Biologically inspired design (BID) is a methodology for designing technological systems by analogy to designs of biological systems. Given that knowledge of many biological systems is available mostly in the form of textual documents, the question becomes how can we extract design knowledge about biological systems from textual documents for potential use in designing engineering systems? In earlier work, we described how annotating biology articles with partial Structure-Behavior-Function models helps users access documents relevant to a given design problem and understand the biological systems for potential transfer of their causal mechanisms to engineering problems. In this paper, we present an automated technique instantiated in the IBID system for extracting partial SBF models of biological systems from their natural language documents for potential use in biologically inspired design.