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Table 1 Detected and corrected problems in the BioMeta database

From: Correcting ligands, metabolites, and pathways

Type of Problem # in KEGG # in BioMeta # Corrected
Structure missing 1239 1106 133
Valence violation(s) 76 0 76
Incorrect constitution unknown unknown 107
Total (constitution) 1315 1106 316
Undefined stereo double bond(s) 35 32 3
Invalid sp3 stereocenter(s) 70 47 23
Ambiguous sp3 stereocenter(s) 46 0 46
Undefined sp3 stereocenter(s) 1398 865 533
Unspecified enantiomer 2326 1840 486
Undefined sp3 stereochemistry 554 366 188
Incorrect stereochemistry unknown unknown 69
Total (stereochemistry) 3990 2907 1152
Total corrected    1468
  1. The table shows the validation and correction results of 12,815 entries present in both the KEGG Compound (version of October 25, 2005) and BioMeta databases. Note that the absence of a structure does not need to be an error – it may be a generic compound such as "acceptor" or "phosphorylated protein". Likewise, not all "unspecified enantiomer" cases need to be errors – a number of drugs may be racemic compounds. The row "total (stereochemistry)" is not the sum of the preceding cases because compounds may have multiple problems. The rows with the totals do not add up because of the "unknown" entries – if these numbers were known then the numbers would add up.