Identifying research gaps and generating research questions are often a first step in developing ideas for writing a research paper or grant proposal. The concept of substance-based bibliometrics uses the counts of substances in the scientific literature to better understand, assess, and clarify the state and impact of information in the chemical sciences. Connecting substances indexed to specific bioactivity or target indicators can lead to assessing the biochemical, biological, and medicinal relevance of substances as well as developing ideas for expanding drug design and discovery through identifying and modifying the structural features of molecules. This study uses Chemical Abstracts through the SciFinder database to count for the occurrence of substances in the scientific literature. The study sets out search strategies for discovering potential research gaps and new ideas through visualization of chemical structures with known bioactivity and target indicators. The author recommends that subject librarians integrate research gap training in their bibliographic instruction classes, particularly to upper-level undergraduate and graduate chemistry students.