GO Rule Violations by Assignment

Generated on 2025-04-14
Rule AgBase ARUK-UCL BHF-UCL CACAO CAFA cgd CollecTF ComplexPortal dictybase DisProt ecocyc EcoliWiki Ensembl FlyBase GDB GeneDB genedb_tbrucei GO_Central GOC HGNC HGNC-UCL HPA IntAct InterPro mgi NTNU_SB ParkinsonsUK-UCL PINC pombase pseudocap reactome rgd RHEA RNAcentral sgd sgn SynGO SYSCILIA_CCNET tair TIGR TreeGrafter UniProt wb xenbase zfin

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

0 8 22 0 0 0 0 1302 24 0 0 0 0 1 0 21 1 6 12 0 0 0 0 0 0 0 0 0 67 1739 0 2 0 1264 8 0 0 0 29 2 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 1 0 0 0 0 0 0 0 0 0 2 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 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 60 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 4 2 0 0 12 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 0 467 0 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 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 1 0 0 0 0 0 0 0 0 0

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

71 6 48 6 12 10000 0 55 47 9 3 8 3708 404 0 482 0 14230 314 1 2 1893 0 1116 16 0 18 84 4 57 18 0 0 0 66 4 0 0 198 16 195 3291 167 0 170

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 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 36 0 0 0 0 0 0 0 0 0 0 0

Dual species taxon check:
gorule-0000015

0 0 2 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 37 0 0 0

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

0 0 5 0 0 0 0 0 0 0 38 0 0 0 0 23 0 0 0 0 1 0 0 0 0 0 0 0 3 0 0 0 0 0 0 6 0 0 0 0 0 191 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 5 0 0 0 8 0 0 0 0 0 0

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

0 0 0 0 0 18 0 2476 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 32 0 0 2 0 0 0

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

6 3 29 1 5 8147 0 116 0 0 61 5 507 121 0 2154 0 11440 119 0 0 0 503 266 17 0 12 4 5 296 82 42 63 0 44 124 12 0 28 0 54 482 61 0 22

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

2 0 0 2 0 1 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 66 0 0 0 0 0 0 0 0 0 0 0 0 0

Each identifier in GAF is valid:
gorule-0000027

11 0 2 1 0 10000 154 0 106 8 6 0 66762 4 16 2261 0 12087 8 1 4 0 68 3026 5 240 0 0 3 75 10000 4387 275 0 2 0 32 4 6421 1 0 9940 13 0 326

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 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

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 6479 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 9628 0 0 9219

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

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

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 1 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

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 14 88 0 53 84 0 0 2 4 365 0 3327 59 0 19 0 1370 0 3 34 0 0 708 13 0 7 0 0 0 0 899 0 0 1 0 0 0 0 0 0 1981 5 0 86

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 3 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 0 194 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 112 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

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 29941 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 0

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

1 0 5 357 1 9597 0 0 2681 6 0 0 1846 84 0 763 0 3448 0 0 2 0 0 4 1 0 1 4 0 14 0 1560 0 0 0 5 0 0 1046 11 0 950 28 0 2716

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

1 0 0 0 0 1441 0 0 97 0 26 0 0 937 0 490 0 0 455 0 0 0 0 0 0 0 0 0 1 971 0 10 0 0 496 94 0 0 5166 0 0 20 192 0 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 10000 0 0 0 0

Annotations to term that are candidates for obsoletion should be removed:
gorule-0000065

124 27 1224 108 100 3302 0 27 39 0 0 0 0 13 3 408 0 5090 378 0 1 0 0 769 167 0 56 161 0 41 43 4567 0 0 248 1 0 0 313 5 0 6612 22 0 3728