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.

Semantic interoperability: ontological unpacking of a viral conceptual model.

BACKGROUND: Genomics and virology are unquestionably important, but complex, domains being investigated by a large number of scientists. The need to facilitate and support work within these domains requires sharing of databases, although it is often difficult to do so because of the different ways in which data is represented across the databases. To foster semantic interoperability, models are needed that provide a deep understanding and interpretation of the concepts in a domain, so that the data can be consistently interpreted among researchers. RESULTS: In this research, we propose the use of conceptual models to support semantic interoperability among databases and assess their ontological clarity to support their effective use. This modeling effort is illustrated by its application to the Viral Conceptual Model (VCM) that captures and represents the sequencing of viruses, inspired by the need to understand the genomic aspects of the virus responsible for COVID-19. For achieving semantic clarity on the VCM, we leverage the "ontological unpacking" method, a process of ontological analysis that reveals the ontological foundation of the information that is represented in a conceptual model. This is accomplished by applying the stereotypes of the OntoUML ontology-driven conceptual modeling language.As a result, we propose a new OntoVCM, an ontologically grounded model, based on the initial VCM, but with guaranteed interoperability among the data sources that employ it. CONCLUSIONS: We propose and illustrate how the unpacking of the Viral Conceptual Model resolves several issues related to semantic interoperability, the importance of which is recognized by the "I" in FAIR principles. The research addresses conceptual uncertainty within the domain of SARS-CoV-2 data and knowledge.The method employed provides the basis for further analyses of complex models currently used in life science applications, but lacking ontological grounding, subsequently hindering the interoperability needed for scientists to progress their research.

Text Analysis of Evolving Emotions and Sentiments in COVID-19 Twitter Communication.

Scientists and regular citizens alike search for ways to manage the widespread effects of the COVID-19 pandemic. While scientists are busy in their labs, other citizens often turn to online sources to report their experiences and concerns and to seek and share knowledge of the virus. The text generated by those users in online social media platforms can provide valuable insights about evolving users' opinions and attitudes. The objective of this research is to analyze text of such user disclosures to study human communication during a pandemic in four primary ways. First, we analyze Twitter tweet information, generated throughout the pandemic, to understand users' communications concerning COVID-19 and how those communications have evolved during the pandemic. Second, we analyze linguistic sentiment concepts (analytic, authentic, clout, and tone concepts) in different Twitter settings (sentiment in tweets with pictures or no pictures and tweets versus retweets). Third, we investigate the relationship between Twitter tweets with additional forms of internet activity, namely, Google searches and Wikipedia page views. Finally, we create and use a dictionary of specific COVID-19-related concepts (e.g., symptom of lost taste) to assess how the use of those concepts in tweets are related to the spread of information and the resulting influence of Twitter users. The analysis showed a surprisingly lack of emotion in the initial phases of the pandemic as people were information seeking. As time progressed, there were more expressions of sentiment, including anger. Further, tweets with and without pictures and/or video had statistically significant differences in text sentiment characteristics. Similarly, there were differences between the sentiment in tweets and retweets and tweets. We also found that Google and Wikipedia searches were predictive of sentiment in the tweets. Finally, a variable representing a dictionary of COVID-related concepts was statistically significant when related to users' Twitter influence score and number of retweets, illustrating the general impact of COVID-19 on Twitter and human communication. Overall, the results provide insights into human communication as well as models of human internet and social media use. These findings could be useful for the management of global challenges beyond, or different from, a pandemic.

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.