GO Rule Violations by Assignment

Generated on 2023-11-06
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 MTBBASE ParkinsonsUK-UCL PHI-base PINC pombase pseudocap reactome rgd RHEA RNAcentral Roslin_Institute sgd sgn SynGO SynGO-UCL SYSCILIA_CCNET tair TIGR UniProt wb zfin

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

0 0 0 0 0 0 0 0 1418 0 0 0 0 0 0 0 0 0 21 1 0 0 0 0 0 0 3 0 0 0 0 0 0 0 1739 3 3 0 0 0 0 0 0 0 0 2 0 2 0 1

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 0 1 0 0 0 0 0 0 0 0 0 0 0 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 6 2 0 0 0 0 9 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 0 0 17 0 0 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 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 1 0 0 0 0 0 0 0 0

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

197 14 472 1283 97 117 10000 0 122 2 5 73 0 0 0 23 619 2 898 0 26845 1419 0 10 107 0 1291 0 3123 0 276 0 158 37 70 108 0 0 0 1 318 17 4 2 0 1329 10 9547 342 5

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 0 18 0 0 0 0 0 0 0 0 0 0 0

Taxon-appropriate annotation check:
gorule-0000013

4 0 0 0 4 0 53 0 8 0 0 0 1 5 0 139 153 0 0 0 7362 0 0 0 0 0 27 0 3 0 0 0 1 31 2 890 2 0 0 0 29 0 2 0 0 16 0 89 69 11

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 0 0 0 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 5 0

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

0 0 0 4 0 0 0 0 0 0 0 0 0 36 0 0 6 0 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 6 0 0 0 0 0 136 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 0 0 5 0 0 0 0 2 0 0 0 0

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

0 0 0 0 0 0 0 0 2790 0 0 0 0 0 0 0 0 0 29 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 18 0 1 0 0

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

0 0 43 32 0 6 10000 0 149 0 0 0 17 8 1 279 27 0 1443 0 5448 141 0 0 0 425 61 0 17 0 41 0 2 6 229 215 31 11 0 0 6 113 0 0 0 5 26 223 93 24

Each identifier in GAF is valid:
gorule-0000027

0 0 0 0 0 0 0 154 0 0 0 0 0 0 0 0 15 57 0 0 0 0 37 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 1 0 0 0 162 0 0 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 0 0

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

0 0 0 0 0 0 10000 0 0 0 0 0 0 0 0 0 0 0 6557 0 0 144 0 0 0 0 8 0 0 0 0 0 0 0 14 0 0 0 59 0 0 0 0 0 0 0 0 0 0 0

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 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 0 0 0 0 0

IBA annotations should ONLY be assigned_by GO_Central and have PMID:21873635 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 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 0 449 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 0 0

Check for valid combination of evidence code and GO_REF:
gorule-0000043

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

47 0 14 94 0 61 91 0 0 0 0 5 0 364 0 2265 63 0 19 0 2030 0 0 3 26 0 857 0 1002 0 7 0 0 0 0 0 954 0 0 0 1 0 0 0 0 0 0 1899 6 81

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 0 0 3 0 0

Some GO terms require a value in the Annotation Extension field:
gorule-0000051

193 1 48 470 1 83 20 0 0 6 0 823 22 948 52 0 870 0 754 0 13 0 0 3 78 34851 0 2 2 1 95 0 0 2045 29 0 1974 0 299 3 149 0 0 5 1 2719 0 10861 539 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 0 108 0 0 0 0 0 0 0 0 0 0 0 0 0

Group specific filter rules should be applied to annotations:
gorule-0000057

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 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 0 3726 0 0 0 0 0 0 1458 0 0 0 0 0 0 0 0

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

1 0 13 7 359 3 6342 0 4623 0 0 4616 1 77 0 0 112 0 0 0 6 0 0 0 2 0 0 0 1838 0 0 0 0 0 0 4526 3381 0 1 0 716 0 0 0 0 1095 11 940 29 2597

Other

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