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Merge pull request #2071 from geneontology/pgaudet-patch-88
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Update gorules_test_errors.gaf
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@pgaudet
pgaudet authored Sep 26, 2023
2 parents 880fdc4 + a8ca3ae commit 93d465c
Showing 1 changed file with 25 additions and 7 deletions.
32 changes: 25 additions & 7 deletions docs/gorules_test_errors.gaf
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Original file line number Diff line number Diff line change
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!gaf-version: 2.2
!generated-by: GOC
!date-generated: 2023-08-25
!date-generated: 2023-09-16
! Dummy GAF file containing deliberate errors to test that GO rules are correctly implemented.

! FAILS GORULE:0000001 - empty col1 and col2
Expand All @@ -25,6 +25,8 @@ PomBase SPAC25B8.17 ypf1 is_active_in GO:0005634 GO_REF:0000024 MADEUP SGD:S0000
PomBase SPAC25B8.17 ypf1 is_active_in GO:0005634 GO_REF:0000024 ISO SGD:S000001583 C GORULE:0000001-6 intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 2015-03-05 PomBase part_of(X:1)
! FAILS GORULE:0000001 - TEST 7 - Bad date, unparsable
PomBase SPAC25B8.17 ypf1 is_active_in GO:0005634 GO_REF:0000024 ISO SGD:S000001583 C GORULE:0000001-7 intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted) ppp81 protein taxon:4896 TODAY PomBase part_of(X:1)
! FAILS GORULE:0000001 - TEST 8 - invalid taxon 0
ZFIN ZDB-GENE-070117-1552 obj_symbol acts_upstream_of_or_within GO:0045601 PMID:17531218 IMP ZFIN:ZDB-GENO-080318-17 P GORULE:0000001-8 gene_product taxon:0 20080326 ZFIN
! FAILS GORULE:0000002 - TEST 1 - has a 'NOT' annotations to 'protein binding ; GO:0005515
UniProtKB O76187 darA NOT|involved_in GO:0005515 PMID:9802899 IPI UniProtKB:P34149 F GORULE:0000002-1 Darlin darA protein taxon:44689 20100205 UniProt
! TBC FAILS GORULE:0000003 - incorrect evidence codes for 'binding ; GO:0005488' and 'protein binding ; GO:0005515'
Expand Down Expand Up @@ -125,27 +127,31 @@ UniProtKB F1N2N9 ODAD1 part_of GO:0120228 PMID:34715025 ISS UniProtKB:F1N2N9 C G
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 - TEST 3 - self-referential ISA annotations
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:0000051 - Pass TEST 51 - Annotation extension for certain GO terms - protein binding; GO:0005515
UniProtKB O76187 darA enables GO:0005515 PMID:9802899 IPI UniProtKB:P34149 F GORULE:0000051-1 Darlin darA protein taxon:44689 20100205 UniProt has_input(GO:0003674)|occurs_in(CL:123456)
! FAILS GORULE:0000051 - TEST 51 - Annotation extension is required for certain terms - binding GO:0005488
UniProtKB O76187 darA enables GO:0005488 PMID:9802899 IPI UniProtKB:P34149 F GORULE:0000051-2 Darlin darA protein taxon:44689 20100205 UniProt
! FAILS GORULE:0000055 - TEST 1 - Two references in the same ID space - PMID
PlasmoDB PF3D7_0200400 PF3D7_0200400 is_active_in GO:0020036 PMID:12477793|PMID:15961998 IDA C GORULE:0000055-1 stevor mRNA taxon:4896 20131007 GeneDB
! FAILS GORULE:0000055 - TEST 2 - Two references in the same ID space - GO_REF
PlasmoDB PF3D7_0200400 PF3D7_0200400 is_active_in GO:0020036 GO_REF:0000044|GO_REF:0000001 IDA C GORULE:0000055-2 stevor mRNA taxon:4896 20131007 GeneDB
! FAILS GORULE:0000059 - TEST 1 - GP2term relation missing
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 - TEST 1 SHOULD NOT FAIL (wrong on snapshot??) the part_of GP2term relation is not allowed for GO:0070865
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
! FAILS GORULE:0000061 - TEST 2 -fails because no data in column 4
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
! FAILS GORULE:0000061 - TEST 2 -fails because no data in column 4. This is GORULE 1
FB FBgn0011273 Acam GO:0070865 FB:FBrf0193169|PMID:16790438 IDA C GORULE:0000061-2 Androcam ACaM|And|CG17769|CalB|Calmodulin-related 97A|Camr97A|androcalmodulin|androcam protein taxon:7227 20180501 FlyBase
