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_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 | 24 | 0 | 1 | 4 | 0 | 18 | 5 | 41 | 7 | 1207 | 40 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1739 | 0 | 6 | 1316 | 0 | 29 | 0 | 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 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae 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 | 1 | 14 | 2 | 0 | 27 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 4 | 0 |
IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC: gorule-0000006 |
1 | 0 | 23 | 2 | 0 | 0 | 0 | 0 | 2 | 0 | 26 | 0 | 0 | 448 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 4 | 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 | 3 | 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 | 0 | 0 | 0 |
No annotations should be made to uninformative high level terms: gorule-0000008 |
10000 | 3 | 0 | 6 | 40 | 146 | 228 | 39 | 42 | 5 | 392 | 10 | 4 | 420 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 38 | 16 | 0 | 55 | 4 | 292 | 320 | 24 | 21 |
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 | 3 | 3 | 4 | 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 |
Dual species taxon check: gorule-0000015 |
0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 38 | 1 | 0 | 35 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 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 | 197 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 6 | 1 | 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 | 5 | 0 | 7 | 0 | 0 | 0 |
IPI annotations require a With/From entry: gorule-0000018 |
3 | 0 | 449 | 0 | 0 | 2 | 27 | 1 | 12 | 0 | 1719 | 2 | 0 | 130 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 118 | 0 | 20 | 0 | 8 | 5 |
Automatic repair of annotations to merged or obsoleted terms: gorule-0000020 |
7367 | 0 | 128 | 75 | 330 | 745 | 1032 | 230 | 285 | 185 | 1226 | 231 | 0 | 1380 | 15 | 28 | 9 | 23 | 47 | 66 | 53 | 4788 | 18 | 54 | 15 | 51 | 26 | 39 | 56 | 1 | 269 | 30 | 472 | 238 | 124 | 137 | 288 | 2 | 53 |
Check for, and filter, annotations made to retracted publications: gorule-0000022 |
1 | 0 | 0 | 0 | 0 | 1 | 0 | 2 | 0 | 0 | 27 | 0 | 0 | 22 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 67 | 0 | 0 | 23 | 0 | 0 | 0 |
Each identifier in GAF is valid: gorule-0000027 |
10000 | 10000 | 973 | 447 | 311 | 710 | 1241 | 10000 | 10000 | 10000 | 10000 | 10000 | 303 | 10000 | 7979 | 10000 | 826 | 10000 | 10000 | 10000 | 10000 | 10000 | 7753 | 10000 | 8536 | 10000 | 10000 | 10000 | 10000 | 3123 | 75 | 10000 | 10000 | 8447 | 0 | 10000 | 10000 | 1425 | 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 | 1 | 0 | 3 | 1 | 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 | 1 |
IEAs should be less than one year old.: gorule-0000029 |
0 | 0 | 0 | 0 | 4 | 6475 | 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 | 0 | 0 | 0 | 0 | 0 | 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 |
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 |
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 | 1 | 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 |
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 | 404 | 102 | 4 | 6 | 9 | 691 | 720 | 584 | 875 | 679 | 0 | 1728 | 1 | 1 | 0 | 2 | 9 | 5 | 16 | 356 | 1 | 15 | 1 | 1 | 4 | 16 | 13 | 0 | 0 | 0 | 1474 | 6 | 0 | 218 | 69 | 140 | 160 |
Annotations to ISS, ISA and ISO should not be self-referential: gorule-0000050 |
0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 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 |
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 | 109 | 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 |
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 | 3726 | 0 | 0 | 0 | 1458 | 0 | 0 | 0 | 0 |
Allowed gene product to term relations (gp2term): gorule-0000061 |
9560 | 4600 | 607 | 1 | 77 | 187 | 499 | 30 | 98 | 7 | 3942 | 19 | 0 | 4878 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 2362 | 0 | 5 | 1105 | 253 | 76 | 2741 |
Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column): gorule-0000063 |
1441 | 97 | 26 | 943 | 104 | 0 | 386 | 1 | 0 | 0 | 12 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 971 | 0 | 12 | 495 | 94 | 5630 | 192 | 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 | 10000 | 0 |