tidysbml

tidysbml extracts compartments, species, and reactions data from Systems Biology Markup Language (SBML) documents into R dataframes for accessible biological information handling and network analysis.

Key Features:

• SBML Parsing: Extracts information from listOfCompartments, listOfSpecies, and listOfReactions elements from SBML files up to Level 3.
• Structured Tabular Output: Generates data frames with one row per entity and dedicated columns for attributes, notes subelement content, and annotation subelement content.
• Network Construction Support: Enables manageable construction and analysis of custom networks through integration with R packages including igraph, RCy3, and biomaRt.

Scientific Applications:

• Metabolic Network Analysis: Facilitates data manipulation and retrieval for analysis of biological networks derived from SBML-encoded models such as those from Reactome.
• Systems Biology Data Integration: Supports extraction and handling of rich biological information from SBML documents for downstream computational analysis in R.

Methodology:

SBML files are parsed to extract listOfCompartments, listOfSpecies, and listOfReactions elements, with each entity saved as a row in a dataframe containing columns for attributes, notes content, and annotation content.