diff --git a/CHANGELOG.md b/CHANGELOG.md index e64d8b9..adf1d1c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,12 @@ ### Manual curation - argannot_curation: (Tet)tetH:EF460464:6286-7839:1554 was incorrectly annotated as ARO:3004797 which is a beta-lactamase due to a loose RGI hit. This was manually curated to ARO:3000175. +- deeparg, megares, resfinderfg & sarg curation: ARO:3004445 -> ARO:3005440, this was due to a change in the ARO and the ARO number for the RSA2 gene changing. **db_harmonisation must change to take this into account** + +#### Incorrectly curated genes. +- Previously, these were directly mapped to drug classes. Correct parent ARO term has now been given. +- resfinder_curation: grdA_1_QJX10702 -> 3007380 & EstDL136_1_JN242251 -> 3000557 +- megares_curation: MEG_2865|Drugs|Phenicol|Chloramphenicol_hydrolase|ESTD -> 3000557 ## 0.4.0 - 10 June diff --git a/argnorm/data/manual_curation/deeparg_curation.tsv b/argnorm/data/manual_curation/deeparg_curation.tsv index 693f9dd..70ce00a 100644 --- a/argnorm/data/manual_curation/deeparg_curation.tsv +++ b/argnorm/data/manual_curation/deeparg_curation.tsv @@ -11,3 +11,4 @@ gi:685904080:ref:WP_031644138.1:|FEATURES|cystathionine_beta-lyase_patB|unclassi NP_253005.1|FEATURES|MvaT|multidrug|MvaT 3004069 MvaT NP_417544.5|FEATURES|patA|fluoroquinolone|patA 3000024 patA NP_416340.1|FEATURES|mgrB|multidrug|mgrB 3003820 mgrB +AUW34359.1|FEATURES|RSA-2|beta-lactam|RSA-2 3005440 RSA2 beta-lactamase ARO number of RSA2 had been changed. \ No newline at end of file diff --git a/argnorm/data/manual_curation/megares_curation.tsv b/argnorm/data/manual_curation/megares_curation.tsv index 7d1ef9a..43ca398 100644 --- a/argnorm/data/manual_curation/megares_curation.tsv +++ b/argnorm/data/manual_curation/megares_curation.tsv @@ -1,7 +1,7 @@ Original ID ARO Description MEG_8443|Drugs|Pleuromutilin|Pleuromutilin-resistant_23S_rRNA_mutation|P23S|RequiresSNPConfirmation 3005083 MEG_4060|Metals|Multi-metal_resistance|Multi-metal_resistance_protein|MREA Metal resistance. No mapping -MEG_2865|Drugs|Phenicol|Chloramphenicol_hydrolase|ESTD 3000387 +MEG_2865|Drugs|Phenicol|Chloramphenicol_hydrolase|ESTD 3000557 MEG_1732|Drugs|Lipopeptides|Daptomycin-resistant_mutant|CLS|RequiresSNPConfirmation 3003092 MEG_2933|Drugs|Mycobacterium_tuberculosis-specific_Drug|Para-aminosalicylic_acid_resistant_mutant|FOLC|RequiresSNPConfirmation 3004157 MEG_8700|Multi-compound|Biocide_and_metal_resistance|Biocide_and_metal_ABC_efflux_pumps|SITABCD Metal + Biocide resistance. No mapping @@ -86,3 +86,4 @@ MEG_2429|Drugs|betalactams|Class_A_betalactamases|CTX 3001943 MEG_5148|Drugs|betalactams|Class_D_betalactamases|OXA 3001555 MEG_7604|Drugs|Glycopeptides|VanD-type_accessory_protein|VANYD 3002957 MEG_8253|Drugs|MLS|Macrolide-resistant_23S_rRNA_mutation|MLS23S|RequiresSNPConfirmation 3004836 +MEG_6148|Drugs|betalactams|Class_A_betalactamases|RSA 3005440 ARO number of RSA2 had been changed. diff --git a/argnorm/data/manual_curation/resfinder_curation.tsv b/argnorm/data/manual_curation/resfinder_curation.tsv index 9629319..dda529c 100644 --- a/argnorm/data/manual_curation/resfinder_curation.tsv +++ b/argnorm/data/manual_curation/resfinder_curation.tsv @@ -9,7 +9,7 @@ VanC2XY_1_EU151754 glycopeptide resistance gene cluster VanC 3000246 https://www VanHAX_PT_1_DQ018710 glycopeptide resistance gene cluster VanA 3000236 https://www.ncbi.nlm.nih.gov/nuccore/DQ018710.1 5109-7715 Part of VanA cluster (ARO:3000236) VanHAX_PA_1_DQ018711 glycopeptide resistance gene cluster VanA 3000236 https://www.ncbi.nlm.nih.gov/nuccore/DQ018711.1?report=fasta 3168-5750 Part of VanA cluster (ARO:3000236) VanHAX_PT_2_AY926880 glycopeptide resistance gene cluster VanA 3000236 https://www.ncbi.nlm.nih.gov/nuccore/AY926880.2?report=fasta 2771-5377 Part of VanA cluster (ARO:3000236) -dldHA2X_1_AL939117 D-Ala-D-Ala ligase 3003970 https://www.ncbi.nlm.nih.gov/nuccore/AL939117.1 53343-56013 +dldHA2X_1_AL939117 D-Ala-D-Ala ligase 3003970 https://www.ncbi.nlm.nih.gov/nuccore/AL939117.1 53343-56013 VanHBX_1_AF192329 glycopeptide resistance gene cluster VanB 3000238 https://www.ncbi.nlm.nih.gov/nuccore/AF192329 27871-30477 Part of VanB cluster (ARO:3000238) VanHBX_2_U35369 glycopeptide resistance gene cluster VanB 3000238 https://www.ncbi.nlm.nih.gov/nuccore/U35369.1?report=fasta 4007-6613 "Part of VanB cluster (ARO:3000238). Contains ARO:3002943, ARO:3002950" VanC4XY_1_EU151752 glycopeptide resistance gene cluster VanC 3000246 https://www.ncbi.nlm.nih.gov/nuccore/EU151752.1?report=fasta 29-1650 Part of VanC cluster (ARO:3000246) @@ -45,6 +45,6 @@ qepA1_1_AB263754 QepA2 3004103 Reverse complement in resfinder db. tet(43)_1_GQ244501 tet(43) 3000573 Reverse complement in resfinder db. blaSPG-1_1_KP109680 SPG-1 3003720 blaBIM-1_1_CP016446 BlaB 3004201 -grdA_1_QJX10702 3007382 Parent ARO mapping +grdA_1_QJX10702 3007380 Parent ARO mapping aac(3)-I_1_AJ877225 AAC(3)-I 3007384 -EstDL136_1_JN242251 3000387 Parent ARO mapping +EstDL136_1_JN242251 3000557 Parent ARO mapping diff --git a/argnorm/data/manual_curation/resfinderfg_curation.tsv b/argnorm/data/manual_curation/resfinderfg_curation.tsv index 2aa446c..ff91181 100644 --- a/argnorm/data/manual_curation/resfinderfg_curation.tsv +++ b/argnorm/data/manual_curation/resfinderfg_curation.tsv @@ -1,2 +1,4 @@ -Original ID ARO Gene Name in CARD -UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase|KF629588.1|pediatric_fecal_sample|CYC 3003970 D-Ala-D-Ala ligase +Original ID ARO Gene Name in CARD Description +UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase|KF629588.1|pediatric_fecal_sample|CYC 3003970 D-Ala-D-Ala ligase +Beta-lactamase OXA-1|KU544700.1|sewage|CAZ 3005440 RSA2 beta-lactamase ARO number of RSA2 had been changed. +Beta-lactamase OXA-1|MG739504.1|river|AMP 3005440 RSA2 beta-lactamase ARO number of RSA2 had been changed. diff --git a/argnorm/data/manual_curation/sarg_curation.tsv b/argnorm/data/manual_curation/sarg_curation.tsv index 953cd02..7352c17 100644 --- a/argnorm/data/manual_curation/sarg_curation.tsv +++ b/argnorm/data/manual_curation/sarg_curation.tsv @@ -1,3 +1,4 @@ -Original ID ARO Gene Name in CARD -gb|AAG57600.1|ARO:3000318|mphB 3000318 mphB -AM180355.1.gene2260.p01 3000250 ErmC +Original ID ARO Gene Name in CARD Description +gb|AAG57600.1|ARO:3000318|mphB 3000318 mphB +AM180355.1.gene2260.p01 3000250 ErmC +gb|AUW34359.1|ARO:3004445|RSA-2 3005440 RSA2 beta-lactamase ARO number of RSA2 had been changed.