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

BMC Bioinformatics

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.

ISSN: 1471-2105