Historians of science have begun to make use of a range of digital techniques to analyse a range of phenomena in the field, including collaborations, interfield connections and influences, and patterns of publications and funding. As part of the ARC-funded Discovery Project “Organisms and Us: How Living Things Help Us To Understand Our World,” we have utilised several digital approaches to map the choice and use of particular organisms by researchers over time, to supplement data generated using more traditional, qualitative techniques such as publication and archival material analysis. This paper explores the advantages of using digital methods for these sorts of broader scope projects in the history of science, and also outlines potential gaps in what can be investigated, with particular focus on the norms of science which privilege certain types of information (e.g., the recording of scientific successes via publications, which are the main textual sources for these types of approaches). We outline our strategies for combining different types of data into historical narratives, and show possible future fruitful directions for these types of approaches in the history of biology.