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Softcite dataset: A dataset of software mentions in biomedical and economic research publications

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  • Caifan Du
  • Johanna Cohoon
  • Patrice Lopez
  • James Howison

Abstract

Software contributions to academic research are relatively invisible, especially to the formalized scholarly reputation system based on bibliometrics. In this article, we introduce a gold‐standard dataset of software mentions from the manual annotation of 4,971 academic PDFs in biomedicine and economics. The dataset is intended to be used for automatic extraction of software mentions from PDF format research publications by supervised learning at scale. We provide a description of the dataset and an extended discussion of its creation process, including improved text conversion of academic PDFs. Finally, we reflect on our challenges and lessons learned during the dataset creation, in hope of encouraging more discussion about creating datasets for machine learning use.

Suggested Citation

  • Caifan Du & Johanna Cohoon & Patrice Lopez & James Howison, 2021. "Softcite dataset: A dataset of software mentions in biomedical and economic research publications," Journal of the Association for Information Science & Technology, Association for Information Science & Technology, vol. 72(7), pages 870-884, July.
    • Handle: RePEc:bla:jinfst:v:72:y:2021:i:7:p:870-884
    DOI: 10.1002/asi.24454
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    References listed on IDEAS

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    Cited by:

    1. Enrique Orduña-Malea & Rodrigo Costas, 2021. "Link-based approach to study scientific software usage: the case of VOSviewer," Scientometrics, Springer;Akadémiai Kiadó, vol. 126(9), pages 8153-8186, September.
    2. Yuzhuo Wang & Chengzhi Zhang & Kai Li, 2022. "A review on method entities in the academic literature: extraction, evaluation, and application," Scientometrics, Springer;Akadémiai Kiadó, vol. 127(5), pages 2479-2520, May.
    3. Yuzhuo Wang & Kai Li, 2024. "How do official software citation formats evolve over time? A longitudinal analysis of R programming language packages," Scientometrics, Springer;Akadémiai Kiadó, vol. 129(7), pages 3997-4019, July.

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