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Table 2 The tagging performance of BANNER and OSCAR3

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

 

Protein names tagged

Small molecule names

 

by BANNER

tagged by OSCAR3

  Pantothenate and coenzyme A biosynthesis pathway

Recall(C) (%)

81 (112/139)

96 (329/343)

Precision (%)

85 (112/132)

86 (329/384)

F-score (%)

83

91

  Tetrahydrofolate biosynthesis pathway

Recall(C) (%)

93 (250/268)

82 (528/647)

Precision (%)

76 (250/327)

95 (528/558)

F-score (%)

84

88

  Aerobic fatty acid β-oxidation I pathway

Recall(C) (%)

91 (341/376)

81 (456/565)

Precision (%)

82 (341/414)

92 (456/494)

F-score (%)

86

86

  1. The tagging performance of the NER tools when applied to the Abstracts and Introductions from papers referenced in EcoCyc with respect to our three evaluation pathways. Taking the BANNER column for the pantothenate and coenzyme A biosynthesis pathway as an example, the numbers in brackets indicate that BANNER correctly identified 112 out of the 139 protein names (recall row); and of the 132 names it tagged, 112 were correct (precision row). The OSCAR3 results are with a confidence threshold of zero.