Table 2

Comparison of the four automated bioassay neighboring methods by using the depositor-defined (human-curated) assay neighbors as a benchmark.

Neighboring method

Recall

Precision

F1 score

Number of common pairs/Number of depositor-specified pairs

Number of common pairs/Number of assay pairs by the method

Harmonic mean(recall, precision)

1. Activity based

41% [3694/8802]

0.5% [4100/671799]

0.99%

2. Target similarity based

46% [4100/8802]

0.6% [4100/66497]

1.18%

3. Biosystems based

34% [3008/8802]

0.2% [3008/160356]

0.39%

4. Text-mining based

86% [7530/8802]

15.0% [7530/50148]

25.50%

Han et al. BMC Bioinformatics 2010 11:549   doi:10.1186/1471-2105-11-549