At the time of publishing SmartGraph, in January 2020, we identified the need for a standalone SmartGraph API that provides programmatic access to most of the functionalities that are accessible via the frontend (see: "Conclusions" in Zahoranszky-Kohalmi et al. ). Little did we know how soon this need would be magnified by the onset of the COVID-19 pandemic, only weeks after the publication of SmartGraph. The pandemic shed light on the pivotal role of rapid data integration and computation-driven hypothesis generation, which were identified as bottlenecks in the translational process . Indeed, our recent work on a semi-automated workflow that addresses biomedical data integration for COVID-19 research demonstrated the drawbacks of lacking an API. Namely, this hiatus of the SmartGraph platform required us to execute certain steps in the workflow manually. This approach is not scalable and is quite error-prone. Therefore, we decided to develop an Application Programming Interface (API) for SmartGraph which provides access to most functions available for the investigators via the GUI. We demonstrate how this improvement enables the execution of the same workflow in a completely automated manner. Furthermore, we hope that this effort further emphasizes the need for the development of APIs, workflows, and standards as best practices, which will be critical for a rapid response to emerging pathogens.