tidysbml: R/Bioconductor package for SBML extraction into dataframes

Area of Science:

• Systems Biology
• Bioinformatics
• Computational Biology

Background:

• Systems Biology Markup Language (SBML) is a standard for representing biochemical models.
• Extracting data from SBML files into usable formats can be challenging for analysis.
• Biological network construction and analysis require efficient data handling.

Purpose of the Study:

• To introduce tidysbml, an R package for extracting data from SBML files.
• To provide a user-friendly method for accessing compartments, species, and reactions.
• To facilitate the construction and analysis of custom biological networks.

Main Methods:

• Developed an R package named tidysbml.
• Implemented functions for parsing SBML documents (up to Level 3).
• Output data in tabular structures (R dataframes) for easy manipulation.

Main Results:

• Successfully extracts compartment, species, and reaction data from SBML files.
• Generated tabular data structures compatible with R's data manipulation tools.
• Demonstrated exemplar data extraction from Reactome SBML files.

Conclusions:

• tidysbml simplifies data extraction from SBML, enhancing biological information accessibility.
• The package supports downstream network analysis through integration with R packages like igraph and RCy3.
• tidysbml offers a valuable tool for systems biology research and custom network construction.