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Update gorules_test_errors.gaf
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pgaudet authored Jun 30, 2023
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Expand Up @@ -40,91 +40,91 @@ GeneDB PF3D7_0507500 SUB1 enables GO:0004672 PMID:12764150 HEP F GORULE:0000006
! FAILS GORULE:0000006 - fails because uses IEP with a cellular component term.
GeneDB PF3D7_0507500 SUB1 enables GO:0005634 PMID:12764150 IEP C GORULE:0000006-3 subtilisin-like protease 1 gene NCBITaxon:36329 20090624 GeneDB
! FAILS GORULE:0000007 IPI used with GO:0003824 catalytic activity or descendents (GO:0004674 protein serine/threonine kinase activity)
UniProtKB A0A078CGE6 M3KE1 enables GO:0004674 PMID:11489177 IPI F protein taxon:3708 20150115 UniProt
UniProtKB A0A078CGE6 M3KE1 enables GO:0004674 PMID:11489177 IPI F GORULE:0000007-1 protein taxon:3708 20150115 UniProt
! FAILS GORULE:0000008 - GO:0005622 is in the subset gocheck_do_not_annotate
UniProtKB Q9DGE2 mapk14a is_active_in GO:0005622 PMID:10995439 IDA C Mitogen-activated protein kinase 14A mapk14a|mapk14 protein taxon:7955 20180129 UniProt
UniProtKB Q9DGE2 mapk14a is_active_in GO:0005622 PMID:10995439 IDA C GORULE:0000008-1 Mitogen-activated protein kinase 14A mapk14a|mapk14 protein taxon:7955 20180129 UniProt
! FAILS GORULE:0000008 - GO:0007049 is in the subset gocheck_do_not_manually_annotate
UniProtKB Q9WVH3 Foxo4 involved_in GO:0007049 PMID:12048180 IDA P Forkhead box protein O4 Foxo4|Afx|Afx1 protein taxon:10090 20110425 MGI
UniProtKB Q9WVH3 Foxo4 involved_in GO:0007049 PMID:12048180 IDA P GORULE:0000008-1 Forkhead box protein O4 Foxo4|Afx|Afx1 protein taxon:10090 20110425 MGI
! FAILS GORULE:0000011 - because the GO ID is not one of GO:0003674, GO:0008150 or GO:0005575
UniProtKB Q4KA26 PFL_3807 is_active_in GO:0016020 GO_REF:0000015 ND C Putative membrane protein PFL_3807 protein taxon:220664 20090717 JCVI
UniProtKB Q4KA26 PFL_3807 is_active_in GO:0016020 GO_REF:0000015 ND C GORULE:0000011-1 Putative membrane protein PFL_3807 protein taxon:220664 20090717 JCVI
! FAILS GORULE:0000011 - fails because the evidence code is not ND, even if the GO ID one of GO:0003674, GO:0008150 or GO:0005575.
