# The Rise of GitHub in Scholarly Publications

arXiv: https://arxiv.org/abs/2208.04895 · HTML: https://mlsanity.com/paper/2208.04895/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 9 Aug 2022.

## Built on by (most cited first, 4 of 4)

- [Interpretable Multimodal Learning for Tumor Protein-Metal Binding: Progress, Challenges, and Perspectives](https://mlsanity.com/paper/2504.03847/) (2025)
- [BARMPy: Bayesian Additive Regression Models Python Package](https://mlsanity.com/paper/2404.04738/) (2024)
- [Ontologies in Motion: A BFO-Based Approach to Knowledge Graph Construction for Motor Performance Research Data in Sports Science](https://mlsanity.com/paper/2510.15983/) (2025)
- [A Two-Dimensional Study of the Model Context Protocol: Publication and Adoption](https://mlsanity.com/paper/2609.14721/) (2026)

## Abstract (arXiv)

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.