GO Rule Violations by Assignment

Generated on 2026-05-07
Rule AgBase ARUK-UCL BHF-UCL CACAO CAFA cgd CollecTF ComplexPortal dictybase DisProt ecocyc EcoliWiki Ensembl EnsemblFungi EnsemblPlants FlyBase GDB GeneDB genedb_tbrucei GO_Central GOC HGNC HGNC-UCL IntAct InterPro mgi NTNU_SB ParkinsonsUK-UCL PHI-base PINC pombase pseudocap reactome rgd RNAcentral sgd SynGO SYSCILIA_CCNET tair TIGR TreeGrafter UniProt UOS_MCB wb xenbase zfin

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

0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 7 0 21 1 0 0 0 0 0 0 21 0 0 0 0 0 0 0 0 478 0 0 0 0 0 0 0 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 0 0 0 0 0 0 0 0 0 0 0

IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations are not allowed for direct annotations to 'protein binding ; GO:0005515 or GO:0005488 binding'':
gorule-0000005

6 0 8 0 4 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 72 0 0 0 0

IEP and HEP usage is restricted to terms from the Biological Process ontology:
gorule-0000006

0 0 0 0 0 6 5 0 0 17 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 1107 0 4 0 0 0 0 0 5 1

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

0 0 0 0 0 1 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0

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

48 20 9 6 0 10000 0 0 4 0 0 0 0 0 0 35 0 544 0 12128 0 0 2 0 17 23 0 0 0 100 0 0 20 0 0 0 0 0 0 0 0 774 0 45 0 0

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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 42 0 0 0 0 0 0 0 0 0 0 0

Taxon-appropriate annotation check:
gorule-0000013

3 0 3 0 0 111 0 16 0 0 0 0 4 0 0 0 0 6 0 4424 0 0 0 0 7 1 0 3 0 1 0 10 1221 0 0 30 2 0 0 0 0 68 0 0 1 0

Dual species taxon check:
gorule-0000015

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 36 0 0 0 0

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

0 0 5 0 0 0 0 0 0 1 38 0 0 0 0 21 0 21 0 0 0 0 1 0 0 1 0 0 0 0 4 0 0 0 0 3 0 0 0 0 0 215 2 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 0 0 0 0 0 0 0 0 0 0 0 0 0

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

0 0 0 0 0 19 0 7225 0 0 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0

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

2 4 2 0 2 964 0 95 0 0 1 1 83 3 0 2 2 2379 0 20303 1 0 0 991 113 8 0 1 0 0 8 1 22 23 0 16 0 0 4 1 7 96 3 1 2 4

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

0 0 0 2 0 1 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

Each identifier in GAF is valid:
gorule-0000027

0 0 0 0 0 10000 459 0 106 38 6 0 69692 10000 4188 0 19 2257 0 136940 0 0 0 0 0 0 315 0 35 0 1 0 10000 2 10 0 0 5 0 0 0 0 0 1 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

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

0 0 0 0 0 10000 0 0 0 0 0 0 0 0 0 0 0 6450 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Only valid GO_REFs are 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

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

Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants:
gorule-0000039

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 1 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

Check for valid combination of evidence code, with/from rules 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

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

39 13 71 0 61 79 0 0 2 8 386 0 2985 4 16 55 0 19 0 1237 0 3 16 0 711 60 0 8 0 0 0 0 0 899 0 5 0 0 0 0 0 2326 0 8 0 1

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 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 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 0 194 0 0 0 0 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

GAF Version 2.0 and 2.1 are converted into GAF Version 2.2:
gorule-0000059

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

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

1 0 5 391 1 10000 0 0 386 14 0 0 1668 12 8 163 0 763 0 286 0 0 2 0 0 1 0 1 0 4 0 0 0 27 0 69 0 0 7 0 0 872 0 9 0 0

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

1 0 0 0 0 1437 0 0 92 0 25 0 0 0 0 738 0 486 0 0 0 0 0 0 0 778 0 0 0 0 0 0 0 0 0 0 0 0 3064 0 0 23 0 163 0 66

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 10000 0 0 0 0 0

Annotations to term that are candidates for obsoletion should be produce a warning:
gorule-0000065

97 1 1 95 1 2729 0 143 36 15 132 0 0 0 0 7 0 406 0 5272 0 0 0 0 0 1633 0 0 0 133 0 30 100 3448 0 210 0 0 253 5 0 4364 0 1 2 81