Leslie Allan demonstrates how human rights are unproblematic for utilitarian moral theory and how, upon consideration, utilitarianism turns out to be the best theory for justifying human rights. Using case studies of historical and contemporary human rights conventions and recent psychological research, he argues how our concept of human rights is founded on the satisfaction of fundamental human needs and the consequences for human happiness.

This tutorial is for beginners wanting to learn the basics of propositional logic; the simplest of the formal systems of logic. Leslie Allan introduces students to the nature of arguments, validity, formal proofs, logical operators and rules of inference. With many examples, Allan shows how these concepts are employed through the application of three different methods for proving the formal validity of arguments.

In this address, Leslie Allan shares his early experiences and how they shape his humanist outlook today. He then outlines what he considers to be the three core principles underlying the humanist world view and illustrates their application with historical and contemporary examples. He concludes by drawing upon each of these principles to tease out what it means to live a good life; a life of meaning and purpose.

Donald Hoffman proposed a bold theory—that objects do not exist independently of us perceiving them and that all that really exists is conscious agents. In this critical review, Leslie Allan examines the three core components of Hoffman's new idealism. He proposes solutions to linguistic absurdities suffered by Hoffman's theory before considering its most serious problems. These include oversimplifications of evolutionary theory, self-refutation, heuristic sterility and dependence on scientific realism.

The author challenges both the eliminative idealist's contention that physical objects do not exist and the phenomenalist idealist's view that statements about physical objects are translatable into statements about private mental experiences. Firstly, he details how phenomenalist translations are parasitic on the realist assumption that physical objects exist independently of experience. Secondly, the author confronts eliminative idealism head on by exposing its heuristic sterility in contrast with realism's predictive success.

In his seminal essay, 'Two Concepts of Rules', John Rawls draws a central distinction between justifying a practice and justifying a particular action falling under it. In this review, Leslie Allan walks through Rawls's essay, highlighting his key arguments for a strengthened version of rule utilitarianism and reflecting on the lasting influence of his analysis.

As a non-cognitivist analysis of moral language, Charles Stevenson's sophisticated emotivism is widely regarded by moral philosophers as a substantial improvement over its historical antecedent, radical emotivism. None the less, it has come in for its share of criticism. In this essay, Leslie Allan responds to the key philosophical objections to Stevenson's thesis, arguing that the criticisms levelled against his meta-ethical theory rest largely on a too hasty reading of his works.

The existence of evil, pain and suffering is considered by many philosophers to be the most vexed question concerning the existence of an omnipotent, omniscient and morally perfect deity. Why would a loving God permit wanton acts of cruelty and misery on the scale witnessed throughout human history? In this essay, Leslie Allan evaluates four common theistic responses to this problem, highlighting the benefits and challenges faced by each approach. He concludes with a critical examination of a theistic (...) defence designed to show that the problem of evil is not a problem at all. (shrink)

In his seminal essay, Harry Frankfurt argued that our exercise of free will and allocation of moral responsibility do not depend on us being able to do other than we did. Leslie Allan defends this moral maxim from Frankfurt's attack. Applying his character-based counterfactual conditional analysis of free acts to Frankfurt's counterexamples, Allan unpacks the confusions that lie at the heart of Frankfurt's argument. The author also explores how his 4C compatibilist theory measures up against Frankfurt’s conclusions.

Leslie Allan defends his thesis that ethics is objective in the sense of requiring moral agents to offer impartial reasons for acting. Radical subjectivists have attacked this requirement for impartiality on a number of grounds. Some critics make the charge that Allan's thesis is simply a version of subjectivism in disguise. He responds by showing how a broadly naturalist view of ethics accommodates objective moral constraints. Allan also counters cases in which impartiality is purportedly not morally (...) required and considers the subjectivists' response to the problem of demarcating moral from non-moral judgements. (shrink)

Absolutist systems of ethics have come in for harsh criticism on a number of fronts. The Principle of Double Effect was formulated by Catholic ethicists to overcome such objections. In this essay, Leslie Allan addresses four of the most prominent problems faced by an absolutist ethic and evaluates the extent to which the Principle of Double Effect is successful in avoiding or mitigating these criticisms.

