GO Rule Violations by Assignment

Generated on 2024-01-04
Rule AgBase Alzheimers_University_of_Toronto ARUK-UCL BHF-UCL CACAO CAFA CollecTF ComplexPortal DFLAT DisProt ecocyc Ensembl FlyBase GO_Central GOC HGNC HGNC-UCL IntAct InterPro mgi ParkinsonsUK-UCL pseudocap Reactome RHEA RNAcentral Roslin_Institute SynGO SynGO-UCL SYSCILIA_CCNET UniProt wb

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

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1739 0 0 0 0 0 0 0 0 0

No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515':
gorule-0000002

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 2 0 0 1 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

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

97 6 93 233 36 36 0 0 1 0 0 0 1 5403 5 2 19 0 690 2931 40 70 0 0 0 1 3 1 0 3167 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 0 0 0 0 0 0 2 0 0 0 0 0 0

Taxon-appropriate annotation check:
gorule-0000013

1 0 0 0 1 0 0 6 0 0 5 107 0 154 0 0 0 0 13 4 0 2 0 0 0 0 2 0 0 15 69

Dual species taxon check:
gorule-0000015

0 0 0 0 0 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

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

0 0 0 1 0 0 0 0 0 0 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 4 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

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

0 0 0 0 0 0 0 592 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

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

1 0 7 3 0 0 0 3 0 0 7 85 0 587 80 0 0 44 102 0 3 229 0 11 0 0 0 0 0 166 135

IBA annotations must have been sourced from the PAINT inference pipeline:
gorule-0000026

0 0 0 0 0 0 0 0 0 0 0 0 0 43247 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

0 0 0 0 0 0 154 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 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

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 0 0 0 14 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

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

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

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

Check for valid combination of evidence code and GO_REF:
gorule-0000043

0 0 0 0 0 0 0 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

28 0 13 28 0 19 0 0 0 0 364 859 1 64 0 0 6 0 295 989 4 0 0 0 0 0 0 0 0 427 6

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

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 0 0 0 0 0 0 0 0 0 0 0 0 0

Group specific filter rules should be applied to annotations:
gorule-0000057

0 0 0 0 0 0 0 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

GAF Version 2.0 and 2.1 are converted into GAF Version 2.2:
gorule-0000059

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3726 0 0 0 0 0 0 0 0 0

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

1 0 0 4 128 2 0 1646 0 0 77 0 0 2 0 0 1 0 0 1867 0 6 4709 0 0 0 0 0 0 209 28

Other

 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0