GO Rule Violations by Group Dataset

Generated on 2026-01-23
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 47 113 0 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 102 0 0 41 6 0 26

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 to 'protein binding ; GO:0005515 or GO:0005488 binding'':
gorule-0000005

0 0 0 1 0 0 0 2 22 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 4 0

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 0 462 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 627 4 0 4 0 4 0

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 1 1 0 0 0 0

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

10000 55 2 130 41 177 265 340 536 355 858 360 13 744 36 188 6 100 155 160 20 209 10000 26 187 28 227 133 198 223 9 44 19 519 19 4 559 136 567 923

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

112 0 4 0 1 2 3 14 2 1 14 2 0 0 26 98 0 25 23 4 19 2 2757 26 2 18 28 21 11 7 1 18 1209 0 10 0 50 0 11 44

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 27 3 3 15 0 0 0 215 1 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 2 0 6 0 0 0 1

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 14 0 0 0

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

19 0 60 7 0 2 27 0 3 0 458 2 0 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 166 0 34 9 0 0

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

25 50 132 80 361 819 1081 86 122 112 663 108 29 217 42 70 32 54 128 115 36 126 10000 39 127 45 121 88 130 156 58 104 8 195 794 125 124 74 135 288

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 21

Each identifier in GAF is valid:
gorule-0000027

10000 106 160 772 310 710 1239 10000 10000 10000 10000 10000 10000 10000 2 16 0 3 14 15 2 15 744 2 2348 4 4 5 14 25 5 313 10000 10000 6 0 10000 0 308 10000

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 2 2 1 3 1 0 4 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

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

10000 339 668 410 4 6472 0 152 768 608 1130 600 239 1110 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 386 511 0 797 501 0 2 415 1407 10000

Obsolete GO_REFs are not 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 17 440 107 4 6 9 678 758 596 1014 713 8 2018 1 1 0 2 3 4 1 15 291 1 11 1 1 4 12 7 10 16 0 1577 22 0 208 76 30 171

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 1458 0 0 0 0

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

10000 395 13 93 77 187 499 335 379 315 715 344 12 836 0 0 0 0 0 1 0 1 44 0 1 0 1 0 1 0 20 2 0 389 86 5 1129 31 65 44

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

1434 96 25 760 103 0 385 1 0 0 12 0 0 776 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 94 5618 174 0 127

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

2569 50 146 87 56 95 253 126 316 53 2164 94 1 4531 0 8 0 4 13 23 0 21 632 0 22 0 6 3 22 23 11 32 48 4074 278 0 818 52 215 4005