The soul-making theodicy seeks to explain how belief in the existence of God is compatible with the evil, pain and suffering we experience in our world. It purports to meet the problem of evil posed by non-theists by articulating a divine plan in which the occurrence of evil is necessary for enabling the greater good of character building of free moral agents. Many philosophers of religion have levelled strong objections against this theodicy. In this essay, Leslie Allan considers (...) the effectiveness of the counterarguments advanced by theist philosopher, Clement Dore, to two key objections to the soul-making theodicy. (shrink)

Enlightenment philosopher, René Descartes, set out to establish what could be known with certainty, untainted by a deceiving demon. With his method of doubt, he rejected all previous beliefs, allowing only those that survived rigorous scrutiny. In this essay, Leslie Allan examines whether Descartes's program of skeptical enquiry was successful in laying a firm foundation for our manifold beliefs. He subjects Descartes's conclusions to Descartes's own uncompromising methodology to determine whether Descartes escaped from a self-imposed radical skepticism.

The author mounts a case against the libertarian and hard determinist's thesis that free will is impossible in a deterministic world. He charges incompatibilists with misconstruing ordinary 'free will' talk by overlaying common language with their own metaphysical presuppositions. Through a review of ordinary discourse and recent developments in jurisprudence and the sciences, he draws together the four key factors required for an act to be free. He then puts his 4C theory to work in giving a credible account of (...) how caused human agents 'could have done otherwise'. (shrink)

Meta-ethics is the area of philosophy in which thinkers explore the language and nature of moral discourse and its relations to other non-moral areas of life. In this introduction to the discipline written explicitly for novices, Leslie Allan outlines the key questions and areas of analysis in contemporary meta-ethics. In clear, tabular format, he summarizes the core concepts integral to each of the major meta-ethical positions and the strengths of each view. To prompt further thinking and reading, (...) class='Hi'>Allan explains briefly the major objections to each theory and lists each view's best known advocates. (shrink)

Some atheistic philosophers have argued that God could have created a world with free moral agents and yet absent of moral evil. Using possible world semantics, Alvin Plantinga sought to defuse this logical form of the problem of evil. In this critical note, Leslie Allan examines the adequacy of Plantinga's argument that the existence of God is logically compatible with the existence of moral evil. The veracity of Plantinga's argument turns on whether his essential use of counterfactual conditionals (...) preserves the logic of this type of conditional. (shrink)

Imre Lakatos holds a well-deserved primary place in current philosophy of science. In this essay, Leslie Allan critically examines Lakatos' theory of knowledge in two key areas. The first area of consideration is Lakatos' notion that knowledge is gained through a process of competition between rival scientific research programmes. Allan identifies and discusses four problems with Lakatos' characterization of a research programme. Next, Allan considers Lakatos' proposed test of adequacy for theories of rationality using his methodology (...) of historiographical research programmes. Allan discovers tensions within Lakatos' criteria and suggests ways of strengthening his test. (shrink)

Drawing on insights from Imre Lakatos' seminal work on theories of rationality, Leslie Allan develops seven criteria for rational theory choice that avoid presuming the rationality of the scientific enterprise. He shows how his axioms of rationality follow from the general demands of an objectivist epistemology. Allan concludes by considering two weighty objections to his framework.

The author contends that classifying theories in the field of meta-ethics along a single dimension misses important nuances in each theory. With the increased sophistication and complexity of meta-ethical analyses in the modern era, the traditional cognitivist–non-cognitivist and realist–anti-realist categories no longer function adequately. The author categorizes the various meta-ethical theories along three dimensions. These dimensions focus on the linguistic analysis offered by each theory, its metaphysical commitments and its degree of normative tolerance.

Leslie Allan reviews Professor Losee's tracing of the history of the philosophy of science from its beginning with Aristotle in Ancient Greece, through the Middle Ages and the Enlightenment to the work of contemporary philosophers. In this review, Allan also provides a summary of each chapter and commentary on Losee's analysis.

