Ontology-based Extraction of Structured Information from Publications on Preclinical Experiments for Spinal Cord Injury Treatments

Abstract

Preclinical research in the field of central nervous system trauma advances at a fast pace, currently yielding over 8,000 new publications per year, at an exponentially growing rate. This amount of published information by far exceeds the capacity of individual scientists to read and understand the relevant literature. So far, no clinical trial has led to therapeutic approaches which achieve functional recovery in human patients. In this paper, we describe a first prototype of an ontology-based information extraction system that automatically extracts relevant preclinical knowledge about spinal cord injury treatments from natural language text by recognizing participating entity classes and linking them to each other. The evaluation on an independent test corpus of manually annotated full text articles shows a macro-average F1 measure of 0.74 with precision 0.68 and recall 0.81 on the task of identifying entities participating in relations.