The integration of bibliographical information of scholarly publications available on the Internet is an important task in academic research. Accurate reference metadata extraction for scholarly publications is essential for the integration of information from heterogeneous reference sources. We propose a knowledge-based approach to literature mining and focus on reference metadata extraction methods for scholarly publications. We adopt an ontological knowledge representation framework called INFOMAP to automatically extract the reference metadata. The experimental results show that, by using INFOMAP, we can extract author, title, journal, volume, number (issue), year, and page information from different reference styles with a high degree of accuracy. The overall average field accuracy of citation extraction for a Bioinformatics dataset is 97.87% for six reference styles.