The ontological argument for the existence of God has enjoyed a recent renaissance among philosophers of religion. Alvin Plantinga's modal version is perhaps the most notable example. This essay critically examines Plantinga's rendition, uncovering both its strengths and weaknesses. The author concludes that while the argument is probably formally valid, it is ultimately unsound. Nonetheless, Plantinga's version has generated much interest and discussion. The author spends some time uncovering the reasons for the argument's powerful intuitive appeal. He concludes his essay (...) by appraising Pruss's recent defence of Plantinga's argument. (shrink)

Conservative and liberal approaches to the problem of abortion are oversimplified and deeply flawed. Accepting that the moral status of the conceptus changes during gestation, the author advances a more nuanced perspective. Through applying a form of rules in practice utilitarianism within the context of overall population policy, he provides a compelling ethical and legal framework for regulating contraception and abortion practices.

The materialist version of the mind/brain identity theory has met with considerable challenges from philosophers of mind. The author first dispenses with a popular objection to the theory based on the law of indiscernibility of identicals. By means of discussing the vexatious problem of phenomenal qualities, he explores how the debate may be advanced by seeing each dualist and monist ontology through the lens of an evolutionary epistemology. The author suggests that by regarding each ontology as the core of a (...) scientific research programme, each of these logically irrefutable hypotheses can be tested rationally. (shrink)

This essay explores the moral reasoning underpinning the common view that it is worse to kill a human compared with killing an animal. After examining the serious deficiencies of traditional approaches, the author develops an alternative utilitarian-based framework that proportions the seriousness of killing to levels of sentience. He demonstrates how this new approach avoids the problems faced by the application of standard utilitarian formulae in weighing the seriousness of killing many low-sentience animals vis-á-vis killing a single human. The author (...) concludes with a discussion of how this new approach overcomes the difficulties faced by Peter Singer’s dualist form of utilitarianism. (shrink)

Moral sentimentalism can be understood as a metaethical theory, a normative theory, or some combination of the two. Metaethical sentimentalism emphasizes the role of affect in the proper psychology of moral judgment, while normative sentimentalism emphasizes the centrality of warm emotions to the phenomena of which these judgments properly approve. Neither form of sentimentalism necessarily implies a commitment to virtue ethics, but both have an elective affinity with it. The classical metaethical sentimentalists of the Scottish Enlightenment—such as David Hume and (...) Adam Smith—were all, to a greater or lesser extent, also virtue theorists. The connection is even stronger in the case of Enlightenment philosophers who were also normative sentimentalists , as with Frances Hutcheson. For Hutcheson, virtue simply is a habit of acting from the warm motive of universal benevolence. Today, neo-sentimentalist metaethicists such as Allan Gibbard, Justin D’Arms and Daniel Jacobson generally remain agnostic on the question of whether virtue ethics is superior to its deontological and consequentialist competitors. Michael Slote, however, has developed a comprehensive theory of sentimentalist care ethics in an unambiguously virtue-centered form. (shrink)

This paper responds to Kevin Krein’s claim in that the particular value of nature sports over traditional ones is that they offer intensity of sport experience in dynamic interaction between an athlete and natural features. He denies that this intensity is derived from competitive conflict of individuals and denies that nature sport derives its value from internal conflict within the athlete who carries out the activity. This paper responds directly to Krein by analysing ‘intensity’ in sport in terms of the (...) relationship between attention and reflection and the interaction between self and environment. I reply directly to Krein’s rejection of self-competition as based on a mischaracterisation of internal struggle and argue that the weighing of incompatible desires does not involve a fragmented self. I argue that the unique intensity to which Krein refers is strongly comparable to the Kantian conception of the sublime and explore how sublime experience fits Krein’s account and outline some serious problems that such an ideal of experience poses for nature sport. (shrink)

In this paper we propose an Ontology of Commercial Exchange (OCE) based on Basic Formal Ontology. OCE is designed for re-use in the Industrial Ontologies Foundry (IOF) and in other ontologies addressing different aspects of human social behavior involving purchasing, selling, marketing, and so forth. We first evaluate some of the design patterns used in the Financial Industry Business Ontology (FIBO) and Product Types Ontology (PTO). We then propose terms and definitions that we believe will improve the representation of contractual (...) obligations, sales processes, and their associated documents. A commercial exchange, for instance, involves mutual agreement to reciprocate actions, such as transferring money, performing a service, or transferring goods. (shrink)

