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Table 3 The performance of our metabolic reaction extraction method on three evaluation pathways

From: A text-mining system for extracting metabolic reactions from full-text articles

  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)
  1. 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.