Hierarchical sequence labeling for extracting BEL statements from biomedical literature

Abstract Background Extracting relations between bio-entities from biomedical literature is often a challenging task and also an essential step towards biomedical knowledge expansion. The BioCreative community has organized a shared task to evaluate the robustness of the causal relationship extraction algorithms in Biological Expression Language (BEL) from biomedical literature. Method We first map the sentence-level BEL statements in the BC-V training corpus to the corresponding text segments, thus generating hierarchically tagged training instances. A hierarchical sequence labeling model was afterwards induced from these training instances and applied to the test sentences in order to construct the BEL statements. Results The experimental results on extracting BEL statements from BioCreative V Track 4 test corpus show that our method achieves promising performance with an overall F-measure of 31.6%. Furthermore, it has the potential to be enhanced by adopting more advanced machine learning approaches. Conclusion We propose a framework for hierarchical relation extraction using hierarchical sequence labeling on the instance-level training corpus derived from the original sentence-level corpus via word alignment. Its main advantage is that we can make full use of the original training corpus to induce the sequence labelers and then apply them to the test corpus