GO Rule Violations by Group Dataset

Generated on 2025-07-27
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 1 0 1 4 0 18 5 44 7 1210 40 0 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 99 6 0 102 24 0 32 6 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

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 14 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

5 0 24 2 0 0 0 0 2 0 27 0 0 463 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 630 2 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 2 1 1 0 0 0 0

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

10000 12 0 8 41 176 265 867 743 734 547 868 0 219 32 160 6 85 133 143 22 201 10000 25 177 29 236 115 184 161 6 0 15 129 6 4 624 41 117 185

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 1 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 0 3 3 15 0 0 0 220 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 10 0 0 0

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

18 0 502 0 0 2 27 1 12 0 1777 3 0 155 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 42 1785 0 33 99 8 5

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

8356 7 74 12 346 777 1058 123 134 109 690 132 3 84 60 58 34 96 171 178 58 218 10000 60 197 67 125 77 192 232 8 5 3 69 476 124 44 16 20 29

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

Each identifier in GAF is valid:
gorule-0000027

10000 106 160 7 310 710 1239 10000 10000 10000 10000 10000 0 10000 0 0 0 0 0 0 0 0 0 0 2182 0 0 0 0 6 7 312 10000 10000 3 0 10000 68 1714 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 379 669 0 4 6472 0 174 869 705 1284 701 70 1262 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 512 0 967 553 0 7588 476 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 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 17 439 102 4 6 9 733 744 599 1030 720 0 2044 1 1 0 2 9 8 1 16 357 1 15 1 1 4 16 13 0 16 0 1554 22 0 213 79 140 169

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 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

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 395 13 1 77 187 499 347 342 296 670 331 0 905 0 1 0 1 1 1 0 1 27 0 1 0 0 1 1 0 0 2 0 350 84 5 1109 33 65 2870

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

1431 96 25 910 104 0 386 1 0 0 12 0 0 789 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 94 5623 174 0 8

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

3302 54 17 100 56 95 255 163 413 70 2644 124 0 1354 0 0 1 0 0 2 0 2 175 0 2 0 3 0 2 1 0 2 47 716 42 1 982 58 253 3965