GO Rule Violations by Group Dataset

Generated on 2020-06-01
Rule aspgd cgd dictybase ecocyc fb genedb_lmajor genedb_pfalciparum genedb_tbrucei goa_chicken goa_chicken_complex goa_chicken_isoform goa_chicken_rna goa_cow goa_cow_complex goa_cow_isoform goa_cow_rna goa_dog goa_dog_complex goa_dog_isoform goa_dog_rna goa_human goa_human_complex goa_human_isoform goa_human_rna goa_pig goa_pig_complex goa_pig_isoform goa_pig_rna mgi paint_cgd paint_dictybase paint_ecocyc paint_fb paint_goa_chicken paint_goa_human paint_mgi paint_other paint_pombase paint_rgd paint_sgd paint_tair paint_wb paint_zfin pombase pseudocap reactome rgd sgd sgn tair wb zfin

GAF lines are parsed according to GAF 2.1 specifications:
gorule-0000001

0 0 0 161 0 3 16 17 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1738 0 0 0 0 0 0 0

No 'NOT' annotations to '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 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:
gorule-0000006

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

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

10000 4314 0 140 28 25 65 202 5 0 3 0 2 0 0 0 0 0 0 0 110 0 0 0 2 0 1 0 919 39 52 39 79 146 157 161 10000 32 169 35 169 133 224 0 25 469 0 0 22 353 3 1

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 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 0 0 0 0

Taxon-appropriate annotation check:
gorule-0000013

358 119 10 1 148 10 13 14 272 0 12 0 15 0 2 0 10 0 0 0 20 0 0 0 13 0 1 0 18 49 61 18 24 48 22 23 8250 41 26 30 101 67 39 0 5 263 17 0 6 61 48 89

Dual species taxon check:
gorule-0000015

0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 2 0 0 0 20 0 4 0 1 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 5 0

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

0 0 0 0 0 4 56 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1

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 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0

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

9 0 0 0 0 1 1 23 0 0 0 0 0 3 0 0 0 0 0 0 0 112 0 0 0 3 0 0 381 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 285 0 3

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

2601 393 0 262 146 59 222 218 266 0 39 0 148 0 29 0 113 0 36 0 375 15 95 12 111 0 57 0 3 36 31 28 53 145 150 147 10000 30 146 29 234 56 183 6 104 34 3 12 94 1503 432 22

Each identifier in GAF is valid:
gorule-0000027

0 0 0 10000 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 209 0 5 0 0 0 0 0 44 0 0 0 0 0 0 0 2269 0 0 0 0 0 0 0 1 0 0 0 0 1 0 53

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 0 0 0 0 0 0 0

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

4980 1 0 10000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 23 0 6510 38 2

Deprecated GO_REFs are not allowed:
gorule-0000030

0 0 0 10000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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

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 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 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 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 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

144 91 21 77 105 4 7 10 629 0 38 0 734 0 87 0 482 0 116 0 752 0 136 0 581 0 158 0 941 3 5 0 8 36 30 54 2102 2 47 4 13 9 46 0 0 0 1283 7 0 281 72 162

Annotations to ISS, ISA and ISO should not be self-referential:
gorule-0000050

0 0 0 0 3 0 0 0 0 0 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 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 0 0 0 0 0 0 0

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 1942 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0