Conceptual Modelling for Life Sciences Based on Systemist Foundations

TL;DR

This paper introduces a systemist approach and new notation for conceptual modeling in life sciences, enhancing representation of complex biological problems and supporting applications like genomics and precision medicine.

Contribution

It proposes a novel systemist perspective and notation grounded in ontological foundations for more effective life sciences conceptual modeling.

Findings

Developed a new systemist notation for life sciences

Applied the approach to genomic information systems

Supported modeling of precision medicine

Abstract

All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support researchers and scientists in conducting their work, conceptual models of the relevant domains are usually designed as both blueprints for a system being developed and as a means of communication between the designer and developer. Most conceptual modelling concepts are generic in the sense that they are applied with the same understanding across many applications. Problems in the life sciences, however, are especially complex and important, because they deal with humans, their well-being, and their interactions with the environment as well as other organisms. This work proposes a systemist perspective for creating a conceptual model of a life scientist's problem. We introduce the notion of a system and then show how it can be applied to the development of an information system for handling genomic-related information. We extend our discussion to show how the proposed systemist perspective can support the modelling of precision medicine. This research recognizes challenges in life sciences research of how to model problems to better represent the connections between physical and digital worlds. We propose a new notation that explicitly incorporates systemist thinking, as well as the components of systems based on recent ontological foundations. The new notation captures important semantics in the domain of life sciences. It may be used to facilitate understanding, communication and problem-solving more broadly. We also provide a precise, sound, ontologically supported characterization of the term system, as a basic construct for conceptual modelling in life sciences.