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Table 4 The performance (precision, recall and F-score) of six GPI extraction methods when applied to five GPI corpora using gold-standard named entities.

From: A realistic assessment of methods for extracting gene/protein interactions from free text

  A B H I L
Precision:      
AkanePPI(A) (57.0) 29.2 61.5 60.2 69.6
AkanePPI(B) 29.1 (56.8) 52.0 66.2 76.7
RelEx 40 39 76 74 82
Baseline(K) 22.8 24 54 44.8 (53.9)
Baseline(C) 17 13 38 41 50
OpenDMAP 61 62.3 77.3 87.5 100
Recall:      
AkanePPI(A) (74.0) 31.8 44.2 32.5 23.8
AkanePPI(B) 52.9 (85.4) 55.8 51.3 40.2
RelEx 50 45 64 61 72
Baseline(K) 51.5 52.2 66.9 56.4 (72)
Baseline(C) 95 99 100 100 100
OpenDMAP 9.1 5.9 10.4 2.1 2.4
F-score:      
AkanePPI(A) (64.4) 30.5 51.4 42.2 35.4
AkanePPI(B) 37.5 (68.2) 53.8 57.8 52.8
RelEx 44 41 69 67 77
Baseline(K) 31.6 32.9 59.7 49.9 (61.6)
Baseline(C) 29 23 55 58 66
OpenDMAP 15.9 10.8 18.4 4.1 4.8
  1. The figures for RelEx and Baseline(C) are taken from Pyysalo et al. (2008). (Note that we use a simplified version of BioInfer compared to the one used in that paper, so the figures for this corpus are not completely comparable.) Figures are given in brackets where a corpus was used to develop a given method. Corpus abbreviations are as follows: A = AIMed; B = BioInfer; H = HPRD50; I = IEPA; L = LLL.