Author summary There is a multitude of publicly available databases that contain information about biological entities (i.e., genes, proteins, and other small molecules) as well as information about how these entities interact together. However, these databases are often incomplete. There is a wealth of information present in the text of the scientific literature that is not yet available in these databases. Using tools that mine the scientific literature we are able to extract some of this potentially relevant information. In this work we show how we can use publicly available databases in conjunction with the information extracted from the scientific literature to infer the networks that are involved in specific biological processes, such as viral replication and cancer tumor growth.
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