Rule | cgd | dictybase | ecocyc | fb | genedb_lmajor | genedb_pfalciparum | genedb_tbrucei | goa_chicken | goa_cow | goa_dog | goa_human | goa_pig | japonicusdb | mgi | paint_cgd | paint_dictybase | paint_ecocyc | paint_fb | paint_goa_chicken | paint_goa_human | paint_japonicusdb | paint_mgi | paint_other | paint_pombase | paint_rgd | paint_sgd | paint_tair | paint_wb | paint_xenbase | paint_zfin | pombase | pseudocap | reactome | rgd | sgd | sgn | tair | wb | xenbase | zfin |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GAF lines are parsed according to GAF 2.2 specifications: gorule-0000001 |
0 | 1 | 0 | 13 | 4 | 0 | 18 | 18 | 39 | 34 | 58 | 114 | 0 | 78 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 99 | 6 | 0 | 102 | 24 | 0 | 0 | 6 | 0 | 0 |
No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515': gorule-0000002 |
0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 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 |
IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations are not allowed for direct annotations to to 'protein binding ; GO:0005515 or GO:0005488 binding'': gorule-0000005 |
0 | 0 | 0 | 1 | 0 | 0 | 0 | 2 | 22 | 2 | 14 | 3 | 0 | 27 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 14 | 0 | 0 | 0 | 1 | 4 | 4 |
IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC: gorule-0000006 |
6 | 0 | 24 | 2 | 0 | 0 | 0 | 0 | 2 | 0 | 29 | 0 | 0 | 463 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 631 | 2 | 0 | 0 | 0 | 4 | 0 |
IPI should not be used with GO:0003824 catalytic activity or descendents: gorule-0000007 |
1 | 0 | 0 | 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 | 2 | 1 | 1 | 0 | 0 | 0 | 0 |
No annotations should be made to uninformative high level terms: gorule-0000008 |
10000 | 13 | 0 | 39 | 41 | 176 | 265 | 88 | 119 | 69 | 436 | 86 | 0 | 223 | 32 | 160 | 6 | 85 | 133 | 143 | 22 | 201 | 10000 | 25 | 177 | 29 | 236 | 115 | 184 | 161 | 6 | 0 | 15 | 131 | 9 | 4 | 20 | 43 | 115 | 64 |
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 | 1 | 0 | 9 | 9 | 12 | 6 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 |
Dual species taxon check: gorule-0000015 |
0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 37 | 1 | 0 | 30 | 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 |
With/From: IC annotations require a With/From GO ID: gorule-0000016 |
0 | 0 | 38 | 2 | 3 | 3 | 15 | 0 | 0 | 0 | 218 | 1 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 6 | 0 | 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 | 0 | 0 | 0 | 0 | 0 |
IPI annotations require a With/From entry: gorule-0000018 |
18 | 0 | 502 | 26 | 0 | 2 | 27 | 1 | 12 | 0 | 1777 | 3 | 0 | 155 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 42 | 1785 | 0 | 26 | 99 | 8 | 5 |
Automatic repair of annotations to merged or obsoleted terms: gorule-0000020 |
3644 | 84 | 43 | 185 | 349 | 780 | 1060 | 204 | 278 | 271 | 839 | 275 | 2 | 420 | 74 | 78 | 36 | 114 | 208 | 218 | 63 | 257 | 10000 | 66 | 236 | 76 | 153 | 161 | 253 | 293 | 9 | 2 | 3 | 347 | 572 | 124 | 208 | 201 | 560 | 280 |
Check for, and filter, annotations made to retracted publications: gorule-0000022 |
1 | 0 | 0 | 0 | 0 | 1 | 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 | 0 | 0 | 0 | 0 | 0 |
Each identifier in GAF is valid: gorule-0000027 |
10000 | 106 | 160 | 753 | 310 | 710 | 1239 | 10000 | 10000 | 10000 | 10000 | 10000 | 0 | 10000 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2182 | 0 | 0 | 0 | 0 | 6 | 5 | 312 | 10000 | 10000 | 5 | 0 | 327 | 0 | 1714 | 98 |
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 | 0 | 0 | 0 | 0 | 0 | 0 | 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 |
10000 | 379 | 668 | 477 | 4 | 6472 | 0 | 179 | 868 | 705 | 1284 | 700 | 71 | 1262 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 53 | 511 | 0 | 967 | 553 | 0 | 1876 | 476 | 1657 | 794 |
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 | 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 | 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 | 1 | 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 |
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 |
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 |
84 | 17 | 439 | 108 | 4 | 6 | 9 | 677 | 741 | 599 | 1031 | 720 | 0 | 2047 | 1 | 1 | 0 | 2 | 9 | 8 | 1 | 16 | 357 | 1 | 15 | 1 | 1 | 4 | 16 | 13 | 0 | 16 | 0 | 1559 | 22 | 0 | 307 | 79 | 140 | 167 |
Annotations to ISS, ISA and ISO should not be self-referential: gorule-0000050 |
0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 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 |
References should have only one ID per ID space: gorule-0000055 |
0 | 0 | 0 | 0 | 65 | 76 | 53 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 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 |
GAF Version 2.0 and 2.1 are converted into GAF Version 2.2: gorule-0000059 |
10000 | 0 | 0 | 0 | 9941 | 10000 | 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 | 1458 | 0 | 0 | 0 | 0 |
Allowed gene product to term relations (gp2term): gorule-0000061 |
6914 | 395 | 13 | 95 | 77 | 187 | 499 | 316 | 340 | 294 | 687 | 329 | 0 | 908 | 0 | 1 | 0 | 1 | 1 | 1 | 0 | 1 | 27 | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 2 | 0 | 350 | 84 | 5 | 32 | 33 | 65 | 46 |
Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column): gorule-0000063 |
1433 | 96 | 25 | 854 | 103 | 0 | 385 | 1 | 0 | 0 | 12 | 0 | 0 | 789 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 94 | 3341 | 174 | 0 | 80 |
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 | 0 | 0 | 0 | 10000 | 0 |
Annotations to term that are candidates for obsoletion should be produce a warning: gorule-0000065 |
3302 | 54 | 11 | 96 | 56 | 95 | 255 | 157 | 392 | 69 | 2489 | 119 | 0 | 1338 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 2 | 175 | 0 | 2 | 0 | 3 | 0 | 2 | 1 | 0 | 2 | 47 | 707 | 40 | 1 | 126 | 57 | 248 | 156 |