GO Rule Violations by Assignment

Generated on 2025-07-01
Rule AgBase ARUK-UCL BHF-UCL CACAO CAFA cgd CollecTF ComplexPortal dictybase DisProt ecocyc Ensembl 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 RHEA RNAcentral sgd sgn SynGO SYSCILIA_CCNET tair TIGR UniProt wb xenbase zfin

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

0 8 22 0 0 0 0 0 0 0 0 0 1 0 21 1 0 1262 0 0 0 0 710 0 0 0 0 1 0 0 0 0 11519 0 0 0 0 30 2 1 0 0 3

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 2 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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 68 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 5 5 0 0 14 21 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 1111 0 0 0 0 0 6 0

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

0 0 0 0 0 1 0 5 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 0 1 0 0 0 0 0 0 0 0

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

73 0 0 6 12 10000 0 0 41 0 0 4133 5 0 482 0 11716 327 0 0 0 66 16 0 0 0 84 0 0 15 0 0 0 0 4 0 0 199 16 662 27 0 136

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 1 0 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

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 38 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 23 0 0 0 0 1 0 0 1 0 0 0 0 6 0 0 0 0 0 0 6 0 0 0 0 218 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 10 0 0 0 0 0

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

0 0 0 0 0 18 0 4426 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 0 33 0 0 0 0 0

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

5 2 8 0 1 5922 0 16 6 0 4 234 2 0 2168 0 11989 6 0 2 963 100 18 0 10 0 3 22 1 8 76 14 0 86 124 0 0 0 0 342 3 0 18

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 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

13 0 2 2 0 10000 459 0 106 16 6 71054 7 16 2261 0 2188 8 1 4 112 2461 0 255 0 7 0 0 0 10000 2 341 0 0 0 0 4 7100 1 9624 0 0 331

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

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

0 0 0 0 0 10000 0 0 0 0 0 0 0 0 6479 0 0 0 0 0 0 6845 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11286 0 0 9175

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

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

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 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

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 55 84 0 0 2 4 385 3086 59 0 19 0 446 0 3 34 0 663 59 0 8 0 0 0 0 0 849 0 0 1 0 0 0 0 0 2238 10 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 5 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 0 194 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

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 29941 0 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

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

1 0 5 396 3 9543 0 0 393 9 0 1753 75 0 763 0 41 0 0 2 0 4 1 0 1 0 4 0 0 0 23 0 0 0 5 0 0 1048 11 855 10 0 2826

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

1 0 0 0 0 1435 0 0 97 0 25 0 910 0 490 0 0 463 0 0 0 0 790 0 0 0 0 0 0 0 0 0 0 0 94 0 0 5166 0 20 174 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 0 0 0

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

104 0 0 116 98 3302 0 0 38 0 0 0 1 3 408 0 383 377 0 1 0 156 167 0 0 0 157 0 0 47 0 0 0 0 1 0 0 318 5 5509 0 0 3810