The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

Originally published in 1958. A study in the logical foundations of modern theoretical semantics, this book is concerned with notions of designation and consistency as well as denotation and truth. It presents several semantical theories, each of which with what were new concepts or treatments from the author. Talking at a time when semantical theory was gained great ground, this book also looks at the methodology of the sciences and the semantics of scientific language alongside analysis of meaning and expression. (...) It is influenced by the writings of Carnap, Church, Frege, Goodman, Quine, Russell and Tarski. (shrink)

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...) are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor – though nevertheless ontologically important – technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

The aim of this paper is to show that we can deny that reality is neatly segmented into natural kinds and still give a plausible view about what science is supposed to do – and the way science in fact works does not rely on the dubious metaphysical assumption that reality is segmented into natural kinds. The score is simple: either there are natural kinds or there aren’t. The former view has been the default position in mainstream analytic metaphysics and (...) philosophy of science. I want to put the latter on the table as a metaphysically and scientifically plausible alternative. (shrink)

In a series of papers over a period of several years Barry Smith andWerner Ceusters have offered a number of cogent criticisms of historical approaches to creating, maintaining, and applying biomedical terminologies and ontologies. And they have urged the adoption of what they refer to as a “realism-based” approach. Indeed, at times they insist that the realism-based approach not only offers clear advantages and a well-founded methodological basis for ontology development and evaluation, but that such a realist perspective is in (...) fact necessary for understanding and using terminologies and ontologies in science. -/- This paper explores a number of questions surrounding such claims, provides a careful characterization of the type of realism recommended by Smith and Ceusters, and evaluates the role that realism plays in the critiques and recommendations that they offer. The conclusion reached is that while Smith’s and Ceusters’ criticisms of prior practice in the treatment of ontologies and terminologies in medical informatics are often both perceptive and well founded, and while at least some of their own proposals demonstrate obvious merit and promise, none of this either follows from or requires the brand of realism that they propose. (shrink)

A scientific community cannot practice its trade without some set of received beliefs. These beliefs form the foundation of the "educational initiation that prepares and licenses the student for professional practice". The nature of the "rigorous and rigid" preparation helps ensure that the received beliefs are firmly fixed in the student's mind. Scientists take great pains to defend the assumption that scientists know what the world is like...To this end, "normal science" will often suppress novelties which undermine its foundations. Research (...) is therefore not about discovering the unknown, but rather "a strenuous and devoted attempt to force nature into the conceptual boxes supplied by professional education". (shrink)

Coherent, well organized text familiarizes readers with complete theory of logical inference and its applications to math and the empirical sciences. Part I deals with formal principles of inference and definition; Part II explores elementary intuitive set theory, with separate chapters on sets, relations, and functions. Last section introduces numerous examples of axiomatically formulated theories in both discussion and exercises. Ideal for undergraduates; no background in math or philosophy required.

Thomas S. Kuhn's classic book is now available with a new index.

It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach – by Cimino, by Wüster, and by Campbell and associates – and surveys (...) some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support. (shrink)

In "Realism and Reason" Hilary Putnam has offered an apparently strong argument that the position of metaphysical realism provides an incoherent model of the relation of a correct scientific theory to the world. However, although Putnam's attack upon the notion of the "intended" interpretation of a scientific theory is sound, it is shown here that realism may be formulated in such a way that the realist need make no appeal to any "intended" interpretation of such a theory. Consequently, it can (...) be shown that realism is immune to Putnam's criticism and that attempts at reformulating this criticism are not likely to meet with success. (shrink)

Summary The concept of unified theory is defined in logical and abstract semantic terms, and employed in the analysis of relations between empirical scientific theories. The conceptual framework of the approach applies to binary relations such as the reduction or replacement of one theory by another, and to multiple intertheory relations. Historically, unified theories tend to arise within the contexts of scientific conflicts which they may show susceptible of solution even in the most controversial cases of the logical incompatibility or (...) conceptual incommensurability of competing theories. These conclusions are exemplified by the Planck-Einstein quantum theory of thermal radiation. The analysis shows in which sense it can, and in which it cannot, be said that this theory unifies Wien's law and the Rayleigh-Jeans law of black-body radiation. (shrink)

The conditions are examined under which one theory is said to be replaceable by another, while preserving those features of the original theory which made it serviceable for a given purpose. Among such replacements, special attention is given to ones which qualify as so-called reductions of a theory, and some theorems are proved concerning the notion of a reduction.

It has long been a standard practice for the natural sciences to classify things. Thus, it is no wonder that, for two and a half millennia, philosophers have been reflecting on classifications, from Plato and Aristotle to contemporary philosophy of science. Some of the results of these reflections will be presented in this chapter. I will start by discussing a parody of a classification, namely: the purportedly ancient Chinese classification of animals described by Jorge Luis Borges. I will show that (...) many of the mistakes that account for the comic features of this parody appear in real-life scientific databases as well. As examples of the latter, I will discuss the terminology database of the National Cancer Institute (NCI) of the United States, the NCI Thesaurus. (shrink)

Since Freges terms were meant to refer always to sets, that is, entities composed of individuals. Classical philosophy up to Leibniz and Kant had a different view on this questionBegriffes syntaxhighercorresponding to the idea which Leibniz used in the construction of his characteristic numbers. Thus, this paper is an addendum to Corcorans theory via predicate logic.

Originally published in 1958. A study in the logical foundations of modern theoretical semantics, this book is concerned with notions of designation and consistency as well as denotation and truth. It presents several semantical theories, each of which with what were new concepts or treatments from the author. Talking at a time when semantical theory was gained great ground, this book also looks at the methodology of the sciences and the semantics of scientific language alongside analysis of meaning and expression. (...) It is influenced by the writings of Carnap, Church, Frege, Goodman, Quine, Russell and Tarski. (shrink)

1. 1. PROGRAM It will be our aim to reconstruct, with precision, certain views which have been traditionally associated with nominalism and to investigate problems arising from these views in the construction of interpreted formal systems. Several such systems are developed in accordance with the demand that the sentences of a system which is acceptable to a nominalist must not imply the existence of any entities other than individuals. Emphasis will be placed on the constructionist method of philosophical analysis. To (...) follow this method is to introduce the central notions of the subject-matter to be investigated into a system governed by exact rules. For example, the constructionist method of investigating the properties of geometric figures may consist in formulating a system of postulates and definitions which, together with the apparatus of formal logic, generates all necessary truths concerning geometric figures. Similarly, a constructionist analysis of the notion of an individual may take the form of an axiomatic theory whose provable assertions are just those which seem essential to the role played by the concept of an individual in system atic contexts. Such axiomatic theories gain in interest if they are supple mented by precise semantical rules specifying the denotation of all terms and the truth conditions of all sentences of the theory. (shrink)

Babylon Knowledge Explorer (BKE) is an integrated suite of tools and information sources developed in GlaxoSmithKline's Analysis, Applications, and Research Technologies Department to support the prototyping and implementation of ontology-driven information systems and ontology-enhanced knowledge applications. In this paper we describe the current state of BKE development and focus on some of its distinctive or novel approaches, highlighting -/- * How BKE makes use of multiple large pre-existing ontologies in support of text and data mining. * The methodology employed for (...) importing an ontology and making it immediately accessible to BKE's tools, interfaces, and API. * A formal description of BKE's ontology-based fact model and how this is employed in implementing information retrieval and data mining capabilities. * A sample application built on BKE that illustrates an ontologyenhanced machine learning tool. (shrink)