GO Rule Violations by Assignment

Generated on 2024-06-17
Rule AgBase Alzheimers_University_of_Toronto ARUK-UCL BHF-UCL CACAO CAFA cgd CollecTF ComplexPortal DFLAT DIBU dictybase DisProt ecocyc EcoliWiki Ensembl FlyBase GDB GeneDB genedb_tbrucei GO_Central GOC GOC-OWL HGNC HGNC-UCL IntAct InterPro mgi ParkinsonsUK-UCL PHI-base PINC pombase pseudocap reactome rgd RHEA RNAcentral sgd sgn SynGO SynGO-UCL SYSCILIA_CCNET tair TIGR TreeGrafter UniProt wb zfin

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

0 0 0 0 0 0 0 0 1294 0 0 1 0 0 0 0 2221 0 21 1 57 0 0 0 0 0 0 0 0 0 0 0 1739 0 6 0 0 0 0 0 0 0 5 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 1 0 0 0 0 0 0 0 0 0 0 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

6 0 0 6 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 35 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 0 2 0 0 0 0 10 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 20 0 0 0 0 0 0 0 0

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

0 0 0 0 0 0 0 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

173 2 420 1186 96 113 10000 0 31 3 5 68 5 0 0 269 56 2 901 0 24451 1503 0 9 64 0 759 2985 214 0 150 8 81 79 0 0 0 312 5 4 1 0 471 14 1 9580 153 299

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 0 1 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 0 0 0 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

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

0 0 0 5 0 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 1 0 0 0 0 0 0 6 1 0 0 0 1 0 176 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 0 5 0 0 0 0 0

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

0 0 0 0 0 0 0 0 2458 0 0 0 0 0 0 0 0 0 29 0 0 4 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 2 0 0 0 0 25 0 0 1 0 0

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

6 0 33 29 3 8 7367 0 156 0 0 6 0 36 1 311 176 0 1973 0 12333 215 0 0 0 429 150 285 10 0 8 8 239 3 121 23 7 23 115 1 0 0 298 28 76 951 227 88

Each identifier in GAF is valid:
gorule-0000027

0 0 0 0 0 0 0 154 0 0 0 0 0 0 0 0 0 60 0 0 0 0 42 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 157 0 0 10000 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 0 0

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

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6482 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 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 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 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 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

40 0 4 78 0 53 84 0 0 0 0 2 1 365 0 1731 61 0 19 0 485 0 0 3 26 0 611 935 7 0 0 0 0 0 882 0 0 1 0 0 0 0 0 0 23 1658 5 82

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 0 3 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 0 194 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 108 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 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 2 16 7 356 2 9307 0 5367 0 0 4606 2 78 0 2 94 0 675 0 233 0 0 0 3 0 36 1862 0 0 4 1 6 4770 3135 0 0 0 5 0 0 0 1097 11 1 1185 31 2810

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

1 0 0 0 0 0 1442 0 0 0 0 97 0 27 0 0 955 0 490 0 0 519 0 0 0 0 0 0 0 0 0 0 972 0 10 0 0 495 94 0 0 0 5173 0 0 17 195 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 0 10050 0 0 0