Table 3

The performance of our metabolic reaction extraction method on three evaluation pathways
Correct reactions Correct
(ignoring enzyme) (including enzyme)
  Pantothenate and coenzyme A biosynthesis pathway
Recall(P) (%) 78 (7/9) 56 (5/9)
Precision (%) 59 (24/41) 41 (17/41)
  Tetrahydrofolate biosynthesis pathway
Recall(P) (%) 90 (9/10) 70 (7/10)
Precision (%) 60 (39/65) 38 (25/65)
  Aerobic fatty acid β-oxidation I pathway
Recall(P) (%) 29 (2/7) 29 (2/7)
Precision (%) 30 (11/37) 14 (5/37)

Taking the “correct reactions (ignoring enzymes)” column for the pantothenate and coenzyme A biosynthesis pathway as an example, the numbers in brackets indicate that our algorithm correctly identified 7 out of the 9 reactions in the curated EcoCyc pathway (recall row), giving 78%; and of the 41 identified interactions (precision row), 24 were valid reactions (irrespective of whether they belong to the pathway or not), giving 68%. A reaction for which the susbtrate(s) and product(s) have been correctly assigned, but not the enzyme, is deemed correct in column two, but incorrect in column three.

Czarnecki et al.

Czarnecki et al. BMC Bioinformatics 2012 13:172   doi:10.1186/1471-2105-13-172

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