! FAILS GORULE:0000061 - TEST 3 - SHOULD NOT FAIL the 'part_of' GP2term relation is allowed for GO:0070864 (CC complex)
FB FBgn0011273 shi part_of GO:0070864 PMID:12432073 IDA C GORULE:0000061-3 Dynamin Protein shibire|dDyn protein taxon:7227 20180501 FlyBase
FB FBgn0011273 shi part_of GO:0070864 PMID:12432073 IDA C GORULE:0000061-3 Dynamin Protein shibire|dDyn protein taxon:7227 20180501 FlyBase
! FAILS GORULE:0000061 - TEST 4 - the 'part_of' GP2term relation is not allowed for GO:0140827 (MF)
UniProtKB A1B2F4 aztD part_of GO:0140827 PMID:26468286 IDA F GORULE:0000061-4 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - TEST 5 - the 'enables' GP2term relation is not allowed for GO:0005856 (CC)
UniProtKB A1B2F4 aztD enables GO:0005856 PMID:26468286 IDA F GORULE:0000061-5 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - TEST 6 - the 'located in' GP2term relation is not allowed for GO:0005575 (root CC)
! FAILS GORULE:0000061 - TEST 6 - the 'located in' GP2term relation is not allowed for GO:0005575 (root CC) - Fails GORULE 11
UniProtKB A1B2F4 aztD located_in GO:0005575 PMID:26468286 IDA F GORULE:0000061-6 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - TEST 7 - the 'contributes_to' GP2term relation is not allowed for GO:0003674 (root MF)
! FAILS GORULE:0000061 - TEST 7 - the 'contributes_to' GP2term relation is not allowed for GO:0003674 (root MF) - Fails GORULE 11
UniProtKB A1B2F4 aztD contributes_to GO:0003674 PMID:26468286 IDA F GORULE:0000061-7 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - TEST 8 - the 'acts upstream of or within' GP2term relation is not allowed for GO:0008150 (root BP)
! FAILS GORULE:0000061 - TEST 8 - the 'acts upstream of or within' GP2term relation is not allowed for GO:0008150 (root BP) - Fails GORULE 11
UniProtKB A1B2F4 aztD acts_upstream_of_or_within GO:0008150 PMID:26468286 IDA F GORULE:0000061-8 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - test 9- 'enables' is not allowed for a GO BP
UniProtKB A1B2F4 aztD enables GO:0043491 PMID:26468286 IDA P GORULE:0000061-9 protein taxon:318586 20230427 UniProt
Expand Down Expand Up @@ -207,3 +213,15 @@ UniProtKB A1B2F4 aztD located_in GO:0043491 PMID:26468286 IDA C GORULE:0000061-
UniProtKB A1B2F4 aztD colocalizes_with GO:0043491 PMID:26468286 IDA C GORULE:0000061-37 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - test 38 - 'part_of' is not allowed for a GO CC - cellular anatomical entity
UniProtKB A1B2F4 aztD part_of GO:0005634 PMID:26468286 IDA C GORULE:0000061-38 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - test 39 - 'part_of' is not allowed for GO CC - cellular anatomical entity
UniProtKB A1B2F4 aztD NOT|part_of GO:0005634 PMID:26468286 IDA C GORULE:0000061-39 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - test 40 - Fail unknown GO id type
FB FBgn0011273 shi NOT|part_of GO:1234567 PMID:12432073 IDA C GORULE:0000061-40 Dynamin Protein shibire|dDyn protein taxon:7227 20180501 FlyBase
! FAILS GORULE:0000061 - test 41 - 'part_of' is not allowed for GO CC - cell plate descendent of cellular anatomical entity
UniProtKB A1B2F4 aztD part_of GO:0009504 PMID:26468286 IDA C GORULE:0000061-41 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - test 42 - 'part_of' is not allowed for GO CC cellular anatomical entity
UniProtKB A1B2F4 aztD part_of GO:0110165 PMID:26468286 IDA C GORULE:0000061-42 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - test 43 - 'part_of' is not allowed for GO CC virion component
UniProtKB A1B2F4 aztD part_of GO:0044423 PMID:26468286 IDA C GORULE:0000061-43 protein taxon:318586 20230427 UniProt
! FAILS GORULE:0000061 - test 44 - 'part_of' is not allowed for a GO CC icosahedral viral capsid, neck descendant of virion component
UniProtKB A1B2F4 aztD part_of GO:0098030 PMID:26468286 IDA C GORULE:0000061-44 protein taxon:318586 20230427 UniProt

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