UniProtKB Q4KA26 PFL_3807 is_active_in GO:0005575 GO_REF:0000015 IDA C Putative membrane protein PFL_3807 protein taxon:220664 20090717 JCVI
UniProtKB Q4KA26 PFL_3807 is_active_in GO:0005575 GO_REF:0000015 IDA C GORULE:0000011-2 Putative membrane protein PFL_3807 protein taxon:220664 20090717 JCVI
! FAILS GORULE:0000013 - fails because GO:0075342 should not be annotated for human gene products
UniProtKB P67870 CSNK2B involved_in GO:0075342 PMID:20719947 IDA P Casein kinase II subunit beta CSNK2B|CK2N|G5A protein taxon:9606 20230307 UniProt
UniProtKB P67870 CSNK2B involved_in GO:0075342 PMID:20719947 IDA P GORULE:0000013-1 Casein kinase II subunit beta CSNK2B|CK2N|G5A protein taxon:9606 20230307 UniProt
! FAILS GORULE:0000015 - GO:0005886 plasma membrane is not a child of "GO:0018995 host cellular component"
UniProtKB O56786 hol187 is_active_in GO:0005886 PMID:10419939 IDA C Holin protein Hol187 hol187 protein taxon:55511|taxon:9696 20170423 CACAO
UniProtKB O56786 hol187 is_active_in GO:0005886 PMID:10419939 IDA C GORULE:0000015-1 Holin protein Hol187 hol187 protein taxon:55511|taxon:9696 20170423 CACAO
! FAILS GORULE:0000015 - "neutrophil chemotaxis" is not a child of "GO:0044419 interspecies interaction between organisms"
UniProtKB A0A0K2S4Q6 CD300H involved_in GO:0030593 PMID:26221034 IDA P Protein CD300H CD300H protein taxon:9606|taxon:55511 20160428 UniProt
UniProtKB A0A0K2S4Q6 CD300H involved_in GO:0030593 PMID:26221034 IDA P GORULE:0000015-2 Protein CD300H CD300H protein taxon:9606|taxon:55511 20160428 UniProt
! FAILS GORULE:0000015 - same taxon in Column 13 for GO:0044158 host cell wall
UniProtKB O56786 hol187 is_active_in GO:0018995 PMID:10419939 IDA C Holin protein Hol187 hol187 protein taxon:9696|taxon:9696 20170423 CACAO
UniProtKB O56786 hol187 is_active_in GO:0018995 PMID:10419939 IDA C GORULE:0000015-3 Holin protein Hol187 hol187 protein taxon:9696|taxon:9696 20170423 CACAO
! FAILS GORULE:0000016 - column 8 (with/from) is null
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 GO_REF:0000036 IC P Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 BHF-UCL
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 GO_REF:0000036 IC P GORULE:0000016-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 BHF-UCL
! FAILS GORULE:0000017 - IDA annotations must not have a with/from entry (column 8)
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 GO_REF:0000036 IDA GO:0004198|GO:0008092 P Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 BHF-UCL
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 GO_REF:0000036 IDA GO:0004198|GO:0008092 P GORULE:0000017-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 BHF-UCL
! FAILS GORULE:0000018 - column 8 (with/from) is null for IPI annotation to 'protein binding ; GO:0005515'
UniProtKB A0A0K3AV08 mlk-1 enables GO:0005080 PMID:23072806 IPI F Mitogen-activated protein kinase kinase kinase mlk-1 mlk-1,K11D12.10 protein taxon:6239 20170322 UniProt
UniProtKB A0A0K3AV08 mlk-1 enables GO:0005080 PMID:23072806 IPI F GORULE:0000018-1 Mitogen-activated protein kinase kinase kinase mlk-1 mlk-1,K11D12.10 protein taxon:6239 20170322 UniProt
! FAILS GORULE:0000018 - 'protein binding ; GO:0005515' annotation not using IPI
UniProtKB Q8IY33 MICALL2 enables GO:0005515 PMID:23072807 IDA F MICAL-like protein 2 JRAB protein taxon:9606 20170322 UniProt
UniProtKB Q8IY33 MICALL2 enables GO:0005515 PMID:23072807 IDA F GORULE:0000018-2 MICAL-like protein 2 JRAB protein taxon:9606 20170322 UniProt
! FAILS GORULE:0000018 - missing Column 8 data ('with' field) for 'binding ; GO:0005488'
