GO Rule Violations by Group Dataset

Generated on 2026-05-07
Rule cgd dictybase ecocyc fb genedb_lmajor genedb_pfalciparum genedb_tbrucei goa_chicken goa_cow goa_dog goa_human goa_pig japonicusdb mgi paint_cgd paint_dictybase paint_ecocyc paint_fb paint_goa_chicken paint_goa_human paint_japonicusdb paint_mgi paint_other paint_pombase paint_rgd paint_sgd paint_tair paint_wb paint_xenbase paint_zfin pombase pseudocap reactome rgd sgd sgn tair wb xenbase zfin

GAF lines are parsed according to GAF 2.2 specifications:
gorule-0000001

0 0 0 13 4 0 18 11 27 33 44 113 0 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 102 0 82 0 6 0 0

No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515':
gorule-0000002

0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations are not allowed for direct annotations to 'protein binding ; GO:0005515 or GO:0005488 binding'':
gorule-0000005

0 0 0 1 0 0 0 2 21 2 14 3 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 1 3 4

IEP and HEP usage is restricted to terms from the Biological Process ontology:
gorule-0000006

6 0 24 2 0 0 0 0 2 0 29 0 0 466 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 630 4 0 4 0 5 1

IPI should not be used with GO:0003824 catalytic activity or descendents:
gorule-0000007

1 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 2 3 0 0 0 0 0

No annotations should be made to uninformative high level terms:
gorule-0000008

10000 10 1 42 46 193 305 43 59 10 448 21 1 185 39 195 8 107 176 168 22 225 10000 27 199 31 234 177 239 272 2 3 20 98 0 0 16 66 70 17

ND evidence code should be to root nodes only, and no terms other than root nodes can have the evidence code ND:
gorule-0000011

0 0 0 0 0 0 1 0 9 9 12 6 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0

Taxon-appropriate annotation check:
gorule-0000013

111 0 4 0 1 2 3 14 3 2 55 2 0 0 18 104 0 44 44 28 24 27 3894 31 27 21 39 42 35 46 0 11 1221 0 41 7 0 0 10 0

Dual species taxon check:
gorule-0000015

0 0 0 0 0 0 0 0 0 0 37 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

With/From: IC annotations require a With/From GO ID:
gorule-0000016

0 0 38 21 3 3 15 0 0 0 219 1 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 2 3 0 0 0 0 0

IDA annotations must not have a With/From entry:
gorule-0000017

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

IPI annotations require a With/From entry:
gorule-0000018

19 0 515 384 0 2 27 15 16 0 3736 15 0 200 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 295 0 0 68 1821 0 46 99 15 5

Automatic repair of annotations to merged or obsoleted terms:
gorule-0000020

964 11 44 37 374 860 1145 40 39 36 578 42 17 112 136 219 94 659 1096 1268 106 1477 10000 125 1374 135 417 477 1118 1386 26 7 19 53 500 30 26 42 30 26

Check for, and filter, annotations made to retracted publications:
gorule-0000022

1 0 0 0 0 1 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Each identifier in GAF is valid:
gorule-0000027

10000 106 160 0 310 710 1237 10000 10000 10000 10000 10000 10000 10000 6411 10000 1245 10000 10000 10000 5498 10000 10000 6672 10000 7114 10000 10000 10000 10000 6 313 10000 10000 6 3996 226 1 39 24

GO aspect should match the term's namespace; otherwise it is repaired to the appropriate aspect:
gorule-0000028

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

IEAs should be less than one year old.:
gorule-0000029

10000 0 0 0 4 6446 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Only valid GO_REFs are allowed:
gorule-0000030

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference:
gorule-0000037

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants:
gorule-0000039

0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0

Qualifier: IKR evidence code requires a NOT qualifier:
gorule-0000042

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Check for valid combination of evidence code, with/from rules and GO_REF:
gorule-0000043

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

The ‘with’ field (GAF column 8) must be the same as the gene product (GAF column 2) when annotating to ‘self-binding’ terms.:
gorule-0000046

79 17 440 110 4 6 9 675 707 583 1015 709 8 2020 1 1 0 2 3 4 1 15 291 1 11 1 1 4 12 7 10 16 0 1569 27 88 306 73 28 158

Annotations to ISS, ISA and ISO should not be self-referential:
gorule-0000050

0 0 0 0 0 0 0 0 0 0 5 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

References should have only one ID per ID space:
gorule-0000055

0 0 0 0 65 76 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Object extensions should conform to the extensions-patterns.yaml file in metadata:
gorule-0000058

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

GAF Version 2.0 and 2.1 are converted into GAF Version 2.2:
gorule-0000059

10000 0 0 0 9941 10000 10000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Allowed gene product to term relations (gp2term):
gorule-0000061

10000 388 13 93 77 187 499 302 323 288 677 329 12 818 0 0 0 0 0 1 0 1 44 0 1 0 1 0 1 0 20 2 0 349 90 7 31 29 63 44

Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column):
gorule-0000063

1437 92 25 738 103 0 383 1 0 0 12 0 0 781 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 3070 163 0 66

TreeGrafter IEAs should be filtered for GO reference species:
gorule-0000064

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0

Annotations to term that are candidates for obsoletion should be produce a warning:
gorule-0000065

2729 49 143 85 56 95 255 126 310 51 2169 94 1 4574 0 21 0 4 15 24 0 22 3039 0 23 0 49 3 23 25 11 32 46 4032 252 2 375 53 206 201