The 2018 Galaxy update paper cites 42 references, of which 27—approximately 64 percent—include at least one author who is also a co-author of the update itself. This unusually high level of author overlap raises important questions about citation balance, transparency, and bibliometric consequences within large consortium-driven research projects. While the Galaxy platform is a major resource for the bioinformatics community, the concentration of citations within the same author group invites a closer look at how these references were selected and how readers should interpret the resulting citation network.

Same pattern is also observed in all papers of the same: https://scholar.google.com/citations?user=3tSiRGoAAAAJ&hl=en

A central concern is citation balance. When the majority of references originate from the same collaborative group, there is a risk that the broader scientific landscape is underrepresented. Although the Galaxy ecosystem is extensive and interconnected, a citation list dominated by internally produced work may not fully acknowledge alternative tools, independent contributions, or parallel developments across the field. Ensuring that references reflect a diverse set of perspectives and sources is essential for accurately situating a project within the wider research environment.

Related to this is the possibility of citation stacking, in which concentrated self-citation—intentional or not—magnifies the apparent scientific influence of a particular team. In large collaborative projects, self-citation is expected to some degree, especially when updates build directly upon earlier work from the same consortium. However, a self-citation rate approaching two-thirds is high enough to warrant clarification. It remains unclear whether this level was a natural outcome of the project’s tightly integrated structure or whether more balanced referencing could have been achieved.

Transparency is another important factor. Most readers will not automatically detect author overlap within a reference list without checking each citation manually. Making this overlap explicit would help readers assess the independence of the referenced work and understand the relationship between cited contributions and the core Galaxy team. Similarly, clearer guidance on internal citation policies—if such policies exist—would support more informed interpretation by reviewers and the broader community.

The issue also intersects with discussions of bibliometric impact. High rates of internal citation can elevate citation counts for both individuals and the consortium as a whole, influencing metrics that are widely used to assess scientific impact. This raises a deeper methodological question: how should self-citation be defined in the context of large, multi-institutional teams? Is citing work produced by related subprojects within the same ecosystem equivalent to traditional self-citation, or should it be understood differently? Clarification from the authors would help readers interpret the bibliometric implications more accurately.

Several questions naturally follow. Was the high self-citation rate unavoidable given the integrated nature of the Galaxy ecosystem? Were external references considered but deemed less relevant? Does the Galaxy consortium follow any internal guidelines regarding citation practices, especially for platform-update papers? And for tools such as ToolShed, deepTools, RNA Workbench, and CloudBridge—each involving overlapping authors—should they be considered independent contributions or coordinated extensions of the same project?

Kind note: This commentary is not intended to diminish the technical achievements of the Galaxy team. Rather, given the substantial author overlap, increased transparency about citation strategy would help readers, reviewers, and the community better understand the independence of the cited work and the rationale behind the observed citation pattern.