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Updated: Jun 4, 2025

Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal
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pyBioPortal: a Python package for simplifying cBioPortal data access in cancer research.

Matteo Valerio1, Alessandro Inno1, Stefania Gori1

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|December 30, 2024
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Summary

A new Python package, pyBioPortal, simplifies accessing cancer genomic and clinical data from cBioPortal. This tool streamlines data retrieval and analysis for researchers, enhancing reproducibility in cancer informatics.

Keywords:
PythonbioinformaticscBioPortalcancer research

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Cancer Genomics

Background:

  • Biomedical research increasingly relies on big data and AI, expanding databases and web services.
  • cBioPortal is a key platform for accessing cancer genomic and clinical data.
  • Programmatic interaction with cBioPortal's web service presents challenges for researchers.

Purpose of the Study:

  • Develop a tool to simplify programmatic interaction with the cBioPortal web service.
  • Facilitate easier access to heterogeneous biological and clinical data.

Main Methods:

  • Developed the pyBioPortal Python package.
  • Leveraged the cBioPortal REST API for data access.
  • Returned retrieved data in Pandas DataFrame format for analysis.

Main Results:

  • pyBioPortal provides an efficient interface for users and the cBioPortal database.
  • Data is delivered in formats suitable for further analysis and visualization.
  • The tool simplifies data extraction, allowing focus on analytical aspects.

Conclusions:

  • pyBioPortal addresses challenges in accessing and processing large biomedical datasets.
  • Enhances data accessibility, analysis, and reproducibility in cancer informatics.
  • Available as an open-source project to the bioinformatics community for collaboration.