GO Rule Violations by Assignment

Generated on 2025-12-22
Rule AgBase ARUK-UCL BHF-UCL CACAO CAFA cgd CollecTF ComplexPortal dictybase DisProt ecocyc EcoliWiki Ensembl EnsemblFungi 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 sgn 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 7 0 21 1 0 0 0 0 0 0 21 0 0 0 0 0 0 0 0 399 0 0 0 0 32 2 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 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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 74 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 15 22 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 1098 0 4 0 0 0 0 0 4 0

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 2 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0

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

45 0 0 7 0 10000 0 0 3 0 0 0 0 0 0 0 482 0 11620 312 0 0 0 66 16 0 0 0 77 0 0 15 0 0 0 4 0 0 199 16 0 618 0 27 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 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 0

Taxon-appropriate annotation check:
gorule-0000013

2 0 0 5 0 112 0 15 0 0 0 0 4 0 0 0 6 0 3354 0 0 0 0 17 0 0 0 0 1 0 10 1210 0 0 0 0 2 0 24 0 0 48 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 94 0 21 0 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0 6 0 0 0 0 0 230 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 0 0 0 0 0 14 0 0 0 0 0 0 0

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

0 0 0 0 0 19 0 754 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 0 0 0 0 33 0 0 0 0 0 0 0

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

5 5 28 6 4 297 0 8 6 2 14 2 394 14 25 2 2244 0 12219 128 0 7 1223 409 34 0 55 0 10 18 4 12 150 0 42 125 37 0 50 0 34 588 0 1 0 2

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 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

Each identifier in GAF is valid:
gorule-0000027

0 0 0 0 0 10000 459 721 106 26 6 0 69965 10000 3 19 2259 0 3422 52 0 0 0 2541 0 313 0 12 0 0 0 10000 1 20 0 0 0 5 7016 1 0 467 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

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 6476 0 0 0 0 0 0 8149 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11583 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 0 0 0 0 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 1 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

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

38 13 71 0 55 79 0 0 2 7 386 0 3059 4 55 0 19 0 1314 0 3 16 0 697 58 0 8 0 0 0 0 0 897 0 0 0 0 0 0 0 0 2187 0 9 0 3

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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 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 0 194 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 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 29941 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1458 0 0 0 0 0 0 0 0 0 0

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

1 0 5 397 0 10000 0 0 386 13 0 0 1945 15 163 0 763 0 238 0 0 2 0 4 107 0 1 0 4 0 0 0 33 0 63 5 0 0 1063 11 0 897 0 11 2 2

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

1 0 0 0 0 1434 0 0 95 0 25 0 0 0 750 0 488 0 0 449 0 0 0 0 773 0 0 0 0 0 0 0 0 0 0 94 0 0 5166 0 0 20 0 173 0 75

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

98 0 0 99 1 2589 0 114 36 14 132 0 0 0 0 0 406 0 2502 375 0 0 0 156 1615 0 0 0 141 0 30 95 3525 0 240 1 0 0 318 5 0 4475 0 0 3 81