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pyBioPortal: a Python package for simplifying cBioPortal data access in cancer research.
Matteo Valerio1, Alessandro Inno1, Stefania Gori1
1Medical Oncology, IRCCS Sacro Cuore Don Calabria Hospital, 37024 Negrar di Valpolicella, Verona, Italy.
JAMIA Open
|December 30, 2024
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.
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.
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