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  3. Momapy: A Python Library To Work With Molecular Maps.
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  3. Momapy: A Python Library To Work With Molecular Maps.

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momapy: a Python library to work with molecular maps.

Adrien Rougny1, Marek Ostaszewski1, Venkata Sagatopam1

  • 1Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.

Bioinformatics (Oxford, England)
|June 3, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

A new Python library, momapy, enables programmatic analysis and comparison of molecular maps. This tool facilitates the extraction of biological concepts from graphical representations, enhancing data analysis and modeling capabilities.

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Molecular maps visualize biological system mechanisms, aiding knowledge curation and data analysis.
  • Existing software supports molecular maps but lacks advanced programmatic analysis and comparison tools.
  • Programmatic access is needed for extracting biological concepts and comparing map representations.

Purpose of the Study:

  • To introduce momapy, a Python library for programmatic interaction with molecular maps.
  • To enable separation of map data models from their graphical representations.
  • To facilitate map manipulation and comparison through a unified interface.

Main Methods:

  • Developed momapy as a generic Python library.
  • Implemented support for Systems Biology Graphical Notation (SBGN) and CellDesigner formats.
  • Designed momapy for extensibility to new formats and functionalities.

    • Main Results:

    • momapy allows programmatic extraction and separation of molecular map data models.
    • Users can perform base operations like manipulation and comparison on map data.
    • The library supports established standards like SBGN and CellDesigner.

    Conclusions:

    • momapy provides essential tools for advanced programmatic analysis of molecular maps.
    • This library enhances the utility of molecular maps for data analysis and modeling.
    • momapy is freely available with comprehensive documentation for researchers.