Researchers at the Chan Zuckerberg Initiative, a U.S.-based philanthropic organization, have created a dataset tracking mentions of open-source software in biomedical research papers. In curating the dataset, the team used an AI system to locate mentions of software in 3.9 million open access biomedical research papers and 16.9 million papers given to the team. In the first subset, the system found over 19 million total mentions and 1.6 million unique mentions of software in 2.5 million papers. The team then provided a repository link for 185,000 of the unique software mentions. In the second subset, the system found 48 million total mentions and 934,704 unique mentions of software in 2.9 million papers. Researchers can use the dataset to identify successful uses of open-source software in the biomedical field and advance science and technology research.