GO Rule Violations by Group Dataset

Generated on 2024-09-29
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 57 0 0 0 0 0 0 0 1 1739 0 6 1298 0 32 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 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 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

0 0 23 2 0 0 0 0 2 0 26 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 0 0

IPI should not be used with GO:0003824 catalytic activity or descendents:
gorule-0000007

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 1 1 0 0 0 0

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

10000 3 0 17 40 146 228 39 41 5 410 10 10 429 9 12 1 80 81 75 78 2631 7 82 10 14 44 72 107 10 39 16 0 55 4 434 692 24 24

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 0 193 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 6 0 0 0

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

0 0 449 0 0 2 27 1 12 0 1707 2 0 130 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 118 0 27 0 8 5

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

7837 2 98 66 330 727 1028 75 173 119 819 165 0 764 35 29 10 68 79 89 87 5651 30 91 45 76 42 86 99 1 243 37 14 147 124 702 441 0 5

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

1 0 0 0 0 1 0 0 0 0 82 0 0 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 65 0 0 23 0 0 0

Each identifier in GAF is valid:
gorule-0000027

10000 10000 948 455 311 710 1241 10000 10000 10000 10000 10000 309 10000 7988 10000 818 10000 10000 10000 10000 10000 7644 10000 8602 10000 10000 10000 10000 3079 75 10000 10000 8363 0 10000 10000 10000 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

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

0 0 0 0 4 6476 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 0 0 0 0 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 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

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 17 402 104 4 6 9 300 552 574 870 670 0 1730 1 1 0 2 9 17 24 383 1 20 1 1 4 14 12 0 0 0 1479 6 0 221 69 149 159

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 0 109 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

9565 4606 607 349 77 187 499 30 97 7 3938 18 0 4908 38 41 0 88 139 167 161 7965 47 164 45 100 90 144 186 0 6 0 2608 0 5 1097 291 76 2741

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

1441 97 27 948 104 0 386 1 0 0 12 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 972 0 12 495 94 5630 195 0 12

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 4 0 0