Rule | AgBase | ARUK-UCL | BHF-UCL | CACAO | CAFA | cgd | CollecTF | ComplexPortal | dictybase | DisProt | ecocyc | Ensembl | FlyBase | GDB | GeneDB | genedb_tbrucei | GO_Central | GOC | HGNC | HGNC-UCL | IntAct | InterPro | mgi | NTNU_SB | ParkinsonsUK-UCL | PHI-base | PINC | pombase | pseudocap | reactome | rgd | RHEA | RNAcentral | sgd | sgn | SynGO | SYSCILIA_CCNET | tair | TIGR | TreeGrafter | UniProt | wb | xenbase | zfin |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GAF lines are parsed according to GAF 2.2 specifications: gorule-0000001 |
0 | 8 | 22 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 21 | 1 | 0 | 12 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1276 | 0 | 0 | 0 | 0 | 29 | 2 | 0 | 0 | 0 | 0 | 3 |
No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515': gorule-0000002 |
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 | 2 | 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 |
7 | 0 | 10 | 0 | 6 | 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 | 92 | 0 | 0 | 0 |
IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC: gorule-0000006 |
0 | 0 | 0 | 0 | 0 | 5 | 5 | 0 | 0 | 15 | 21 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1558 | 0 | 0 | 0 | 0 | 0 | 0 | 7 | 0 |
IPI should not be used with GO:0003824 catalytic activity or descendents: gorule-0000007 |
0 | 0 | 0 | 0 | 0 | 1 | 0 | 5 | 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 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
No annotations should be made to uninformative high level terms: gorule-0000008 |
76 | 0 | 0 | 7 | 13 | 10000 | 0 | 0 | 41 | 0 | 0 | 4881 | 405 | 0 | 482 | 0 | 11799 | 314 | 0 | 0 | 0 | 124 | 16 | 0 | 0 | 0 | 85 | 0 | 0 | 15 | 0 | 0 | 0 | 0 | 4 | 0 | 0 | 198 | 16 | 0 | 856 | 27 | 0 | 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 | 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 | 42 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Dual species taxon check: gorule-0000015 |
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 | 39 | 0 | 0 | 0 |
With/From: IC annotations require a With/From GO ID: gorule-0000016 |
0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 38 | 0 | 0 | 0 | 23 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 0 | 0 | 0 | 0 | 0 | 218 | 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 | 8 | 0 | 0 | 0 | 0 | 0 | 0 |
IPI annotations require a With/From entry: gorule-0000018 |
0 | 0 | 0 | 0 | 0 | 18 | 0 | 4574 | 0 | 0 | 0 | 0 | 0 | 0 | 29 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 32 | 0 | 0 | 0 | 0 | 0 | 0 |
Automatic repair of annotations to merged or obsoleted terms: gorule-0000020 |
5 | 2 | 8 | 1 | 0 | 5694 | 0 | 16 | 5 | 0 | 4 | 242 | 69 | 0 | 2161 | 0 | 12005 | 92 | 0 | 3 | 963 | 124 | 24 | 0 | 11 | 0 | 2 | 17 | 1 | 74 | 68 | 17 | 0 | 25 | 124 | 0 | 0 | 52 | 8 | 34 | 388 | 3 | 0 | 18 |
Check for, and filter, annotations made to retracted publications: gorule-0000022 |
2 | 0 | 0 | 2 | 0 | 1 | 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 | 0 | 0 |
Each identifier in GAF is valid: gorule-0000027 |
14 | 0 | 2 | 1 | 0 | 10000 | 459 | 0 | 106 | 20 | 6 | 71114 | 7 | 16 | 2261 | 0 | 2188 | 8 | 1 | 4 | 111 | 3022 | 0 | 269 | 0 | 7 | 0 | 0 | 0 | 10000 | 2 | 340 | 0 | 0 | 0 | 0 | 4 | 6421 | 1 | 0 | 9736 | 0 | 0 | 339 |
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 | 0 | 0 | 0 |
IEAs should be less than one year old.: gorule-0000029 |
0 | 0 | 0 | 0 | 0 | 10000 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6479 | 0 | 0 | 0 | 0 | 0 | 0 | 7572 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 13621 | 0 | 0 | 9175 |
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 | 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 | 0 | 0 | 0 |
Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants: gorule-0000039 |
0 | 0 | 1 | 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 |
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 |
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 |
44 | 17 | 112 | 0 | 57 | 84 | 0 | 0 | 2 | 7 | 385 | 3617 | 59 | 0 | 19 | 0 | 446 | 0 | 3 | 46 | 0 | 805 | 104 | 0 | 12 | 0 | 0 | 0 | 0 | 0 | 854 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 2771 | 10 | 0 | 86 |
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 | 6 | 0 | 0 | 0 |
References should have only one ID per ID space: gorule-0000055 |
0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 194 | 0 | 0 | 0 | 0 | 0 | 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 |
GAF Version 2.0 and 2.1 are converted into GAF Version 2.2: gorule-0000059 |
0 | 0 | 0 | 0 | 0 | 10000 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 29941 | 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 | 0 | 0 | 0 | 0 |
Allowed gene product to term relations (gp2term): gorule-0000061 |
1 | 0 | 5 | 508 | 3 | 9545 | 0 | 0 | 393 | 10 | 0 | 2048 | 84 | 0 | 763 | 0 | 43 | 0 | 0 | 2 | 0 | 4 | 1 | 0 | 1 | 0 | 4 | 0 | 0 | 0 | 22 | 0 | 0 | 0 | 5 | 0 | 0 | 1046 | 11 | 0 | 1081 | 10 | 0 | 2826 |
Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column): gorule-0000063 |
1 | 0 | 0 | 0 | 0 | 1434 | 0 | 0 | 97 | 0 | 25 | 0 | 937 | 0 | 490 | 0 | 0 | 464 | 0 | 0 | 0 | 0 | 1200 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 94 | 0 | 0 | 5166 | 0 | 0 | 23 | 174 | 0 | 0 |
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 | 0 | 0 | 0 |
Annotations to term that are candidates for obsoletion should be produce a warning: gorule-0000065 |
116 | 0 | 0 | 145 | 106 | 3302 | 0 | 0 | 38 | 0 | 0 | 0 | 1 | 3 | 408 | 0 | 385 | 377 | 0 | 1 | 0 | 158 | 168 | 0 | 0 | 0 | 157 | 0 | 0 | 43 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 313 | 5 | 0 | 7010 | 0 | 0 | 3810 |