GO Rule Violations by Group Dataset

Generated on 2025-10-03
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 4386 4 0 18 11 27 33 47 113 6 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 102 24 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 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

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, except when assigned by GOC:
gorule-0000006

6 0 24 2 0 0 0 0 2 0 29 0 0 463 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 622 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 42 55 6 373 23 6 152 32 159 6 84 123 130 20 183 10000 24 156 26 221 115 177 156 8 0 15 76 1 4 609 34 34 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

Dual species taxon check:
gorule-0000015

0 0 0 0 0 0 0 0 0 0 37 1 0 30 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

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

0 0 38 6 3 3 15 0 0 0 228 1 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 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

18 0 512 27 0 2 27 1 13 0 1873 4 0 157 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 46 0 0 42 1809 0 33 99 8 5

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

1299 0 40 9 349 782 1061 25 32 22 518 25 62 47 16 54 5 35 72 87 7 87 4274 8 84 12 52 87 79 101 94 0 53 37 723 124 0 4 0 13

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 1239 10000 10000 10000 10000 10000 10000 10000 3 17 0 4 15 16 4 16 936 4 2346 6 8 6 15 26 5 312 10000 10000 5 0 10000 0 1734 151

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 0 152 771 608 1130 600 258 1110 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 420 511 0 811 499 0 9029 413 1407 690

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

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 17 440 108 4 6 9 679 738 601 1033 718 8 2041 1 1 0 2 9 8 1 16 357 1 15 1 1 4 16 13 7 16 0 1506 22 0 213 76 30 165

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 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

6724 388 13 95 77 187 499 349 366 326 734 356 17 936 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 2 0 380 84 5 1124 31 65 46

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

1433 95 25 796 103 0 385 1 0 0 12 0 0 780 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 81

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

3298 52 11 94 56 95 255 150 378 68 2423 116 1 1310 0 1 0 2 11 20 0 18 424 0 19 0 2 1 20 21 11 2 47 674 38 1 981 56 247 153