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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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    1. Park, Hyoungjoo & Wolfram, Dietmar, 2019. "Research software citation in the Data Citation Index: Current practices and implications for research software sharing and reuse," Journal of Informetrics, Elsevier, vol. 13(2), pages 574-582.
    2. James Howison & Julia Bullard, 2016. "Software in the scientific literature: Problems with seeing, finding, and using software mentioned in the biology literature," Journal of the Association for Information Science & Technology, Association for Information Science & Technology, vol. 67(9), pages 2137-2155, September.
    3. Matthew S. Mayernik & David L. Hart & Keith E. Maull & Nicholas M. Weber, 2017. "Assessing and tracing the outcomes and impact of research infrastructures," Journal of the Association for Information Science & Technology, Association for Information Science & Technology, vol. 68(6), pages 1341-1359, June.
    4. Xuelian Pan & Erjia Yan & Weina Hua, 2016. "Disciplinary differences of software use and impact in scientific literature," Scientometrics, Springer;Akadémiai Kiadó, vol. 109(3), pages 1593-1610, December.
    5. Pan, Xuelian & Yan, Erjia & Wang, Qianqian & Hua, Weina, 2015. "Assessing the impact of software on science: A bootstrapped learning of software entities in full-text papers," Journal of Informetrics, Elsevier, vol. 9(4), pages 860-871.
    6. Andrea K. Thomer & Karen M. Wickett & Karen S. Baker & Bruce W. Fouke & Carole L. Palmer, 2018. "Documenting provenance in noncomputational workflows: Research process models based on geobiology fieldwork in Yellowstone National Park," Journal of the Association for Information Science & Technology, Association for Information Science & Technology, vol. 69(10), pages 1234-1245, October.
    7. Susan Leigh Star & Karen Ruhleder, 1996. "Steps Toward an Ecology of Infrastructure: Design and Access for Large Information Spaces," Information Systems Research, INFORMS, vol. 7(1), pages 111-134, March.
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    Cited by:

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