UniProtKB O76187 darA GO:0005488 PMID:9802899 IPI UniProtKB:Q23862 F protein taxon:44689 20230513 IntAct
UniProtKB O76187 darA GO:0005488 PMID:9802899 IPI UniProtKB:Q23862 F GORULE:0000018-3 protein taxon:44689 20230513 IntAct
! FAILS GORULE:0000020 - obsolete term with no replacement
UniProtKB P04995 sbcB involved_in GO:0090503 GO_REF:0000108 IEA GO:0000175 P Exodeoxyribonuclease I sbcB|cpeA|xonA|JW1993|b2011 protein taxon:83333 20230509 GOC
UniProtKB P04995 sbcB involved_in GO:0090503 GO_REF:0000108 IEA GO:0000175 P GORULE:0000020-1 Exodeoxyribonuclease I sbcB|cpeA|xonA|JW1993|b2011 protein taxon:83333 20230509 GOC
! FAILS GORULE:0000020 - obsolete term with a replacement term
TriTrypDB Tb11.02.5420b Tb11.02.5420b located_in GO:0016021 GO_REF:0000002 ISO GeneDB:Tb11.02.5420 C NADPH-cytochrome p450 reductase, putative mRNA taxon:185431 20130726 GeneDB
TriTrypDB Tb11.02.5420b Tb11.02.5420b located_in GO:0016021 GO_REF:0000002 ISO GeneDB:Tb11.02.5420 C GORULE:0000020-2 NADPH-cytochrome p450 reductase, putative mRNA taxon:185431 20130726 GeneDB
! FAILS GORULE:0000027 - bad GO ID syntax
PomBase SPAC25B8.17 ypf1 is_active_in BAD_GO_ID GO_REF:0000024 ISO SGD:S000001583 C intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 20150305 PomBase
PomBase SPAC25B8.17 ypf1 is_active_in BAD_GO_ID GO_REF:0000024 ISO SGD:S000001583 C GORULE:0000027-1 intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 20150305 PomBase
! FAILS GORULE:0000027 - bad GO ID syntax; no colon
PomBase SPAC25B8.18 ypf2 is_active_in GO0006921 GO_REF:0000024 ISO SGD:S000001583 C intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 20150305 PomBase
PomBase SPAC25B8.18 ypf2 is_active_in GO0006921 GO_REF:0000024 ISO SGD:S000001583 C GORULE:0000027-2 intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 20150305 PomBase
! FAILS GORULE:0000027 - bad GO ID syntax; bas namespace
PomBase SPAC25B8.19 ypf3 is_active_in RO:0006921 GO_REF:0000024 ISO SGD:S000001583 C intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 20150305 PomBase
PomBase SPAC25B8.19 ypf3 is_active_in RO:0006921 GO_REF:0000024 ISO SGD:S000001583 C GORULE:0000027-3 intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 20150305 PomBase
! FAILS GORULE:0000027 - Prefix not in /db-xrefs.yaml
UniPotKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA P Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 BHF-UCL
UniPotKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA P GORULE:0000027-4 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 BHF-UCL
! FAILS GORULE:0000027 - Assigned_by not in /groups.yaml
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA P Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA P GORULE:0000027-5 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
! FAILS GORULE:0000027 - Bad reference format
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:PMID:14561399 IDA P Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:PMID:14561399 IDA P GORULE:0000027-6 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
! FAILS GORULE:0000027 - Bad reference format
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:unpublished IDA P Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:unpublished IDA P GORULE:0000027-7 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
! FAILS GORULE:0000027 - Bad reference format
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID: IDA P Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID: IDA P GORULE:0000027-8 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
! FAILS GORULE:0000027 - Bad reference format
