CODA-ML

CODA-ML encodes biological models in an XML-based markup language to integrate and represent high-resolution molecular and contextual information for systemic physiology and multi-organ disease analysis.

Key Features:

• Unified Representation: Integrates signaling pathways, metabolic pathways, and gene regulatory networks into a unified XML representation for combined analysis.
• Molecular Specification: Specifies entities including genes/proteins, compounds, cellular functions, and diseases with high resolution, including isoforms and modifications.
• Contextual Differentiation: Represents biological events with explicit context such as cell types and disease conditions and distinguishes intra-cellular and inter-cellular events to resolve contradictory associations across models.
• Comprehensive Coverage: Supports heterogeneous entity types and enables descriptions of disease mechanisms and drug actions from molecular, functional, and pathological perspectives.

Scientific Applications:

• Computational biology and systems physiology: Supports integrated, context-aware modeling for computational biology and systems physiology investigations.
• Multi-organ disease analysis: Enables analysis of complex, multi-organ diseases beyond single-cell studies, including cancer, by unifying diverse biological data.
• Drug and disease mechanism description: Facilitates representation of drug actions and disease mechanisms across molecular, functional, and pathological scales.

Methodology:

Defines an XML-based markup language for high-resolution representation of molecular entities and their interactions within specified biological contexts, preserving contextual information when different models are combined.