parse_reactome_pathway: Parse Reactome Pathway SBML File

In tidymass/massdatabase: Play with databases about mass spectrometry

Parse Reactome Pathway SBML File

Description

This function extracts pathway details, including description, metabolites, and proteins from an SBML file.

Usage

parse_reactome_pathway(file_name)

Arguments

file_name

Character. The file path of the SBML file.

Value

A list containing:

pathway_name	Character. Name of the pathway.
pathway_id	Character. Reactome pathway ID.
pathway_description	Character. Text description of the pathway.
component_info	Data frame containing metabolites (CHEBI) and proteins (UniProt) involved in the pathway.

Author(s)

Xiaotao Shen ([e-mail])

Examples

# Download a sample SBML file from Reactome and parse it
pathway_info <- request_reactome_pathway("R-HSA-5652084")
print(pathway_info$pathway_name)
print(pathway_info$component_info)

tidymass/massdatabase documentation built on March 29, 2025, 10:51 p.m.