There is a common misconception across the lntelligence Community (IC) to the effect that information trapped within multiple heterogeneous data silos can be semantically integrated by the sorts of meaning-blind statistical methods employed in much of artificial intelligence (Al) and natural language processlng (NLP). This leads to the misconception that incoming data can be analysed coherently by relying exclusively on the use of statistical algorithms and thus without any shared framework for classifying what the data are about. Unfortunately, such approaches (...) do not yield sustainable results where we are dealing with widely distributed, highly heterogeneous and often changing bodies of data. We argue here that the needed integration requires the use of what we call an lntegrating Semantic Framework (ISF), which provldes a consistent set of categories and relationships that can be reused over and over again to tag successive bodies of data in ways which foster more coherent representation and reasoning. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

Mental health research faces a suite of unresolved challenges that have contributed to a stagnation of research efforts and treatment innovation. One such challenge is how to reliably and validly account for the subjective side of patient symptomatology, that is, the patient’s inner experiences or patient phenomenology. Providing a structured, standardised semantics for patient phenomenology would enable future research in novel directions. In this contribution, we aim at initiating a standardized approach to patient phenomenology by sketching a tentative formalisation within (...) the framework of an applied ontology, in the broader context of existing open-source Open Biomedical Ontologies resources such as the Mental Functioning Ontology. We further discuss a number of prevailing challenges and observations bearing on this task. (shrink)

This paper explains conceptual modeling within the framework of Frame-Based Terminology (Faber, 2012; 2015; 2022), as applied to EcoLexicon (ecolexicon.ugr.es), a specialized knowledge base on the environment (León-Araúz, Reimerink &, Faber, 2019; Faber & León-Araúz, 2021). It describes how a frame-based terminological resource is currently being restructured and reengineered as an initial step towards its formalization and subsequent transformation into an ontology. It also explains how the information in EcoLexicon can be integrated in environmental ontologies such as ENVO (Buttigieg, Morrison, (...) Smith, Mungall & Lewis, 2013; Buttigieg, Pafilis, Lewis, Schildhauer, Walls & Mungall, 2016), particularly at the bottom tiers of the Ontology Learning Layer Cake (Cimiano, 2006; Cimiano, Maedche, Staab & Volker, 2009). The assumption is that frames, as a conceptual modeling tool, and information extracted from corpora can be used to represent the conceptual structure of a specialized domain. (shrink)

Recent contributions in moral philosophy have raised questions concerning the prevalent assumption that moral judgments are typologically discrete, and thereby distinct from ordinary and/or other types of judgments. This paper adds to this discourse, surveying how attempts at defining what makes moral judgments distinct have serious shortcomings, and it is argued that any typological definition is likely to fail due to certain questionable assumptions about the nature of judgment itself. The paper concludes by raising questions for future investigations into the (...) nature of moral judgment. (shrink)

Advances in machine learning and the development of very large knowledge graphs have accompanied a proliferation of ontologies of many types and for many purposes. These ontologies are commonly developed independently, and as a result, it can be difficult to communicate about and between them. To address this difficulty of communication, ontologies and the communities they serve must agree on how their respective terminologies and formalizations relate to each other. The process of coming into accord and agreement is called “harmonization.” (...) The Ontology Summit 2021 examined the overall landscape of ontologies, the many kinds of ontology generation and harmonization, as well as the sustainability of ontologies. The Communiqué synthesizes and summarizes the findings of the summit as well as earlier summits on related issues. One of the major impediments to harmonization is the relatively poor quality of natural language definitions in many ontologies. The summit surveyed the state of the art in natural language definition development, based on lexicographic principles, as well as examples of ongoing projects that are explicitly dealing with harmonization and sustainability. (shrink)