GO Rule Violations by Assignment

Generated on 2024-12-15
Rule AgBase Alzheimers_University_of_Toronto ARUK-UCL BHF-UCL CACAO CAFA CollecTF ComplexPortal DFLAT DIBU DisProt ecocyc EcoliWiki Ensembl FlyBase GDB GO_Central GOC HGNC HGNC-UCL IntAct InterPro mgi NTNU_SB ParkinsonsUK-UCL PHI-base PINC pseudocap Reactome RHEA RNAcentral SynGO SYSCILIA_CCNET UniProt wb

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

0 0 8 22 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 0 0 1739 0 0 1258 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 2 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 53 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 0 11 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 465 0 0 0

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

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

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

49 0 33 81 4 9 0 0 0 0 0 0 0 0 0 0 285 0 0 5 0 67 12 0 28 0 11 38 0 0 0 0 0 499 145

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 0 0 0 0 0 0 12 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 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 40 0

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

0 0 0 5 0 0 0 0 0 0 0 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 193 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

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

0 0 0 0 0 0 0 2313 0 0 0 0 0 0 0 0 0 0 0 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

21 0 25 131 6 18 0 65 0 0 6 28 1 806 2 0 6799 451 0 1 491 105 18 0 16 0 7 271 19 19 0 0 0 699 41

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

2 0 25 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 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 16 6 0 59526 0 8 14295 0 0 0 0 0 0 441 0 4 0 75 0 0 0 0 5 66 13

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 3 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 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 0 0 0 0 0 0 14 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

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

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

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

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

38 0 14 85 0 41 0 0 0 0 4 365 0 2392 1 0 1365 0 2 32 0 435 13 0 4 0 0 0 0 0 0 0 0 1395 5

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 3 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 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

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

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

1 2 9 8 297 0 0 5057 0 0 8 80 0 0 75 0 3389 0 0 2 0 0 1 0 0 0 4 6 0 0 0 0 0 831 70

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

1 0 0 0 0 0 0 0 0 0 0 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 971 0 0 0 0 0 15 192

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

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

111 2 397 1031 92 102 0 51 3 5 0 0 0 477 0 2 2930 0 0 49 0 610 131 0 184 0 130 42 0 0 0 0 0 4825 17