Table 5

Performance comparison of gene/protein extraction tools with our metabolic reaction extraction method

Range of scores on

different corpora (%)

Method Interaction type Precision Recall
RelEx Protein-protein 39-80 45-72
Baseline(k) Protein-protein 23-54 52-67
AkanePPI
 (trained on BioInfer) Protein-protein 29-77 40-56
Method described
 in this paper Substrate-product 40-88 20-82
Method described
 in this paper Substrate-enzyme 62-80 37-64
Method described
 in this paper Product-enzyme 58-67 36-70

The range of scores for the gene/protein extraction tools are for five corpora as evaluated in [20]. The scores for our metabolic reaction extraction method summarize those in Table 4, i.e. they are broken down into the same three binary interactions and the range is for the three evaluation corpora and the Reactome dataset.

Czarnecki et al.

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

Open Data