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Table 2 Biological-domain-inconsistent annotations in biological databases

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

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 Ensembla 09/01/09 01/01/10 711 1,891,586 760 4,395,125 13 12,309
  Geneb 12/15/09 01/01/10 1,517 2,391,443 1,647 1,133,060 34 14,762
  AspGDc 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 Genebb 12/15/09 01/01/10 53,088 3,595,041 76,597 101,160 319 2,497
  EcoCycc 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
  1. a http://www.ensembl.org/index.html
  2. b http://www.ncbi.nlm.nih.gov/gene
  3. c http://www.geneontology.org/GO.current.annotations.shtml