GO Rule Violations by Group Dataset

Generated on 2019-11-01
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 gonuts gramene_oryza jcvi 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 pamgo_atumefaciens pamgo_ddadantii pamgo_mgrisea pamgo_oomycetes pombase pseudocap reactome rgd sgd sgn tair wb zfin

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

0 0 0 109 0 3 16 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 1 0 0 0 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 0 65 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 1 1 0

IPI should not be used with catalytic activity molecular function terms:
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 1 0 0 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 2

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

10000 4340 0 140 30 25 65 202 9 0 3 0 7 0 0 0 2 0 0 0 113 0 0 0 6 0 1 0 7 1935 6578 785 28 44 39 83 172 174 179 10000 26 182 27 191 133 231 68 1 1382 1 1 25 469 0 0 22 168 26 1

ND annotations to root nodes only; and only 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 9798 0 0 0 0 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

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

Dual species taxon check:
gorule-0000015

0 0 0 0 0 0 0 0 3 0 0 0 6 0 4 0 4 0 0 0 296 0 137 6 5 0 1 0 0 0 204 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 91 5 0 0 0 0 0 0 0 183 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 1 2575 81 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 4 0 0 0 0 0 0 0 6 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 3 0 4 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 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 0 108 0 0 0 3 0 0 4 1 0 427 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 5 0 260 1 0

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

0 21 0 207 28 41 184 173 68 0 2 0 85 0 6 0 60 0 4 0 115 0 1 0 70 0 20 0 45 10000 6616 6 1 0 0 7 14 20 20 324 0 19 2 1 3 19 6 55 2862 2 0 62 0 10 0 93 0 168 0

Each identifier in GAF is valid:
gorule-0000027

0 0 0 10000 0 1 0 1 37 0 1 0 120 0 0 0 28 0 0 0 2941 0 52 0 67 0 0 0 1 10000 2 497 0 0 0 0 0 0 0 12 0 0 0 0 0 0 248 0 10000 126 0 1 0 0 0 0 7 0 60

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 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

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

130 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 10000 641 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10000 0 0 0 0 0 0 0 10000 33 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Public Reference IDs (PMID, PMC, doi, or GO_REF) should be preferred over group specific Reference IDs:
gorule-0000033

10000 10000 0 50 10000 0 0 0 358 0 13 0 574 0 0 0 18 0 0 0 10000 0 828 0 9 0 1 0 2 10000 1 10000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 223 52 0 0 10000 10000 0 26 10000 10000 10000

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 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 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 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 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

155 106 47 87 162 4 7 10 766 0 41 0 897 0 109 0 568 0 75 0 1315 0 149 0 687 0 205 0 1 0 4 905 3 7 1 11 66 69 77 2219 2 67 4 14 11 89 0 0 0 0 0 0 0 2288 6 0 272 118 163

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 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 0 0 0 0 0 0 0