Tracing database usage: Detecting main paths in database link networks

This paper presents a database link network to measure the impact of databases on biological research. To this end, we used the 20,861 full-text articles from PubMed Central in the field of Bioinformatics. We then extracted databases from the methodology sections of these articles and their references. The list of databases was built with The 2013 Nucleic Acids Research Molecular Biology Database Collection (available online), which includes 1512 databases. The database link network was constructed from sets of pairs of databases mentioned in the methodology sections of full-text PubMed Central articles. The edges of the database link network represent the link relationships between two databases. The weight of each edge is determined either by the link frequency of the two databases (i.e., in the link-weighted database link network) or the topic similarity between two databases (i.e., in the similarity-weighted database link network). With the database link network, we analyzed the topological structure and main paths of the database link network to trace the usage, connection, and evolution of databases. We also conducted content analysis by comparing content similarities among the papers citing databases.