GO Rule Violations by Group Dataset

Generated on 2025-05-04
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 24 0 1 4 0 18 5 44 7 1210 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 76 1739 0 2 1313 0 31 0 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 2 0 0 0 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

IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0

IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC:
gorule-0000006

4 0 23 2 0 0 0 0 2 0 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0

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

10000 232 112 553 41 176 265 1263 1262 1177 3075 1315 6 1143 32 160 6 85 133 143 22 201 10000 25 177 29 236 115 184 161 8 57 15 0 457 4 610 498 872 441

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

Dual species taxon check:
gorule-0000015

0 0 0 0 0 0 0 0 0 0 37 1 0 29 0 0 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 0 4 3 16 0 0 0 195 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 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 5 0 8 0 0 0

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

18 0 447 0 0 2 27 1 12 0 1744 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 121 0 32 0 8 5

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

8161 1 164 129 339 769 1046 344 330 277 1859 342 1 150 32 40 31 80 145 151 41 191 10000 40 169 37 103 63 167 200 5 296 64 1 247 124 137 467 0 62

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

1 0 0 0 0 1 0 2 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 66 0 0 0 0 0 0

Each identifier in GAF is valid:
gorule-0000027

10000 106 160 7 311 710 1240 10000 10000 10000 10000 10000 0 0 0 0 0 0 0 0 0 0 0 0 2180 0 0 0 0 6 3 75 10000 10000 2 0 10000 10000 1473 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 0 0 0 0 0 0 0 0 0 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 379 673 0 4 6475 0 174 870 705 1284 700 74 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 58 14 0 0 554 0 8424 479 1658 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 0 0 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

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

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

84 17 404 102 4 6 9 715 727 582 993 703 0 889 1 1 0 2 9 8 1 16 357 1 15 1 1 4 16 13 0 0 0 1792 6 0 213 69 140 162

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

0 0 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

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 0 112 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 3726 0 0 0 1458 0 0 0 0

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

9597 2684 13 11 77 187 499 347 343 296 671 330 0 1411 0 1 0 1 1 1 0 1 27 0 1 0 0 1 1 0 0 14 0 1986 0 5 1107 85 72 2760

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

1441 97 26 937 104 0 386 1 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 971 0 12 496 94 5624 192 0 9

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 removed:
gorule-0000065

3302 55 19 103 57 96 255 169 424 71 2847 127 0 2430 5 0 1 0 0 2 6 2 328 6 2 9 6 0 2 1 0 41 43 5235 275 1 984 1348 259 3872