GO Rule Violations by Group Dataset

Generated on 2024-11-03
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_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 1 1739 0 6 1313 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 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

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 4 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 6 40 146 228 39 42 5 392 10 14 423 13 9 0 76 79 74 76 2538 10 80 14 12 41 64 95 14 38 16 0 55 4 434 681 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 0 197 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 1719 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

7707 2 57 18 330 735 1028 16 15 10 506 12 0 776 42 34 15 76 99 121 116 7237 33 126 52 84 47 105 141 1 266 27 25 75 124 714 500 3 18

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

1 0 0 0 0 1 0 0 0 0 23 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 973 447 311 710 1241 10000 10000 10000 10000 10000 302 10000 7829 10000 815 10000 10000 10000 10000 10000 7605 10000 8404 10000 10000 10000 10000 3073 75 10000 10000 8294 0 10000 10000 1419 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 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 9 691 720 584 875 679 0 1728 1 1 0 2 9 5 15 356 1 15 1 1 4 16 13 0 0 0 1474 6 0 221 69 140 159

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

9563 4603 607 1 77 187 499 30 97 7 3939 18 0 4898 38 42 0 85 147 166 159 8372 47 163 45 94 89 139 189 0 6 0 2362 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 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 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 10000 0