Logic-Based Representation of Connectivity Routes in the Immune System

This work is part of a general treatment of physiological phenomena grounded on connectivity between anatomical compartments. As a number of immune-related mechanisms may be formally described in terms of white cell movement across body compartments, this paper is concerned with the representation of routes of connectivity in the immune system, focusing on its lymphatic part. The approach relies on ontologies and their expression in a logic-based language supporting spatial knowledge representation and reasoning. The paper discusses informally, and provides elements of formalisation for, a core ontology of the immune system. This ontology is designed to support the representation of topological aspects of immune phenomena at the levels of systems and subsystems of connected tissues, organs, and conduits. The result is a theory i) grounding the representation of immune-related mechanisms on spatial relationships between immunological sites and ii) allowing to infer affordances that relations between sites create for agents.