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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.