Concept mapping One-Carbon Metabolism to model future ontologies for nutrient-gene-phenotype interactions

Area of Science:

• Bioinformatics
• Nutrigenomics
• Systems Biology

Background:

• Bioinformatic tools often require advanced skills, limiting accessibility for life scientists.
• User-friendly methods for visualizing nutrigenomics data are lacking.
• Understanding nutrient-gene/polymorphism-phenotype interactions is crucial for personalized nutrition and health.

Purpose of the Study:

• To develop a low-barrier-to-entry method for visualizing nutrigenomics information.
• To create a conceptual model for future nutrigenomics ontologies.
• To facilitate the understanding of diet and health-related data.

Main Methods:

• Utilized concept mapping software to build a conceptual model of diet and health data.
• Visualized interactions between phenotype, nutrient, gene product, and genetic polymorphism as "knowledge propositions" (triples).
• Mapped genes within the One-Carbon Metabolism (OCM) pathway, their variants, and associated concepts from literature.

Main Results:

• Developed knowledge maps visualizing OCM pathway genes, polymorphisms, and nutrition/phenotype/health associations.
• Identified incongruities between pathway databases and literature data.
• Highlighted the importance of considering upstream and downstream pathways (e.g., TCN2, FUT2) and substrate availability (e.g., B12) for OCM functionality.

Conclusions:

• The conceptual model provides a foundation for developing nutrient-gene/polymorphism-phenotype ontologies.
• Visualized knowledge maps aid in understanding complex gene-diet-phenotype relationships.
• This approach supports systems visualization for nutrigenomics research.