GO Rule Violations by Assignment

Generated on 2025-05-25
Rule AgBase ARUK-UCL BHF-UCL CACAO CAFA cgd COLLECTF ComplexPortal dictybase DisProt ecocyc EcoliWiki Ensembl FLYBASE GDB GeneDB genedb_tbrucei GO_Central GOC HGNC HGNC-UCL IntAct InterPro mgi NTNU_SB ParkinsonsUK-UCL PINC pombase pseudocap reactome rgd RHEA RNAcentral sgd sgn SynGO SYSCILIA_CCNET tair TIGR TreeGrafter UniProt UniProtKB wb xenbase zfin

GAF lines are parsed according to GAF 2.2 specifications:
gorule-0000001

0 8 22 0 0 0 0 1305 24 0 204 0 0 1 0 21 1 44 14 0 0 4 47 0 0 0 0 76 1739 0 2 0 1264 8 0 0 0 29 2 0 0 42 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 1 0 0 0 0 0 0 0 0 0 2 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

5 0 8 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 0 0 0 0 0 0 0 0 0 0 0 60 0 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 2 0 0 12 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 467 0 0 0 0 0 0 0 4 0

IPI should not be used with GO:0003824 catalytic activity or descendents:
gorule-0000007

0 0 0 0 0 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 0 0 1 0 0 0 0 0 0 0 0 0 0

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

71 0 0 6 12 10000 0 8 5 0 51 8 3688 404 0 482 0 12102 314 0 0 0 293 14 0 0 84 4 57 15 0 0 0 74 4 0 0 198 16 0 720 31 167 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 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 36 0 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 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 37 0 0 0 0

With/From: IC annotations require a With/From GO ID:
gorule-0000016

0 0 5 0 0 0 0 0 0 0 39 0 0 0 0 23 0 0 0 0 1 0 0 0 0 0 0 4 0 0 0 0 0 0 6 0 0 0 0 0 216 0 0 0 0

IDA annotations must not have a With/From entry:
gorule-0000017

0 0 0 0 0 0 0 0 0 0 164 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 8 0 0 0 0 0 0 0

IPI annotations require a With/From entry:
gorule-0000018

0 0 0 0 0 18 0 2511 0 0 167 0 0 0 0 29 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 32 0 0 2 0 0 0 0

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

5 0 0 2 0 8171 0 81 0 0 15 14 31 61 0 2154 0 11832 149 0 0 465 132 0 0 1 0 5 296 64 15 16 0 3 124 0 0 30 0 4 143 40 66 0 0

Check for, and filter, annotations made to retracted publications:
gorule-0000022

2 0 0 2 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Each identifier in GAF is valid:
gorule-0000027

13 0 2 1 0 10000 0 0 106 50 257 0 66772 12 16 2261 0 12107 8 1 4 111 3026 5 240 0 0 3 75 10000 4388 344 0 0 0 32 4 6421 1 0 9798 9695 13 0 360

GO aspect should match the term's namespace; otherwise it is repaired to the appropriate aspect:
gorule-0000028

0 0 0 1 0 0 0 1 0 0 1 9 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 0 0 0

IEAs should be less than one year old.:
gorule-0000029

0 0 0 0 0 10000 0 0 0 0 9 0 0 0 0 6479 0 0 150 0 0 0 10541 0 0 0 0 0 14 0 0 439 0 4012 0 0 0 0 0 0 9862 6425 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 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 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 41 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

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

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

42 14 88 0 52 84 0 0 2 4 420 0 3325 59 0 19 0 1335 0 3 34 0 704 13 0 7 0 0 0 0 897 0 0 0 0 0 0 0 0 0 2128 11 5 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 5 0 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 0 194 0 0 0 0 0 0 0 0 0 0 0 0 0 0 112 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 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 0 29941 0 0 0 0 0 0 0 0 0 0 0 0 3726 0 0 0 0 0 1458 0 0 0 0 0 0 0 0 0 0

Allowed gene product to term relations (gp2term):
gorule-0000061

1 0 5 352 1 9597 0 2 2679 6 81 0 1848 84 0 763 0 1450 0 0 2 0 4 1 0 1 4 0 14 0 1558 0 0 0 5 0 0 1046 11 0 944 0 28 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 1441 0 0 96 0 207 0 0 937 0 490 0 0 464 0 0 0 0 0 0 0 0 1 971 0 10 0 0 494 94 0 0 5166 0 0 20 0 192 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 0

Annotations to term that are candidates for obsoletion should be produce a warning:
gorule-0000065

115 0 0 107 97 3302 0 27 38 0 150 0 0 1 3 408 0 2678 378 0 1 0 765 167 0 0 157 0 41 43 4343 0 0 246 1 0 0 313 5 0 6285 6 17 0 3810