GO Rule Violations by Assignment

Generated on 2025-03-16
Rule AgBase Alzheimers_University_of_Toronto ARUK-UCL BHF-UCL CACAO CAFA cgd CollecTF ComplexPortal DFLAT dictybase DisProt ecocyc EcoliWiki Ensembl FlyBase GDB GeneDB genedb_tbrucei GO_Central GOC HGNC HGNC-UCL 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 0 8 22 0 0 0 0 1300 0 24 0 0 0 0 1 0 21 1 6 12 0 0 0 0 0 0 0 0 2 1739 0 6 0 1264 8 0 0 0 32 1 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 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 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 0 4 2 0 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 0 467 0 1 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 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

60 0 4 37 6 10 10000 0 18 0 0 0 1 3 25 9 0 415 0 1471 102 0 2 0 84 12 0 16 11 4 39 21 9 0 0 55 4 0 0 153 9 0 424 137 0 24

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 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 0 2 0 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 38 0 0 0

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

0 0 0 5 0 0 0 0 0 0 0 0 38 0 0 0 0 23 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 6 0 0 0 1 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 0 5 0 0 0 7 0 0 0 0 0 0

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

0 0 0 0 0 0 18 0 2478 0 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 28 0 0 2 0 0 0

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

5 0 4 5 1 0 7927 0 78 0 0 0 5 1 117 42 0 2136 0 12975 275 0 0 503 137 3 0 0 1 5 295 77 45 41 0 28 124 0 0 10 26 0 308 54 0 2

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

2 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 67 0 0 0 0 0 0 2 0 0 0 0 0 0

Each identifier in GAF is valid:
gorule-0000027

33 0 0 4 2 0 10000 154 0 0 106 14 6 0 63585 5 16 2262 0 12096 8 1 14 221 2478 5 284 0 0 1 75 10000 7481 170 0 1 0 52 4 7017 1 0 9851 13 0 294

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 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

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 6479 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 0 9908 0 0 9399

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 0 0 0 0 0 0 0 0 0 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 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

42 0 14 88 0 53 84 0 0 0 2 4 365 0 2762 59 0 19 0 1365 0 3 34 0 694 13 0 7 0 0 0 0 898 0 0 1 0 0 0 0 0 0 1979 5 0 83

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 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 0 0 194 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 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 29941 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 2 5 5 357 1 9597 0 0 0 4596 6 0 0 1267 75 0 763 0 3413 0 0 2 0 4 1 0 1 4 0 14 0 1566 0 0 0 5 0 0 1042 11 0 950 28 0 2681

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

1 0 0 0 0 0 1441 0 0 0 97 0 26 0 0 937 0 490 0 0 455 0 0 0 0 0 0 0 0 2 971 0 10 0 0 495 94 0 0 5169 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 0 10000 0 0 0 0

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

124 2 71 1416 107 103 3339 0 49 2 39 0 0 0 30 13 3 410 0 5857 378 0 26 0 796 167 0 88 162 1 42 45 5107 0 0 253 1 0 0 314 5 0 6770 22 0 3556