GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products

BMC Bioinformatics

Table 2 Biological-domain-inconsistent annotations in biological databases

Biological Domain	Databases	DB version mm/dd/yy	GO version mm/dd/yy	No. of gene products annotated with GO terms		No. of GO annotations applied to gene products		No. of GO terms used in gene product annotations
				Biological-domain inconsistent	Total gene product	Biological-domain inconsistent	Total GO annotation	Biological-domain inconsistent	Total GO terms
Non-prokaryotic gene product	Ensembl^a	09/01/09	01/01/10	711	1,891,586	760	4,395,125	13	12,309
	Gene^b	12/15/09	01/01/10	1,517	2,391,443	1,647	1,133,060	34	14,762
	AspGD^c	12/21/09	01/01/10	2	3,425	2	15,340	1	3,259
	dictyBase	12/27/09	01/01/10	1	7,489	1	31,064	1	2,403
	FB	10/30/09	01/01/10	1	12,509	1	68,316	1	4,924
	GeneDB_Tbrucei	07/18/07	01/01/10	2	2,977	2	10,414	1	935
	MGI	12/17/09	01/01/10	2	18,167	2	151,652	2	7,327
	PDB	12/17/09	01/01/10	26	9,170	26	31,686	3	1,024
	RGD	10/02/09	01/01/10	2	18,363	4	180,606	3	9,094
	TAIR	12/23/09	01/01/10	3	51,713	3	149,466	1	4,103
	UniProtKB/Swiss-Prot	12/17/09	01/01/10	2,680	122,261	3,803	1,035,209	17	10,589
	UniProtKB/TrEMBL	12/17/09	01/01/10	20,573	2,333,592	23,876	12,234,060	24	8,586
	WB	11/26/09	01/01/10	12	15,667	13	91,611	5	2,738
Non-eukaryotic gene product	Geneb^b	12/15/09	01/01/10	53,088	3,595,041	76,597	101,160	319	2,497
	EcoCyc^c	12/14/09	01/01/10	2	1,869	2	4,992	1	1,388
	JCVI_CMR	07/22/09	01/01/10	16	21,271	16	54,398	3	2,350
	PDB	12/17/09	01/01/10	83	16,580	85	66,027	12	1,689
	TIGR_CMR	11/14/07	01/01/10	70	40,653	70	101,965	4	2,441
	UniProt	12/17/09	01/01/10	48	248	67	7,870	3	44
	UniProtKB/Swiss-Prot	12/17/09	01/01/10	4,454	324,523	5,297	2,581,774	30	3,306
	UniProtKB/TrEMBL	12/17/09	01/01/10	77,047	4,459,834	83,965	20,009,318	49	4,048

ISSN: 1471-2105