; 1. +DR NCBIfam; NF03025; EPS_sugtrans; 1. PE 3: Inferred from homology; KW Capsule biogenesis/degradation; Cell membrane; Complete proteome; KW Exopolysaccharide synthesis; Membrane; Transferase; Transmembrane; diff --git a/ff-parser/src/test/resources/entryIT/Q1MS15.txl b/ff-parser/src/test/resources/entryIT/Q1MS15.txl index 71726c7e3..96cf0ea4d 100644 --- a/ff-parser/src/test/resources/entryIT/Q1MS15.txl +++ b/ff-parser/src/test/resources/entryIT/Q1MS15.txl @@ -61,7 +61,7 @@ DR InterPro; IPR036467; LS/RS_sf. DR PANTHER; PTHR21058; PTHR21058; 1. DR Pfam; PF00885; DMRL_synthase; 1. DR SUPFAM; SSF52121; SSF52121; 1. -DR TIGRFAMs; TIGR00114; lumazine-synth; 1. +DR NCBIfam; NF00114; lumazine-synth; 1. PE 3: Inferred from homology; KW Reference proteome; Riboflavin biosynthesis; Transferase. FT CHAIN 1..157 diff --git a/ff-parser/src/test/resources/entryIT/Q32K04.dat b/ff-parser/src/test/resources/entryIT/Q32K04.dat index e27e253e5..e038241ec 100644 --- a/ff-parser/src/test/resources/entryIT/Q32K04.dat +++ b/ff-parser/src/test/resources/entryIT/Q32K04.dat @@ -77,7 +77,7 @@ DR Pfam; PF02875; Mur_ligase_C; 1. DR Pfam; PF08245; Mur_ligase_M; 1. DR SUPFAM; SSF53244; SSF53244; 1. DR SUPFAM; SSF53623; SSF53623; 1. -DR TIGRFAMs; TIGR01087; murD; 1. +DR NCBIfam; NF01087; murD; 1. ** PROSITE; PS00012; PHOSPHOPANTETHEINE; 1; FALSE_POS. ** PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1; FALSE_POS. PE 3: Inferred from homology; diff --git a/ff-parser/src/test/resources/entryIT/Q66GB9.txl b/ff-parser/src/test/resources/entryIT/Q66GB9.txl index 66f69309c..78216d6b3 100644 --- a/ff-parser/src/test/resources/entryIT/Q66GB9.txl +++ b/ff-parser/src/test/resources/entryIT/Q66GB9.txl @@ -55,7 +55,7 @@ DR PANTHER; PTHR36918; PTHR36918; 1. DR Pfam; PF02556; SecB; 1. DR PRINTS; PR01594; SECBCHAPRONE. DR SUPFAM; SSF54611; SSF54611; 1. -DR TIGRFAMs; TIGR00809; secB; 1. +DR NCBIfam; NF00809; secB; 1. PE 3: Inferred from homology; KW Chaperone; Complete proteome; Cytoplasm; Protein transport; Translocation; KW Transport.