GO Rule Violations by Assignment

Generated on 2024-07-21
Rule AgBase Alzheimers_University_of_Toronto ARUK-UCL BHF-UCL CACAO CAFA cgd CollecTF ComplexPortal DFLAT DIBU dictybase DisProt ecocyc EcoliWiki Ensembl FlyBase GDB GeneDB genedb_tbrucei GO_Central GOC GOC-OWL HGNC HGNC-UCL IntAct InterPro japonicusdb mgi ParkinsonsUK-UCL PHI-base PINC pombase pseudocap reactome rgd RHEA RNAcentral sgd sgn SynGO SYSCILIA_CCNET tair TIGR TreeGrafter UniProt wb zfin

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

0 0 8 22 0 0 0 0 1294 0 0 24 0 0 0 0 1 0 21 1 57 12 0 0 0 0 0 0 0 0 0 0 1 1739 0 6 0 1258 0 0 0 0 31 1 0 0 0 0

No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515':
gorule-0000002

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 0 0 0 0 1 0 0 0 0 0 0 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

5 0 0 8 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 57 0 0

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

0 0 0 0 0 0 0 2 0 0 0 0 10 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 467 0 1 0 0 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 4 0 0 0 0 0 0 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 0 0 0

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

173 2 463 1220 102 121 10000 0 41 3 5 45 5 0 0 773 69 2 901 0 27813 1506 0 11 75 0 715 0 147 233 0 149 6 81 68 326 0 0 290 5 5 0 469 14 19 7835 169 300

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 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 12 0 0 0 0 0 0 0 0 0 0

Dual species taxon check:
gorule-0000015

0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 0 0

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

0 0 0 5 0 0 0 0 0 0 0 0 0 38 0 0 0 0 23 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 6 2 0 0 1 0 185 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 0 0 5 0 0 0 6 0 0 0 0 0

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

0 0 0 0 0 0 0 0 2506 0 0 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 27 0 0 1 0 0

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

14 0 20 142 4 0 7764 0 229 0 0 1 0 50 3 206 234 0 2067 0 13514 126 0 0 1 507 398 1 1 11 0 10 10 242 22 21 82 0 6 115 0 0 195 26 42 789 238 416

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

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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

0 0 0 0 0 0 0 154 0 0 0 0 0 0 0 0 0 60 0 0 0 0 42 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 157 0 0 10000 0 0 0

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 0 0 0 0 0 0 0

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

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6482 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 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 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 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 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 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

41 0 14 88 0 53 84 0 0 0 0 2 1 365 0 2007 61 0 19 0 1409 0 0 3 33 0 675 0 13 7 0 0 0 0 0 886 0 0 1 0 0 0 0 0 7 1949 5 82

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

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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

References should have only one ID per ID space:
gorule-0000055

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 194 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 108 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

0 0 0 0 0 0 10000 0 0 0 0 0 0 0 0 0 0 0 29941 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3726 0 0 0 0 0 1458 0 0 0 0 0 0 0 0

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

1 3 18 8 357 2 9634 0 4793 0 0 4608 3 78 0 5 94 0 755 0 3398 0 0 0 3 0 24 0 0 0 0 4 0 6 0 2237 0 0 6 5 0 0 1076 11 0 1226 31 2810

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

1 0 0 0 0 0 1441 0 0 0 0 97 0 27 0 0 954 0 490 0 0 473 0 0 0 0 0 0 0 0 0 0 0 972 0 10 0 0 495 94 0 0 5172 0 0 20 195 0

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 0 0 0 0 0 10050 0 0 0