libsbgnpy: Python library for SBGN

Python library to work with the Systems Biology Graphical Notation (SBGN). This library is based on the SBGN XML schema and supports reading, writing and validation of SBGN files.

The initial library was generated using generateDS. Additional utility functions for reading, writing, and rendering SBGN documents are provided.

Documentation with examples is available at https://libsbgnpy.readthedocs.io.

libsbgn.py python library
libsbgnTypes.py SBGN type definitions (GlyphClasses, ArcClasses, Languages)
utils.py SBGN utility function like writing & reading of files
render.py SBGN rendering
test/ unittests
examples/ python examples
validation/ validation of SBGN files

How to cite

Installation

libsbgnpy is available from pypi and can be installed via

pip install libsbgnpy

License

Source Code: MIT
Documentation: CC BY-SA 4.0

Funding

Matthias König (MK) was supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054). MK is supported by the Federal Ministry of Education and Research (BMBF, Germany) within ATLAS by grant number 031L0304B and by the German Research Foundation (DFG) within the Research Unit Program FOR 5151 QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach) by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).

Software using libsbgnpy

Mimoza takes a model in SBML format and visualizes it in several formats (downloadable as a COMBINE archive).

Python Language Bindings

The python language bindings were created from the XML schema using generateDS and than adapted to include GlyphClasses and ArcClasses.

generateDS.py -o "libsbgn.py" -s "libsbgnSubs.py" SBGN.xsd

The necessary constraints for GlyphClasses, ArcClasses and Languages were added and some utility functions created.

matthiaskoenig/libsbgnpy