GO Rule Violations by Group Dataset

Generated on 2025-06-22
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 xenbase_alt zfin

GAF lines are parsed according to GAF 2.2 specifications:
gorule-0000001

0 0 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 1 12 0 0 0 0 31 0 0 0 3

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 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 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 1 1 2 0

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

5 0 23 2 0 0 0 0 2 0 27 0 0 917 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 630 2 0 0 0 6 1 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 1 0 0 2 1 1 0 0 0 0 0

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

10000 47 0 554 41 176 265 829 687 674 502 810 0 1846 32 160 6 85 133 143 22 201 10000 25 177 29 236 115 184 161 0 0 15 510 1 4 610 38 9 32 136

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 0

Dual species taxon check:
gorule-0000015

0 0 0 0 0 0 0 0 0 0 37 1 0 2 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 0

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

0 0 38 0 4 3 16 0 0 0 220 1 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 2 0 6 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 8 0 0 0 0

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

18 0 502 0 0 2 27 1 12 0 1777 3 0 290 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 48 0 0 44 1785 0 32 99 0 8 5

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

5694 34 56 163 340 773 1048 73 83 67 608 81 0 245 41 53 34 93 163 171 47 211 10000 47 189 47 114 74 186 220 42 18 69 148 517 124 185 43 40 89 30

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 0 0 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 10000 0 0 0 0 0 0 0 0 0 0 2182 0 0 0 0 6 1 312 10000 10000 3 0 10000 0 1421 0 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 0

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

10000 379 670 0 4 6475 0 174 869 705 1284 701 70 2495 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 420 512 0 966 553 0 8441 476 710 943 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 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 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 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 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 17 439 102 4 6 9 733 744 599 1030 720 0 2292 1 1 0 2 9 8 1 16 357 1 15 1 1 4 16 13 10 16 0 1521 22 0 213 79 118 170 169

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

0 0 0 0 0 0 0 0 0 0 4 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

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 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 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 0

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

9545 395 13 11 77 187 499 347 342 296 670 331 0 1203 0 1 0 1 1 1 0 1 27 0 1 0 0 1 1 0 21 2 0 351 23 5 1107 31 22 33 2870

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

1434 97 25 937 104 0 386 1 0 0 12 0 0 1206 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 94 5624 174 0 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 0 10000 0

Annotations to term that are candidates for obsoletion should be produce a warning:
gorule-0000065

3302 55 17 103 57 96 255 163 413 70 2644 124 0 2777 5 0 1 0 0 2 6 2 328 6 2 9 6 0 2 1 14 2 43 725 46 1 984 62 82 177 3965