The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by Brentano’s students (...) Twardowski, Husserl and Meinong, and finally, Adolf Reinach’s addition of a linguistic dimension to the Brentano-Husserlian theory of judgment – an account of judgments as ways of doing things with words in what Reinach called ‘social acts’. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The aim of this paper is to show that the account of objective truth taken for granted by logicians at least since the publication in 1933 of Tarski’s “The Concept of Truth in Formalized Languages” arose out of a tradition of philosophical thinking initiated by Bolzano and Brentano. The paper shows more specifically that certain investigations of states of affairs and other objectual correlates of judging acts, investigations carried out by Austrian and Polish philosophers around the turn of the century, (...) formed part of the background of views that led to standard current accounts of the objectivity of truth. It thus lends support to speculations on the role of Brentano and his heirs in contemporary logical philosophy advanced by Jan Wolenski in his masterpiece of 1989 on the Logic and philosophy in the Lvov-Warsaw School. (shrink)

The dominant theory of judgment in 1870 was one or other variety of combination theory: the act of judgment is an act of combining concepts or ideas in the mind of the judging subject. In the decades to follow a succession of alternative theories arose to address defects in the combination theory, starting with Bolzano’s theory of propositions in themselves, Brentano’s theory of judgment as affirmation or denial of existence, theories distinguishing judgment act from judgment content advanced by Brentano’s students (...) Twardowski, Husserl and Meinong, and finally, Adolf Reinach’s addition of a linguistic dimension to the Brentano-Husserlian theory of judgment – an account of judgments as ways of doing things with words in what Reinach called ‘social acts’. (shrink)

This is a review article on Franz Brentano’s Descriptive Psychology published in 1982. We provide a detailed exposition of Brentano’s work on this topic, focusing on the unity of consciousness, the modes of connection and the types of part, including separable parts, distinctive parts, logical parts and what Brentano calls modificational quasi-parts. We also deal with Brentano’s account of the objects of sensation and the experience of time.

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon previous work in this field by evaluating prospects of implementing (...) International Technology Alliance Controlled English (ITACE) as a middleware for ontology editing. We also discuss at length a prototype of a natural language conversational interface application designed to facilitate ontology editing via the formulation of CNL constructs. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition is (...) based in order to allow integration efforts to be applied in similar ways to other EHR applications. We find that an ordinary statement from an EHR contains a surprising amount of “hidden” data that are only revealed by its decomposition according to these principles. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

Historical research has recently made it clear that, prior to Austin and Searle, the phenomenologist Adolf Reinach (1884-1917) developed a full-fledged theory of speech acts under the heading of what he called "social acts". He we consider a second instance of a speech act theory avant la lettre, which is to be found in the common sense philosophy of Thomas Reid (1710-1796). Reid’s s work, in contrast to that of Reinach, lacks both a unified approach and the detailed analyses of (...) pertinent examples. But his writings leave no doubt that he is acutely aware of the very problems concerning language structure and use out of which contemporary speech act theory has evolved and that he goes a good way towards solving these problems in the spirit of the modern theory. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s (...) Logical Investigations, and Husserl, especially in his later writings, was in some respects closer to Kant than were the Neo-Kantians. The contrast between the two philosophers can be illustrated by looking at their view of the objects of judgment; for Lask, as for Kant, judgment can relate to the thing as such only in an indirect way. The world of judgment is a collection of ‘imitations holding a secondary position’. It is cut apart from the plain world of real things by what Lask calls a ‘chasm of artificiality and imagery’. For Husserl, in contrast, the object of judgment is a ‘Sachverhalt’ or state of affairs, something ontologically ‘positive’ in the sense that it is an entity in its own right and does not point beyond itself in the manner of a mere sign or proxy for something else. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...) the ACGT project thus far. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

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. (shrink)