Annotating the literature with disease ontology

Abstract

With the rapid growth of inquiry in biomedicine concerning diseases, the recognition of diseases becomes especially important. But only the recognition of the biomedical concepts in literature is not enough, annotations and normalizations of the concepts with normalized Metathesaurus get even more important. This paper proposes a system to annotate the literature with normalized Metathesaurus. First, a two-phase Conditional random fields (CRFs) is used to recognize the disease mentions, including the location and identification. Then, the paper adapts the Disease ontology (DO) to annotate the diseases recognized for normalization by computing the similarity between disease mentions and concepts. According to the similarities, the disease mentions are denoted as disease concepts and instances distinctively. The experiments carried out on the Arizona disease corpus show that our system makes a good achievement and outperforms the other works.