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:0. IDA P Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:0. IDA P GORULE:0000027-9 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
! FAILS GORULE:0000028 - Bad GO aspect, C instead of P
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA C GORULE:0000028-1 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
! FAILS GORULE:0000028 - Bad GO aspect, F instead of P
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA F Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
UniProtKB Q9HC96 CAPN10 involved_in GO:0006921 PMID:23072806 IDA F GORULE:0000028-2 Calpain-10 CAPN10,KIAA1845 protein taxon:9606 20140213 SGDDB
! FAILS GORULE:0000028 - Bad GO aspect, P instead of F
UniProtKB A0A0K3AV08 mlk-1 enables GO:0005080 PMID:23072806 IDA P Mitogen-activated protein kinase kinase kinase mlk-1 mlk-1,K11D12.10 protein taxon:6239 20170322 UniProt
UniProtKB A0A0K3AV08 mlk-1 enables GO:0005080 PMID:23072806 IDA P GORULE:0000028-3 Mitogen-activated protein kinase kinase kinase mlk-1 mlk-1,K11D12.10 protein taxon:6239 20170322 UniProt
! FAILS GORULE:0000029 - IEA older than 1 year
UniProtKB P77335 hlyE located_in GO:0020002 GO_REF:0000044 IEA UniProtKB-SubCell:SL-0375 C protein taxon:83333 20210507 UniProt
UniProtKB P77335 hlyE located_in GO:0020002 GO_REF:0000044 IEA UniProtKB-SubCell:SL-0375 C GORULE:0000029-1 protein taxon:83333 20210507 UniProt
! FAILS GORULE:0000030 - Deprecated GO_REF
UniProtKB P77335 hlyE located_in GO:0020002 GO_REF:0000045 IEA UniProtKB-SubCell:SL-0375 C protein taxon:83333 20230607 UniProt
UniProtKB P77335 hlyE located_in GO:0020002 GO_REF:0000045 IEA UniProtKB-SubCell:SL-0375 C GORULE:0000030-1 protein taxon:83333 20230607 UniProt
! FAILS GORULE:0000037 - IBA with Assigned_by other than GO_Central
UniProtKB A0A024BTL2 PHKG1 is_active_in GO:0005634 PMID:21873635 IBA FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 C protein taxon:9823 20221009 FlyBase
UniProtKB A0A024BTL2 PHKG1 is_active_in GO:0005634 PMID:21873635 IBA FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 C GORULE:0000037-1 protein taxon:9823 20221009 FlyBase
! FAILS GORULE:0000037 - IBA with reference other than PMID:21873635
UniProtKB A0A024BTL2 PHKG1 is_active_in GO:0005634 PMID:26221034 IBA FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 C protein taxon:9823 20221009 GO_Central
UniProtKB A0A024BTL2 PHKG1 is_active_in GO:0005634 PMID:26221034 IBA FB:FBgn0019686|FB:FBgn0028360|FB:FBgn0032677|PANTHER:PTN005196447|PomBase:SPAC14C4.03|PomBase:SPCC1322.08|PomBase:SPCC18B5.11c|RGD:621543|SGD:S000006074|UniProtKB:O96017|UniProtKB:Q5AVW7 C GORULE:0000037-2 protein taxon:9823 20221009 GO_Central
! FAILS GORULE:0000039 Protein complex annotated to GO:0032991 protein-containing complex
ComplexPortal CPX-102 dapk-calm_human part_of GO:0032991 PMID:10629061 IMP C complex taxon:9606 20200218 ComplexPortal
ComplexPortal CPX-102 dapk-calm_human part_of GO:0032991 PMID:10629061 IMP C GORULE:0000039-1 complex taxon:9606 20200218 ComplexPortal
! FAILS GORULE:0000039 Protein complex annotated to an is_a descendant of GO:0032991 protein-containing complex
ComplexPortal CPX-102 dapk-calm_human part_of GO:0043020 PMID:10629061 IMP C complex taxon:9606 20200218 ComplexPortal
ComplexPortal CPX-102 dapk-calm_human part_of GO:0043020 PMID:10629061 IMP C GORULE:0000039-2 complex taxon:9606 20200218 ComplexPortal
! FAILS GORULE:0000042 - IKR evidence, no negation (NOT) in column 4
UniProtKB A0A0B4JCV5 CG9898 enables GO:0004252 PMID:30367934 IKR F protein taxon:7227 20190311 FlyBase
