Toward an Intermediate Structural Representation of Organization in Complex Systems

Organization is widely recognized as a fundamental concept in complex systems science, yet it rarely appears as an explicit object of scientific representation. Existing approaches successfully represent components, interactions, mechanisms, dynamical states, networks, or functions, but organizational properties are generally inferred from these representations rather than represented directly. As a consequence, systematic comparison of organization across heterogeneous systems remains difficult and often relies on domain‐specific descriptions or informal analogies. This paper proposes an intermediate structural representational framework in which organization becomes an explicit representational object situated between local mechanisms and global system behaviour. The framework introduces Structural Configurations as elementary organizational representations, criterion‐relative Structural Equivalence as the basis for comparison, Structural Signatures as equivalence classes of organizational configurations and Signature Space as the representational environment in which these signatures are organized. A formal construction based on equivalence relations and quotient spaces establishes the mathematical foundations of the framework while distinguishing empirical structural extraction from formal organizational composition. A complete methodological workflow is developed, linking empirical observations to Structural Configurations and Structural Signatures through explicit organizational coding and declared comparison criteria. The framework is illustrated through independently constructed representations of heterogeneous systems, demonstrating how organizational similarities, partial correspondences, and criterion‐dependent equivalence can be represented transparently without requiring common physical substrates or mechanistic explanations. Rather than proposing a new theory of organization, the paper establishes the conceptual, formal, and methodological foundations of a representational framework through which organizational structures can become explicit objects of scientific observation, comparison, and cumulative investigation across domains.