GO Rule Violations by Group Dataset

Generated on 2025-12-22
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 34 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 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 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 0 623 2 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 8 0 5 41 176 265 37 51 6 360 17 0 148 32 159 7 84 123 130 20 183 10000 24 156 26 221 115 177 156 0 0 15 72 1 4 609 34 33 12

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 15 2 0 0 29 101 0 26 25 13 20 4 3009 28 4 20 31 22 13 9 1 11 1209 0 10 0 59 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 94 3 3 15 0 0 0 233 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 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 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 33 9 0 0

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

297 79 105 100 360 806 1078 136 182 153 787 162 68 429 42 109 16 69 156 158 32 166 10000 28 165 36 124 146 166 199 82 40 7 335 824 125 136 80 126 95

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 106 160 769 310 710 1239 10000 10000 10000 10000 10000 10000 10000 3 17 0 4 15 16 4 16 936 4 2346 6 8 6 15 26 5 313 10000 10000 5 0 10000 0 308 67

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 334 668 409 4 6472 0 152 768 608 1130 600 235 1110 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 386 511 0 788 499 0 9045 413 1407 669

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 9 676 758 595 1012 712 8 2014 1 1 0 2 9 8 1 16 357 1 15 1 1 4 16 13 10 16 0 1569 22 0 213 76 30 161

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

0 0 0 0 0 0 0 0 0 0 3 0 0 3 0 0 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 388 13 93 77 187 499 351 390 330 729 358 15 934 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 2 0 390 84 5 1124 31 65 46

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

1434 95 25 750 103 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 173 0 75

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

2589 50 146 89 56 95 255 128 319 53 2184 95 1 4539 0 1 0 2 11 19 0 17 409 0 18 0 2 1 19 20 11 32 48 4107 279 1 972 53 217 213