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 | xenbase_alt | zfin |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GAF lines are parsed according to GAF 2.2 specifications: gorule-0000001 |
0 | 0 | 0 | 1 | 4 | 0 | 18 | 5 | 44 | 7 | 1210 | 40 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 12 | 0 | 0 | 0 | 0 | 31 | 0 | 0 | 0 | 3 |
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 | 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 | 54 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 14 | 0 | 0 | 0 | 1 | 1 | 2 | 0 |
IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC: gorule-0000006 |
5 | 0 | 23 | 2 | 0 | 0 | 0 | 0 | 2 | 0 | 27 | 0 | 0 | 917 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 630 | 2 | 0 | 0 | 0 | 6 | 1 | 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 | 1 | 0 | 0 | 2 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
No annotations should be made to uninformative high level terms: gorule-0000008 |
10000 | 47 | 0 | 554 | 41 | 176 | 265 | 829 | 687 | 674 | 502 | 810 | 0 | 1846 | 32 | 160 | 6 | 85 | 133 | 143 | 22 | 201 | 10000 | 25 | 177 | 29 | 236 | 115 | 184 | 161 | 0 | 0 | 15 | 510 | 1 | 4 | 610 | 38 | 9 | 32 | 136 |
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 | 0 | 0 | 0 | 3 | 0 | 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 | 2 | 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 |
With/From: IC annotations require a With/From GO ID: gorule-0000016 |
0 | 0 | 38 | 0 | 4 | 3 | 16 | 0 | 0 | 0 | 220 | 1 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 0 | 0 | 2 | 0 | 6 | 0 | 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 | 8 | 0 | 0 | 0 | 0 |
IPI annotations require a With/From entry: gorule-0000018 |
18 | 0 | 502 | 0 | 0 | 2 | 27 | 1 | 12 | 0 | 1777 | 3 | 0 | 290 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 48 | 0 | 0 | 44 | 1785 | 0 | 32 | 99 | 0 | 8 | 5 |
Automatic repair of annotations to merged or obsoleted terms: gorule-0000020 |
5694 | 34 | 56 | 163 | 340 | 773 | 1048 | 73 | 83 | 67 | 608 | 81 | 0 | 245 | 41 | 53 | 34 | 93 | 163 | 171 | 47 | 211 | 10000 | 47 | 189 | 47 | 114 | 74 | 186 | 220 | 42 | 18 | 69 | 148 | 517 | 124 | 185 | 43 | 40 | 89 | 30 |
Check for, and filter, annotations made to retracted publications: gorule-0000022 |
1 | 0 | 0 | 0 | 0 | 1 | 0 | 2 | 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 |
Each identifier in GAF is valid: gorule-0000027 |
10000 | 106 | 160 | 7 | 311 | 710 | 1240 | 10000 | 10000 | 10000 | 10000 | 10000 | 0 | 10000 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2182 | 0 | 0 | 0 | 0 | 6 | 1 | 312 | 10000 | 10000 | 3 | 0 | 10000 | 0 | 1421 | 0 | 10000 |
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 | 0 |
IEAs should be less than one year old.: gorule-0000029 |
10000 | 379 | 670 | 0 | 4 | 6475 | 0 | 174 | 869 | 705 | 1284 | 701 | 70 | 2495 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 420 | 512 | 0 | 966 | 553 | 0 | 8441 | 476 | 710 | 943 | 10000 |
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 | 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 | 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 | 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 |
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 | 102 | 4 | 6 | 9 | 733 | 744 | 599 | 1030 | 720 | 0 | 2292 | 1 | 1 | 0 | 2 | 9 | 8 | 1 | 16 | 357 | 1 | 15 | 1 | 1 | 4 | 16 | 13 | 10 | 16 | 0 | 1521 | 22 | 0 | 213 | 79 | 118 | 170 | 169 |
Annotations to ISS, ISA and ISO should not be self-referential: gorule-0000050 |
0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 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 |
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 | 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 |
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 | 0 |
Allowed gene product to term relations (gp2term): gorule-0000061 |
9545 | 395 | 13 | 11 | 77 | 187 | 499 | 347 | 342 | 296 | 670 | 331 | 0 | 1203 | 0 | 1 | 0 | 1 | 1 | 1 | 0 | 1 | 27 | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 21 | 2 | 0 | 351 | 23 | 5 | 1107 | 31 | 22 | 33 | 2870 |
Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column): gorule-0000063 |
1434 | 97 | 25 | 937 | 104 | 0 | 386 | 1 | 0 | 0 | 12 | 0 | 0 | 1206 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 94 | 5624 | 174 | 0 | 0 | 9 |
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 | 0 | 10000 | 0 |
Annotations to term that are candidates for obsoletion should be produce a warning: gorule-0000065 |
3302 | 55 | 17 | 103 | 57 | 96 | 255 | 163 | 413 | 70 | 2644 | 124 | 0 | 2777 | 5 | 0 | 1 | 0 | 0 | 2 | 6 | 2 | 328 | 6 | 2 | 9 | 6 | 0 | 2 | 1 | 14 | 2 | 43 | 725 | 46 | 1 | 984 | 62 | 82 | 177 | 3965 |