Reports

Rule	AgBase	Alzheimers_University_of_Toronto	ARUK-UCL	BHF-UCL	CACAO	CAFA	cgd	CollecTF	ComplexPortal	DFLAT	DIBU	dictybase	DisProt	ecocyc	EcoliWiki	Ensembl	FlyBase	GDB	GeneDB	genedb_tbrucei	GO_Central	GOC	GOC-OWL	HGNC	HGNC-UCL	IntAct	InterPro	mgi	ParkinsonsUK-UCL	PHI-base	PINC	pombase	pseudocap	reactome	rgd	RHEA	RNAcentral	Roslin_Institute	sgd	sgn	SynGO	SynGO-UCL	SYSCILIA_CCNET	tair	TIGR	TreeGrafter	UniProt	wb	zfin
GAF lines are parsed according to GAF 2.2 specifications: gorule-0000001	0	0	0	0	0	0	0	0	1289	0	0	1	0	0	0	0	2087	0	21	1	57	0	0	0	0	0	0	0	0	0	0	0	1739	0	6	0	0	0	0	0	0	0	0	5	0	0	9096	0	1
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	1	0	0	0	0	0	0	0	0	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	6	0	0	6	0	1	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	0	0	0	0	0	0	0	0	0	0	39	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	0	0	2	0	0	0	0	10	20	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	20	0	0	0	0	0	0	0	0
IPI should not be used with GO:0003824 catalytic activity or descendents: gorule-0000007	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	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	206	2	432	1225	98	132	10000	0	72	3	5	74	5	4	0	313	625	2	927	0	26098	1643	0	10	65	0	925	3183	230	0	157	8	82	133	0	0	0	1	417	5	4	1	0	485	14	21	10872	424	1933
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	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	0	0	0
Taxon-appropriate annotation check: gorule-0000013	4	0	0	0	4	0	111	0	9	0	0	0	1	7	0	118	142	0	3	0	6705	18	0	0	0	0	47	6	0	0	1	4	2	1054	2	5	0	0	12	0	3	0	0	16	0	161	124	71	21
Dual species taxon check: gorule-0000015	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	39	0	0
With/From: IC annotations require a With/From GO ID: gorule-0000016	0	0	0	5	0	0	0	0	0	0	0	0	0	37	0	0	6	0	23	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	6	1	0	0	0	1	0	180	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	5	0	0	0	0	5	0	0	0	0	0
IPI annotations require a With/From entry: gorule-0000018	0	0	0	0	0	0	0	0	2417	0	0	0	0	0	0	0	0	0	29	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	25	0	0	1	0	0
Automatic repair of annotations to merged or obsoleted terms: gorule-0000020	2	0	54	28	1	4	7223	0	190	0	0	1	0	3	2	88	97	0	1940	0	10084	211	0	0	0	425	128	128	10	0	0	23	237	212	11	27	0	0	3	115	0	0	0	147	28	23	494	245	52
Each identifier in GAF is valid: gorule-0000027	0	0	0	0	0	0	0	154	0	0	0	0	0	0	0	0	0	60	0	0	0	0	30	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	162	0	0	10000	0	0	0
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	0	0	0	0	0
IEAs should be less than one year old.: gorule-0000029	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6484	0	0	121	0	0	0	0	0	0	0	0	0	0	14	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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	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	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	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	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	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	0	0	0	0
Check for valid combination of evidence code and GO_REF: gorule-0000043	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	0	14	85	0	53	84	0	0	0	0	2	1	364	0	2028	61	0	19	0	485	0	0	3	26	0	855	935	7	0	0	0	0	0	881	0	0	0	1	0	0	0	0	0	0	111	1732	5	82
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	0	0	0	0	0	0	3	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	0	0	0	194	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	108	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	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	0	10000	0	0	0	0	0	0	0	0	0	0	0	29941	0	0	0	0	0	0	0	0	0	0	0	0	0	3726	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	2	16	8	358	2	9235	0	4781	0	0	4607	3	78	0	0	95	0	644	0	10	0	0	0	3	0	0	1860	0	0	0	0	6	4770	3135	0	0	0	0	5	0	0	0	1097	11	0	949	29	2971
Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column): gorule-0000063	1	0	0	0	0	0	1443	0	0	0	0	97	0	28	0	0	999	0	490	0	0	512	0	0	0	0	0	0	0	0	0	0	972	0	10	0	0	0	495	94	0	0	0	5173	0	0	17	198	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	0	0	0	0	0	0	37055	0	0	0
Other	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

GO Rule Violations by Assignment