Conceptual modelling for life sciences based on systemist foundations.

BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.

Foundations of information technology based on Bunge's systemist philosophy of reality.

General ontology is a prominent theoretical foundation for information technology analysis, design, and development. Ontology is a branch of philosophy which studies what exists in reality. A widely used ontology in information systems, especially for conceptual modeling, is the BWW (Bunge-Wand-Weber), which is based on ideas of the philosopher and physicist Mario Bunge, as synthesized by Wand and Weber. The ontology was founded on an early subset of Bunge's philosophy; however, many of Bunge's ideas have evolved since then. An important question, therefore, is: do the more recent ideas expressed by Bunge call for a new ontology? In this paper, we conduct an analysis of Bunge's earlier and more recent works to address this question. We present a new ontology based on Bunge's later and broader works, which we refer to as Bunge's Systemist Ontology (BSO). We then compare BSO to the constructs of BWW. The comparison reveals both considerable overlap between BSO and BWW, as well as substantial differences. From this comparison and the initial exposition of BSO, we provide suggestions for further ontology studies and identify research questions that could provide a fruitful agenda for future scholarship in conceptual modeling and other areas of information technology.