UniProtKB A0A0B4JCV5 CG9898 enables GO:0004252 PMID:30367934 IKR F GORULE:0000042-1 protein taxon:7227 20190311 FlyBase
! FAILS GORULE:0000046 - self-binding’ term, no data in Column 8
UniProtKB A4D126 CRPPA enables GO:0042803 PMID:26687144 IDA F protein taxon:9606 20170627 UniProt
UniProtKB A4D126 CRPPA enables GO:0042803 PMID:26687144 IDA F GORULE:0000046-1 protein taxon:9606 20170627 UniProt
! FAILS GORULE:0000046 - self-binding’ term, annotated to a protein other than 'self'
UniProtKB A4D126 CRPPA enables GO:0042803 PMID:26687144 IDA P35555 F protein taxon:9606 20170627 UniProt
UniProtKB A4D126 CRPPA enables GO:0042803 PMID:26687144 IDA P35555 F GORULE:0000046-2 protein taxon:9606 20170627 UniProt
! FAILS GORULE:0000050 - self-referential ISS annotations
UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISS UniProtKB:F1N2N9 C Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 protein taxon:9913 20220422 UniProt
UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISS UniProtKB:F1N2N9 C GORULE:0000050-1 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 protein taxon:9913 20220422 UniProt
! FAILS GORULE:0000050 - self-referential ISO annotations
UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISO UniProtKB:F1N2N9 C Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 protein taxon:9913 20220422 UniProt
UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISO UniProtKB:F1N2N9 C GORULE:0000050-2 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 protein taxon:9913 20220422 UniProt
! FAILS GORULE:0000050 - self-referential ISA annotations
UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISA UniProtKB:F1N2N9 C Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 protein taxon:9913 20220422 UniProt
UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISA UniProtKB:F1N2N9 C GORULE:0000050-3 Outer dynein arm-docking complex subunit 1 ODAD1|CCDC114 protein taxon:9913 20220422 UniProt
! FAILS GORULE:0000055 - Two references in the same ID space - PMID
PlasmoDB PF3D7_0200400 PF3D7_0200400 GO:0020036 PMID:12477793|PMID:15961998 IDA C stevor PFB0025c|PF02_0004 mRNA taxon:36329 20131007 GeneDB
PlasmoDB PF3D7_0200400 PF3D7_0200400 GO:0020036 PMID:12477793|PMID:15961998 IDA C GORULE:0000055-1 stevor PFB0025c|PF02_0004 mRNA taxon:36329 20131007 GeneDB
! FAILS GORULE:0000055 - Two references in the same ID space - GO_REF
PlasmoDB PF3D7_0200400 PF3D7_0200400 GO:0020036 GO_REF:0000044|GO_REF:0000001 IDA C stevor PFB0025c|PF02_0004 mRNA taxon:36329 20131007 GeneDB
PlasmoDB PF3D7_0200400 PF3D7_0200400 GO:0020036 GO_REF:0000044|GO_REF:0000001 IDA C GORULE:0000055-1 stevor PFB0025c|PF02_0004 mRNA taxon:36329 20131007 GeneDB
! FAILS GORULE:0000059 - GP2term relation missing
SGN 235 cpk1 GO:0005886 PMID:12011347 IDA C calcium-dependent protein kinase LeCPK1|Solyc03g031670 gene taxon:4081 20080616 SGN
SGN 235 cpk1 GO:0005886 PMID:12011347 IDA C GORULE:0000059-1 calcium-dependent protein kinase LeCPK1|Solyc03g031670 gene taxon:4081 20080616 SGN
! FAILS GORULE:0000061 - the part_of GP2term relation is not allowed for GO:0070865
FB FBgn0011273 Acam part_of GO:0070865 FB:FBrf0193169|PMID:16790438 IDA C Androcam ACaM|And|CG17769|CalB|Calmodulin-related 97A|Camr97A|androcalmodulin|androcam protein taxon:7227 20180501 FlyBase
FB FBgn0011273 Acam part_of GO:0070865 FB:FBrf0193169|PMID:16790438 IDA C GORULE:0000061-1 Androcam ACaM|And|CG17769|CalB|Calmodulin-related 97A|Camr97A|androcalmodulin|androcam protein taxon:7227 20180501 FlyBase

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