GO Rule Violations by Group Dataset

Generated on 2026-03-25
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 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 4 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 0 462 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 616 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 0 0 0 0 0

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

10000 34 18 61 45 193 304 68 88 50 471 51 8 212 39 189 8 105 160 164 22 213 10000 27 191 31 234 137 202 228 9 18 20 125 16 62 56 84 95 42

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 43 44 28 24 27 3884 32 27 21 39 42 35 46 0 11 1209 0 18 7 0 0 11 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 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 3 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 60 10 0 2 27 0 3 0 517 2 0 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 14 178 0 37 9 0 0

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

268 105 177 1337 367 822 1085 1614 1942 1543 4464 1963 41 4523 84 150 72 581 976 1146 63 1347 10000 74 1247 81 283 363 990 1224 81 103 26 3123 524 135 215 337 6 906

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 106 160 774 310 710 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 3972 230 0 305 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 6472 0 0 0 0 0 0 0 0 0 0 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 17 440 111 4 6 9 675 707 584 1014 709 8 1999 1 1 0 2 3 4 1 15 291 1 11 1 1 4 12 7 10 16 0 1518 23 88 308 74 30 158

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 395 13 93 77 187 499 306 325 290 685 330 12 820 0 0 0 0 0 1 0 1 44 0 1 0 1 0 1 0 20 2 0 353 90 7 46 31 65 46

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

1442 95 25 756 103 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 0 3344 174 0 68

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 95 255 137 319 63 2177 106 2 4549 0 21 0 4 15 24 0 22 3039 0 23 0 49 3 23 25 11 32 54 3933 251 2 420 53 209 195