How to translate biological knowledge into a graph

The first step toward building a model is to translate biological knowledge into a basic graphical representation of the system: a graph showing the model components and how they interact. This step focuses on identifying the key elements and their relationships, and can be performed without having a specific mathematical modelling framework in mind (as described in a section later in this tutorial – Introduction to three mathematical model formalisms).

This initial graph-based representation is often referred to as ‘conceptual modelling’. It captures the structure of the system in a way that is accessible and intuitive. Only in the later step — formal modelling — are these interactions translated into mathematical equations tailored to a chosen modelling framework. 

Building Steps

1. Define the question the model should answer
   What do we need the model for — what can it help us understand that cannot be answered directly from data? This question should be clearly formulated before making any modelling decisions.
   
2. Identify the biological players involved
   List the core components of the system — such as genes, proteins, metabolites, signalling molecules or disease states (Fig 4A). For an example, when modelling a signalling pathway, key players might include receptors, enzymes, and messengers. The selection of components should follow the principle “as simple as possible, as complex as necessary.” The scope of the model depends heavily on the question being asked. Deciding what to include or exclude is part of defining the model’s boundaries.
   
3. Identify the interactions and assign directionality
   Once the components are chosen, determine how they influence one another (Fig 5B) and assign directions to these interactions — e.g., which protein interacts with which gene, or which metabolite influences the activity of an enzyme (Fig 4B). Indicate whether each interaction is activating, inhibiting, or neutral  by using different arrow types (Fig 4C).
   

These steps result in a conceptual model graph — a visual structure of the system — that defines the basic architecture of the model. This conceptual model graph remains flexible with respect to mathematical formalism and serves as a foundation for choosing and applying a suitable modelling framework.
Later in this tutorial we will introduce three modelling formalisms that each use different kinds of equations to quantify the interactions between components in such a graph (Introduction to three mathematical model formalisms).