KNeXT

KNeXT parses KGML files and reconstructs topologically accurate gene and gene–compound networks from KEGG pathway maps, preserving node coordinates and preventing artificial neighborhood collapse due to overlapping accession numbers.

Key Features:

• KGML parsing: Parses Kyoto Encyclopedia of Genes and Genomes Markup Language (KGML) map data to extract nodes and relationships from KEGG pathways.
• Topology preservation: Preserves the topological environment of gene and mixed gene–compound networks to maintain original pathway context.
• Overlap resolution: Detects and resolves overlapping accession numbers that can cause artificial collapsing of network neighborhoods.
• Mixed-to-gene conversion: Converts mixed gene–compound networks into gene-only formats while retaining topological fidelity.
• Network construction: Leverages the NetworkX framework to dynamically create high-fidelity topological graph representations.
• Node coordinates: Retains programmatic access to original node coordinates from KEGG pathway maps.
• Output formats: Exports tab-separated files for import into other graph frameworks.
• ID mapping: Supports conversion of output identifiers to NCBI and UniProt IDs.
• Batch parsing and aggregation: Supports parsing of individual KGML files or entire local folders and downloading and aggregation of KGML files to recreate pathways based on user settings.
• Implementation: Implemented as a Python 3 package that integrates with NetworkX for computational graph operations.

Scientific Applications:

• Pathway reconstruction: Recreates KEGG pathways with preserved spatial and topological context for accurate pathway-level analyses.
• Network topology analysis: Enables topology-aware network analyses that avoid artifacts from collapsed neighborhoods in KGML-derived graphs.
• Cross-database integration: Facilitates integration of KEGG pathway data with external resources via NCBI and UniProt identifier mapping and TSV exports.

Methodology:

Parses KGML map data, uses NetworkX to construct graph representations while preserving node coordinates, resolves overlapping accession numbers to prevent neighborhood collapse, converts mixed gene–compound networks to gene-only formats, exports tab-separated files, maps identifiers to NCBI/UniProt, and supports parsing individual files or folders plus downloading and aggregation of KGML files.