Table 2

The tagging performance of BANNER and OSCAR3
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

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.

Czarnecki et al.

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

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