Developing an ontological sandbox : investigating multi-level modelling’s possible Metaphysical Structures

One of the central concerns of the multi-level modelling (MLM) community is the hierarchy of classifications that appear in conceptual models; what these are, how they are linked and how they should be organised into levels and modelled. Though there has been significant work done in this area, we believe that it could be enhanced by introducing a systematic way to investigate the ontological nature and requirements that underlie the frameworks and tools proposed by the community to support MLM (such as Orthogonal Classification Architecture and Melanee). In this paper, we introduce a key component for the investigation and understanding of the ontological requirements, an ontological sandbox. This is a conceptual framework for investigating and comparing multiple variations of possible ontologies – without having to commit to any of them – isolated from a full commitment to any foundational ontology. We discuss the sandbox framework as well as walking through an example of how it can be used to investigate a simple ontology. The example, despite its simplicity, illustrates how the constructional approach can help to expose and explain the metaphysical structures used in ontologies, and so reveal the underlying nature of MLM levelling

Overcoming the Newtonian Paradigm: The Unfinished Project of Theoretical Biology from a Schellingian Perspective

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics

Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes

Philosophy of Blockchain Technology - Ontologies

About the necessity and usefulness of developing a philosophy specific to the blockchain technology, emphasizing on the ontological aspects. After an Introduction that highlights the main philosophical directions for this emerging technology, in Blockchain Technology I explain the way the blockchain works, discussing ontological development directions of this technology in Designing and Modeling. The next section is dedicated to the main application of blockchain technology, Bitcoin, with the social implications of this cryptocurrency. There follows a section of Philosophy in which I identify the blockchain technology with the concept of heterotopia developed by Michel Foucault and I interpret it in the light of the notational technology developed by Nelson Goodman as a notational system. In the Ontology section, I present two developmental paths that I consider important: Narrative Ontology, based on the idea of order and structure of history transmitted through Paul Ricoeur's narrative history, and the Enterprise Ontology system based on concepts and models of an enterprise, specific to the semantic web, and which I consider to be the most well developed and which will probably become the formal ontological system, at least in terms of the economic and legal aspects of blockchain technology. In Conclusions I am talking about the future directions of developing the blockchain technology philosophy in general as an explanatory and robust theory from a phenomenologically consistent point of view, which allows testability and ontologies in particular, arguing for the need of a global adoption of an ontological system for develop cross-cutting solutions and to make this technology profitable. CONTENTS: Abstract Introducere Tehnologia blockchain - Proiectare - Modele Bitcoin Filosofia Ontologii - Ontologii narative - Ontologii de intreprindere Concluzii Note Bibliografie DOI: 10.13140/RG.2.2.24510.3360

A model-driven approach to the conceptual modeling of situations : from specification to validation

A modelagem de situações para aplicações sensíveis ao contexto, também chamadas de aplicações sensíveis a situações, é, por um lado, uma tarefa chave para o funcionamento adequado dessas aplicações. Por outro lado, essa também é uma tafera árdua graças à complexidade e à vasta gama de tipos de situações possíveis. Com o intuito de facilitar a representação desses tipos de situações em tempo de projeto, foi criada a Linguagem de Modelagem de Situações (Situation Modeling Language - SML), a qual se baseia parcialmente em ricas teorias ontológicas de modelagem conceitual, além de fornecer uma plataforma de detecção de situação em tempo de execução. Apesar do benefício da existência dessa infraestrutura, a tarefa de definir tipos de situação é ainda não-trivial, podendo carregar problemas que dificilmente são detectados por modeladores via inspeções manuais. Esta dissertação tem o propósito de melhorar e facilitar ainda mais a definição de tipos de situação em SML propondo: (i) uma maior integração da linguagem com as teorias ontológicas de modelagem conceitual pelo uso da linguagem OntoUML, visando aumentar a expressividade dos modelos de situação; e (ii) uma abordagem para validação de tipos de situação usando um método formal, visando garantir que os modelos criados correspondam à intenção do modelador. Tanto a integração quanto a validação são implementadas em uma ferramenta para especificação, verificação e validação de tipos de situação ontologicamente enriquecidos.The modeling of situation types for context-aware applications, also called situationaware applications, is, on the one hand, a key task to the proper functioning of those applications. On the other hand, it is also a hard task given the complexity and the wide range of possible situation types. Aiming at facilitating the representation of those types of situations at design-time, the Situation Modeling Language (SML) was created. This language is based partially on rich ontological theories of conceptual modeling and is accompanied by a platform for situation-detection at runtime. Despite the benefits of the availability of this suitable infrastructure, the definition of situation types, being a non-trivial task, can still pose problems that are hardly detected by modelers by manual model inspection. This thesis aims at improving and facilitating the definition of situation types in SML by proposing: (i) the integration between the language and the ontological theories of conceptual modeling by using the OntoUML language, with the purpose of increasing the expressivity of situation type models; and (ii) an approach for the validation of situation type models using a lightweight formal method, aiming at increasing the correspondence between the created models’ instances and the modeler’s intentions. Both the integration and the validation are implemented in a tool for specification, verification and validation of ontologically-enriched situation types.CAPE

Ontology, Ontologies and the "I" of FAIR

According to the FAIR guiding principles, one of the central attributes for maximizing the added value of information artifacts is interoperability. In this paper, I discuss the importance, and propose a characterization of the notion of Semantic Interoperability. Moreover, I show that a direct consequence of this view is that Semantic Interoperability cannot be achieved without the support of, on one hand, (i) ontologies, as meaning contracts capturing the conceptualizations represented in information artifacts and, on the other hand, of (ii) Ontology, as a discipline proposing formal meth- ods and theories for clarifying these conceptualizations and articulating their representations. In particular, I discuss the fundamental role of formal ontological theories (in the latter sense) to properly ground the construction of representation languages, as well as methodological and computational tools for supporting the engineering of ontologies (in the former sense) in the context of FAIR

O4OA Specification

This document is the reference ontology specification for the Ontology for Ontological Analysis (O4OA) version 2.6.This work has been developed under the project Digital Knowledge Graph – Adaptable Analytics API with the financial support of Accenture LTD, the Generalitat Valenciana through the CoMoDiD project (CIPROM/2021/023), the Spanish State Research Agency through the DELFOS (PDC2021-121243-I00) and SREC (PID2021-123824OB-I00) projects, MICIN/AEI/10.13039/501 100011033 and co-financed with ERDF and the European Union Next Generation EU/PRTR.Franco Martins Souza, B.; Guizzardi, R.; Pastor López, O. (2023). O4OA Specification. http://hdl.handle.net/10251/19672

Developing situation-aware applications for disaster management with a distributed rule-based platform

In order to enhance interoperability and productivity in the develop-ment of situation-aware applications for disaster management, proper mecha-nisms and guidelines are required. They must address the lack of semantics in modelling emergency situations. In addition, the ever changing and unpredicta-ble nature of disaster scenarios present challenges for information processing and collaboration. This paper proposes a framework that combines the follow-ing elements: (i) a foundational ontology for temporal conceptualization; (ii) well-founded specifications of structural and behavioral models; (iii) a CEP en-gine based on a distributed rule-based platform for situation management; (iv) a model-driven approach. We illustrate the operation of the framework with a scenario for monitoring tuberculosis epidemy