GO Rule Violations by Group Dataset

Generated on 2020-03-23
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 3 0 0 0 1 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 1 1 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 4639 0 140 28 25 65 202 5 0 3 0 2 0 0 0 0 0 0 0 111 0 0 0 2 0 1 0 950 44 53 39 87 193 192 196 10000 37 199 40 194 135 254 1 25 469 361 0 22 337 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

484 240 13 26 180 10 13 14 270 0 10 0 13 0 2 0 10 0 0 0 20 0 0 0 13 0 1 0 19 52 59 20 28 55 30 29 6695 55 29 40 89 73 50 25 19 263 16 32 6 86 49 91

Dual species taxon check:
gorule-0000015

0 0 0 0 0 0 0 0 0 0 0 0 3 0 3 0 2 0 0 0 168 0 146 0 1 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 14 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 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 1 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 0 110 0 0 0 3 0 0 379 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 274 0 2

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

212 85 0 224 42 54 219 211 4 0 0 0 5 0 2 0 4 0 7 0 18 0 3 0 4 0 6 0 0 12 9 8 15 19 21 16 2033 13 20 19 26 11 21 10 64 19 0 1 93 17 46 1

Each identifier in GAF is valid:
gorule-0000027

0 0 0 10000 0 1 0 0 37 0 1 0 120 0 0 0 27 0 0 0 2931 0 52 0 61 0 0 0 510 0 0 0 0 0 0 0 12 0 0 0 0 0 0 0 1 0 0 0 0 1 14 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

All IEAs over a year old are removed:
gorule-0000029

143 220 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 0 37 1

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 95 18 77 105 4 7 10 628 0 38 0 733 0 87 0 482 0 116 0 745 0 136 0 581 0 157 0 931 3 4 0 8 37 23 39 1763 2 39 4 13 10 55 0 0 0 1396 7 0 282 80 152

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