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The Rise of GitHub in Scholarly Publications

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Linking Theory and Practice of Digital Libraries (TPDL 2022)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 13541))

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Abstract

The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs). Similarly, the Software Heritage Foundation is working to archive public source code, but there is value in archiving the issue threads, pull requests, and wikis that provide important context to the code while maintaining their original URLs. In current implementations, source code and its ephemera are not preserved, which presents a problem for scholarly projects where reproducibility matters. To understand and quantify the scope of this issue, we analyzed the use of GHP URIs in the arXiv and PMC corpora from January 2007 to December 2021. In total, there were 253,590 URIs to GitHub, SourceForge, Bitbucket, and GitLab repositories across the 2.66 million publications in the corpora. We found that GitHub, GitLab, SourceForge, and Bitbucket were collectively linked to 160 times in 2007 and 76,746 times in 2021. In 2021, one out of five publications in the arXiv corpus included a URI to GitHub. The complexity of GHPs like GitHub is not amenable to conventional Web archiving techniques. Therefore, the growing use of GHPs in scholarly publications points to an urgent and growing need for dedicated efforts to archive their holdings in order to preserve research code and its scholarly ephemera.

Supported by the Alfred P. Sloan Foundation.

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Notes

  1. 1.

    https://github.com.

  2. 2.

    https://zenodo.org.

  3. 3.

    https://softwareheritage.org/.

  4. 4.

    https://www.ncbi.nlm.nih.gov/pmc/pub/addjournal/.

  5. 5.

    https://arxiv.org/help/arxiv_identifier.

  6. 6.

    https://pypi.org/project/PyPDF2/.

  7. 7.

    https://pypi.org/project/pypdfium2/.

  8. 8.

    https://refhub.elsevier.com.

  9. 9.

    http://tracer.mementoweb.org.

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Authors and Affiliations

  1. Old Dominion University, Norfolk, VA, USA

    Emily Escamilla, Michele C. Weigle & Michael L. Nelson

  2. Los Alamos National Laboratory, Los Alamos, NM, USA

    Martin Klein

  3. New York University, New York, NY, USA

    Talya Cooper & Vicky Rampin

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  1. Emily Escamilla
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  2. Martin Klein
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  4. Vicky Rampin
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  5. Michele C. Weigle
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  6. Michael L. Nelson
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Corresponding author

Correspondence to Emily Escamilla .

Editor information

Editors and Affiliations

  1. University of Padua, Padua, Italy

    Gianmaria Silvello

  2. Universidad Politécnica de Madrid, Madrid, Spain

    Oscar Corcho

  3. CNR-ISTI – National Research Council, Pisa, Italy

    Paolo Manghi

  4. University of Padua, Padua, Italy

    Giorgio Maria Di Nunzio

  5. Linnaeus University, Växjö, Sweden

    Koraljka Golub

  6. University of Padua, Padua, Italy

    Nicola Ferro

  7. Sapienza University of Rome, Rome, Italy

    Antonella Poggi

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Escamilla, E., Klein, M., Cooper, T., Rampin, V., Weigle, M.C., Nelson, M.L. (2022). The Rise of GitHub in Scholarly Publications. In: Silvello, G., et al. Linking Theory and Practice of Digital Libraries. TPDL 2022. Lecture Notes in Computer Science, vol 13541. Springer, Cham. https://doi.org/10.1007/978-3-031-16802-4_15

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  • DOI: https://doi.org/10.1007/978-3-031-16802-4_15

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