GO Rule Violations by Assignment

Generated on 2025-02-18
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 GOC-OWL 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 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 1301 0 24 0 0 0 0 1 0 21 1 6 12 0 0 0 0 0 0 0 0 0 0 2 1739 0 6 0 1258 8 0 0 0 32 1 0 1 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 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 0 0 58 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 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 0 0 1 0 0 0 0 0 0 0 0 0

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

54 0 25 75 6 10 10000 0 2 0 0 0 0 0 0 1 0 414 0 285 91 0 0 5 0 75 12 0 25 0 11 4 39 19 0 0 0 53 4 0 0 153 9 0 519 145 0 21

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 0 0 12 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 0 0 40 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 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 6 0 0 0 1 0 198 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 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 2477 0 0 0 0 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 28 0 0 1 0 0 0

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

5 0 0 0 3 0 7840 0 82 0 0 0 23 11 352 150 0 2134 0 13251 570 2 0 0 503 260 8 0 1 0 0 5 279 102 44 17 0 148 124 0 0 5 26 0 589 57 0 163

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 0 0 71 0 0 0 0 0 0 2 0 0 0 0 0 0

Each identifier in GAF is valid:
gorule-0000027

41 0 0 6 1 0 10000 154 0 0 105 18 6 0 63421 5 8 2262 0 12096 8 0 1 14 259 2478 5 441 0 4 0 1 75 10000 7482 192 0 1 0 52 5 7017 1 0 9728 13 0 348

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 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 0 0 14 0 0 0 0 0 0 0 0 0 0 0 8586 0 0 9375

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 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 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 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 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 0 14 88 0 53 84 0 0 0 2 4 365 0 2582 59 0 19 0 1365 0 0 3 33 0 663 13 0 7 0 0 0 0 0 904 0 0 1 0 0 0 0 0 0 1961 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 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 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 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 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 3 12 5 357 1 9597 0 0 0 4596 6 0 0 0 75 0 763 0 3389 0 0 0 2 0 4 1 0 0 0 4 0 14 0 1566 0 0 0 5 0 0 1042 11 0 1074 70 0 2696

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 0 943 0 490 0 0 464 0 0 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 0 0 10000 0 0 0 0

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

126 3 188 1981 106 105 3339 0 105 4 39 0 0 0 110 16 2 410 0 5857 377 1 0 60 0 899 167 0 156 0 130 0 42 45 5111 0 0 253 1 0 0 314 5 0 6274 22 0 3596