GO Rule Violations by Group Dataset

Generated on 2025-02-18
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_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 41 7 1207 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 1739 0 6 1316 0 33 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 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 1 14 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 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 0 448 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 1 1 0 0 0 0

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

10000 3 0 6 40 146 228 39 42 5 371 11 0 411 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 39 15 0 55 4 273 320 24 21

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 3 3 4 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

Dual species taxon check:
gorule-0000015

0 0 0 0 0 0 0 0 1 0 38 1 0 35 0 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 0 202 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 6 1 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 5 0 7 0 0 0

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

18 0 447 0 0 2 27 1 12 0 1747 2 0 136 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 118 0 28 0 8 5

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

7840 44 157 260 336 760 1038 176 228 177 828 244 43 1359 63 75 28 76 114 134 123 10000 67 137 64 151 89 98 132 5 279 66 111 630 124 69 449 3 177

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 71 0 0 2 0 0 0

Each identifier in GAF is valid:
gorule-0000027

10000 105 160 3 311 710 1241 10000 10000 10000 10000 10000 0 10000 0 0 0 0 0 0 0 0 0 2167 0 0 0 0 6 1 75 10000 10000 1 0 10000 10000 1468 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 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

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

10000 379 673 0 4 6475 0 129 599 483 757 457 75 808 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 60 14 0 0 554 0 850 479 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

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

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 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

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 9 687 698 563 877 661 0 1728 1 1 0 2 9 5 16 356 1 15 1 1 4 16 13 0 0 0 1479 6 0 213 69 140 161

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 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

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 0 112 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

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 3726 0 0 0 1458 0 0 0 0

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

9597 4600 13 1 77 187 499 26 84 7 589 19 0 3696 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 1712 0 5 1103 253 72 2740

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

1441 97 26 943 104 0 386 1 0 0 12 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 971 0 12 495 94 5627 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 10000 0

Annotations to term that are candidates for obsoletion should be removed:
gorule-0000065

3339 56 20 125 57 98 255 227 534 110 4668 191 0 4989 5 0 0 20 112 101 97 2236 6 97 9 0 9 133 165 0 42 45 6044 281 1 986 723 298 3765