Abstract
We present a framework for the topological and semantic assembly of multiscale physiology route maps. The framework, called ApiNATOMY, consists of a knowledge representation (KR) model and a set of knowledge management (KM) tools. Using examples of ApiNATOMY route maps, we present a KR format that is suitable for the analysis and visualization by KM tools. The conceptual KR model provides a simple method for physiology experts to capture process interactions among anatomical entities. In this paper, we outline the KR model, modeling format, and the KM procedures to translate concise abstraction-based specifications into fully instantiated models of physiology processes.
Highlights
Physiology process models take into account the anatomical routes of communication that are necessary for mechanisms to occur
The requirements collected in previous work identified two core sets of knowledge representation (KR) organizing principles for physiology processes, namely: 1. A first set of organizing principles for flow processes is drawn from: (a) Fick’s Law, which emphasizes the dependency of exchange between conduit compartments on the surface area and permeability of the interface between them; (b) Poiseuille equation, which links the resistance of a fluid conduit to its length and internal radius; and (c) LaPlace’s work, which relates the pressure in the lumen of a conduit to the tension in the wall based on he internal radius and wall thickness
We presented the KR model for the ApiNATOMY framework, a modeling methodology of multi-scale physiology systems
Summary
Physiology process models take into account the anatomical routes of communication that are necessary for mechanisms to occur. The development of ApiNATOMY is a work-inprogress and is coupled to integrative efforts by communities in physiology and medicine [e.g., SPARC (National Institutes of Health), HuBMAP (Snyder et al, 2019)] In this context, the requirements collected in previous work (de Bono et al, 2012, 2017) identified two core sets of KR organizing principles for physiology processes, namely: 1. The first set of principles suggests that describing conduits that broker flow processes should take into account radius, length, wall thickness and surface area of these compartments. The KR schema for this model provides a contract between the input data used in route map construction and the ApiNATOMY KM toolset (Kokash) that validates and transforms the data into an expanded entity-relationship model. The paper is organized as follows: section 2 provides a high-level description of sample physiology models represented as route maps in ApiNATOMY.
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