GO Rule Violations by Assignment

Generated on 2023-05-10
Rule AgBase ARUK-UCL BHF-UCL CACAO CAFA cgd CollecTF ComplexPortal dictybase DisProt ecocyc Ensembl EnsemblFungi FlyBase GDB GeneDB genedb_tbrucei GO_Central GOC GOC-OWL HGNC HGNC-UCL IntAct InterPro japonicusdb mgi ParkinsonsUK-UCL PHI-base PINC pombase pseudocap reactome rgd RHEA RNAcentral sgd sgn SynGO SYSCILIA_CCNET tair TIGR UniProt wb xenbase zfin

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

0 0 0 0 0 0 0 1316 0 0 0 0 0 0 0 21 1 0 0 0 0 0 0 0 0 0 0 0 0 5 1739 3 2 0 0 0 0 0 0 0 0 0 0 10 1

No 'NOT' annotations to '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 0 0 0

IEP and HEP usage is restricted to terms from the Biological Process ontology:
gorule-0000006

0 0 0 0 0 6 2 0 0 6 21 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 21 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 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 1 0 0 0 0 0 0 0 0

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

49 0 0 0 0 7074 0 1 0 0 0 0 0 50 0 367 0 12860 275 0 0 0 0 48 0 34 0 0 2 6 22 39 0 0 0 3 16 0 0 711 7 1169 21 0 0

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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 0 0 0

Taxon-appropriate annotation check:
gorule-0000013

4 0 0 4 0 53 0 8 0 1 5 143 0 155 0 2 0 7159 0 0 0 0 0 17 0 4 0 0 0 0 2 889 1 0 0 1 0 2 0 15 0 94 69 0 6

Dual species taxon check:
gorule-0000015

0 5 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 44 0 0 0

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

0 0 4 0 0 0 0 23 0 0 36 0 0 6 0 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 127 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 1 0 0 0 0 0

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

0 0 0 0 0 0 0 2904 0 0 0 0 0 0 0 29 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 6 0 1 0 0 0

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

3 24 24 2 5 10000 0 134 0 0 5 427 0 34 0 1607 0 1531 42 0 0 1 0 132 0 0 33 0 5 4 227 188 6 38 1 55 113 0 0 73 26 357 105 0 159

Each identifier in GAF is valid:
gorule-0000027

0 0 0 0 0 0 154 0 0 0 0 0 1973 15 57 0 0 0 0 35 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 162 0 0 0 0 0 0

Aspect can only be one of C, P, F and should be repaired using the GO term:
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

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

0 0 0 0 0 10000 0 0 0 0 0 0 0 0 0 6326 0 0 144 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 59 0 0 0 0 0 0 8341 0 0 0

Deprecated 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

IBA annotations should ONLY be assigned_by GO_Central and have PMID:21873635 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

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

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

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 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 colummn 2) when annotating to ‘self-binding’ terms.:
gorule-0000046

50 29 94 0 61 91 0 0 5 0 364 2099 0 67 0 24 0 2030 0 0 3 26 0 865 0 989 7 0 0 0 0 0 941 0 0 1 0 0 0 1 0 1880 6 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 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 0 194 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 132 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 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 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 2 0 10000 0 0 2412 1 0 0 0 0 0 29941 0 2184 115 0 0 0 10 1780 0 0 0 0 0 0 3726 0 0 138 0 0 1458 0 0 0 0 3358 0 0 0

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

34 898 553 359 9 6338 0 4846 2295 1 77 1068 2 300 0 0 0 4594 53 0 3 11 0 339 1 2206 16 0 4 14 0 4380 4050 0 7 5818 0 0 0 448 11 5518 71 0 2671

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