The code accompanying our new dataset of software mentions in biomedical papers (dataset, preprint). Plain-text software mentions are extracted with a trained SciBERT model from several sources: the NIH PubMed Central collection and from papers provided by various publishers to the Chan Zuckerberg Initiative. The dataset provides sources, context and metadata, and, for a number of mentions, the disambiguated software entities and links.

{"references": ["Istrate et al (2022), A large dataset of software mentions in the biomedical literature, \tarXiv:2209.00693"]}