Ranking Interactions for a Curation Task

Abstract

One of the key pieces of information which biomedical text mining systems are expected to extract from the literature are interactions among different types of biomedical entities (proteins, genes, diseases, drugs, etc.). Different types of entities might be considered, for example protein-protein interactions have been extensively studied as part of the Bio Creative competitive evaluations. However, more complex interactions such as those among genes, drugs, and diseases are increasingly of interest. Different databases have been used as reference for the evaluation of extraction and ranking techniques. The aim of this paper is to describe a machine-learning based reranking approach for candidate interactions extracted from the literature. The results are evaluated using data derived from the Pharm GKB database. The importance of a good ranking is particularly evident when the results are applied to support human curators.