Applied Ontology: An Introduction," edited by Katherine Munn and Barry Smith.

The following is a comprehensive book review of "Applied Ontology: An Introduction," edited by Katherine Munn and Barry Smith. This volume presents a powerful argument for the systematic application of philosophical ontology to the practical challenges of modern information management, particularly within the domains of medicine and biology.

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An Overview of Themes, Arguments, and Structure

"Applied Ontology: An Introduction" is a collaborative volume that asserts the necessity of integrating rigorous philosophical methods, particularly those derived from ontology, into the development of automated information systems. The book's central argument is that current information systems (such as electronic databases, terminologies, and taxonomies) are often designed idiosyncratically, making them unable to share data (interoperable) or serve as reliable inputs for automated reasoning.

The volume introduces the core theme that ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. The goal of the contributors is to show how philosophical insights can inform the creation of structured, automated representations, also called 'ontologies'.

The key arguments revolve around advocating for the realist orientation as an antidote to prevailing deficiencies. This orientation holds that sound knowledge representation must aim to represent the world itself, not merely convenient conceptualizations of it (a methodology critiqued as "pragmatist conceptualism"). The book emphasizes the doctrine of realist fallibilism, which combines a "healthy intellectual humility" with the conviction that humans can take measures to procure true beliefs about the world.

The book is organized into an introduction and thirteen chapters contributed by various philosophers and information scientists. The chapters systematically explore the theoretical foundation (formal ontology and realism), essential structural tools (granular partitions and classification theory), and deep ontological distinctions (continuants vs. occurrents, universals vs. particulars, and relational logic). Although the methods are intended to be broadly applicable, the book limits its focus primarily to the domains of biology and medicine.

Analysis of Style, Tone, and Perspective

The overall tone of "Applied Ontology" is urgent, expert, and reformative. The contributors stress the "urgency of applying rigorous philosophical methods" because doing so has "vast potential" for making information systems interoperable and efficient.

The perspective is consistently one of realist ontological perspectivalism, which argues that we can gain knowledge of reality via a multiplicity of veridical granular partitions. This stance is consciously pitted against conceptualism, a view widespread in information science where the definition of 'concept' is often loosely applied, leading to confusion about the representation target.

The writing style is designed to bridge the gap between abstract philosophy and practical engineering. Katherine Munn’s introduction is explicitly non-technical, using accessible metaphors, such as imagining a brilliant scientist scribbling a theory on a beer mat. However, the volume quickly moves toward rigorous, formalized treatments, including discussions of first-order logic (FOL) and description logics (DLs), making the style necessarily dense in later chapters. The clarity is enhanced by drawing on a deep tradition, particularly Aristotelian methodology concerning categories and hierarchical taxonomy, which is shown to have new relevance for modern bioinformatics.

Evaluation of Strengths and Weaknesses

Strengths: A major strength is the book’s unwavering commitment to foundational rigor. The authors provide crucial clarity on distinctions often blurred in information science, such as the difference between universals (kinds) and particulars (instances) or the critical difference between sets and classes.

The critique of existing biomedical terminologies (the "concept orientation") is a strong point, yielding critical insights:

• The volume addresses why systems like the UMLS Metathesaurus fail to provide true integration, sometimes treating non-interchangeable entities (like 'aspirin' and 'Aspergum') as if they referred to the same concept in an "artificial world".
• It exposes the flaws in systems like the National Cancer Institute Thesaurus (NCIT), demonstrating how it violates fundamental criteria for good classifications, such as disjointness or uniformity. For example, classifying 'cancer patient' and 'outpatient' as disjoint subtypes of 'patient' is problematic because many cancer patients are treated as outpatients.
• The argument that type-level relations (such as $part_of$ between universals) must be rigorously defined by reverting to consideration of their instances is foundational. The precise delineation of four distinct $is_a$ relations—genus-subsumption, determinable-subsumption, specification, and specialization—resolves ambiguities that plague information systems.

Weaknesses: The authors acknowledge that the proposed transition to a realist orientation would be arduous, necessitating a global paradigm shift. Furthermore, the complexity of the domain—for example, the challenge of defining biological kinds given the "sheer number" of animal kinds (estimated at 30 million) and the existence of borderline cases—means that no classification system can be perfectly exhaustive. The core ideas, being novel in application, are still "being developed".

Connections to Broader Academic and Social Contexts

The book grounds its methodology in a broad sweep of philosophical history. It draws heavily on Aristotle's Categories to build a reliable top-level ontology, recommending the adoption of the Basic Formal Ontology (BFO) structure, influenced by Aristotelian ideas. The discussion of the four-category ontology (the ontological square, later expanded to a sextet) highlights the deep metaphysical concerns underlying effective information structure.

Academically, the volume directly combats influential non-realist positions. Ingvar Johansson's chapter explicitly clarifies and rejects alternative philosophies of science that discourage the pursuit of objective reality, specifically critiquing Myrdal’s Biasism and Vaihinger’s Fictionalism, in favor of Popper’s Epistemological Realism and its central notion of truthlikeness.

In a social and practical context, the book highlights immediate applications in health management. The lack of interoperability caused by non-standardized systems is a critical barrier. The proposed realist approach, particularly using Referent Tracking (assigning an instance unique identifier, or IUI, to every clinically relevant real-world entity), is presented as essential for linking information in Electronic Health Records (EHRs) to general scientific knowledge, thereby supporting diagnostics, scientific discovery, and public health surveillance.

Overall Contribution and Significance

"Applied Ontology: An Introduction" constitutes a seminal contribution to the emerging discipline of applied ontology. Its significance lies in its uncompromising stance that the intellectual rigor of philosophy is not a luxury but a necessary condition for overcoming the limitations of current, non-interoperable information systems. The book provides a theoretical blueprint, formal methodology, and clear practical guidelines for building reference ontologies that mirror reality.

The volume successfully demonstrates that foundational philosophical problems—such as what constitutes a natural kind or how processes unfold in time (occurrents)—have tangible practical consequences when building computerized systems. As the complexity and volume of scientific data continue to increase, the book’s argument that "the means by which knowledge is conveyed are every bit as important as that knowledge itself" serves as a powerful call to action.

Conclusion

This book is indispensable reading for information scientists, knowledge engineers, and bioinformaticians who are involved in developing, curating, or implementing controlled vocabularies and ontologies, particularly those within the biomedical domain.

It is also highly recommended for philosophers—especially those working in metaphysics, philosophy of science, and logic—as it showcases the profound and urgent practical relevance of their disciplines in the 21st century. The explicit intention of the volume is to improve systems for everyone whose life may be affected by scientific research, making its core principles vital for anyone concerned with the quality and reliability of digitally stored scientific knowledge.