Extracting phenotypic information from the literature via natural language processing.

In recent years, the amount of biomedical knowledge has been increasing exponentially. Several Natural Language Processing (NLP) systems have been developed to help researchers extract, encode and organize new information automatically from textual literature or narrative reports. Some of these systems focus on extracting biological entities or molecular interactions while others retrieve and encode clinical information. To exploit gene functions in the post-genome era, it is necessary to extract phenotypic information automatically from the literature as well. However, few NLP projects have focused on this. We present the development of a system called BioMedLEE that extracts a broad variety of phenotypic information from the biomedical literature. The system was developed by adapting MedLEE, an existing clinical information extraction NLP engine. A feasibility evaluation study of BioMedLEE was performed using 300 randomly chosen journal titles. Results showed that experts achieved an average precision rate of 65.4%, (95%CI: [58.0%, 72.8%]) and a recall rate of 73.0%, (95%CI: [66.2%, 80.0%]). BioMedLEE had 64.0% precision and 77.1% recall respectively, according to expert agreements.