Software Dependency Network for Biomedical Research Papers

A weighted graph dataset mapping upstream dependencies of software used in biomedical papers, derived from the CZ Software Mentions Dataset. It was created by Eva Maxfield Brown and last updated on 2026-05-13. The dataset analyzes centrality metrics for packages within the PyPi, CRAN, and Bioconductor ecosystems.

Use Cases

• Identify critical packages in scientific software ecosystems based on dependency network centrality.
• Analyze the hidden structure of foundational libraries underpinning published biomedical research.
• Compare the dependency networks and key packages across the PyPi, CRAN, and Bioconductor ecosystems.

Strengths

• Derived from the established CZ Software Mentions Dataset.
• Analyzes three major software ecosystems: PyPi, CRAN, and Bioconductor.
• Provides centrality metrics for dependency networks.

Limitations

• The dataset is very small at 9.5 KB, indicating limited scope.
• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.

Provenance

Source

CZ Software Mentions Dataset

Collection Method

Network mapping of upstream software dependencies from biomedical papers.

Freshness

Last updated 2026-05-13 17:51:32.