The rapid advancement of Artificial Intelligence (AI) and the developments of Large Language Models (LLMs) like Generative Pretrained Transformers (GPTs) have significantly influenced content creation in scholarly communication and across various fields. This paper presents a comparative analysis of the content reliability between human-generated and GPT-generated scholarly articles. Recent developments in AI suggest that GPTs have become capable in generating content that can mimic human language to a greater extent. This highlights and raises questions about the quality, accuracy, and reliability (...) of such content, especially in academic contexts. Statistical evaluations and quantitative assessments conducted in this study uncover key differences in content accuracy, coherence, citation usage, and overall reliability between human and GPT-generated articles. The paper also examines the potential biases, the role of context, and the implications of AI-generated content for the future of scholarly communication. The study concludes with framework for predictive model indicating the potential future impact of GPT-driven content creation and recommendations for ensuring content quality and ethical considerations in AI usage. (shrink)

In this essay, I investigate if self-respect as Robin Dillon conceives of it in her essay “Self-Respect: Moral, Emotional, Political” can be taught if we presuppose Barbara Herman’s theory of moral education. For Dillon, self-respect is a nonpropositionally held and emotionally forged interpretive orientation that determines one’s understanding of oneself. Further, it cannot be reconstituted through reason if it has been damaged. The claim that reason cannot remedy a lack of self-respect in persons is at odds with Herman’s reason-based training (...) in value. I argue that we do not have sufficient grounds to think that Herman’s reason-based training in value cannot help instil Dillon-type self-respect. (shrink)

Arguments attempting to debunk moral beliefs, by showing they are unjustified, have tended to be global, targeting all moral beliefs or a large set of them. Popular debunking arguments point to various factors purportedly influencing moral beliefs, from evolutionary pressures, to automatic and emotionally-driven processes, to framing effects. We show that these sweeping arguments face a debunker’s dilemma: either the relevant factor is not a main basis for belief or it does not render the relevant beliefs unjustified. Empirical debunking arguments (...) in ethics can avoid this predicament, but only if they are refocused on highly selective classes of moral belief. Experimental data can combine with familiar consistency reasoning to reveal that like cases are not being treated alike. Selective debunking arguments are unlikely to yield sweeping sceptical conclusions, but they can lead to rational moral change. (shrink)

An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).

Andrea Kern contends that perceptual experience is perceptual knowledge if our self-consciously held capacity for perceptual knowledge is “perfectly” actualized. I argue that this view requires further justification. First, Kern is unable to support her claim that an awareness of our self-conscious capacity for perceptual knowledge is “contained” in all our perceptions. Second, Kern’s claim that perception includes the idea of the conditions of perception is potentially inconsistent with her denial that perceptual experience enables perceptual knowledge.

The International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.

Can reasoning improve moral judgments and lead to moral progress? Pessimistic answers to this question are often based on caricatures of reasoning, weak scientific evidence, and flawed interpretations of solid evidence. In support of optimism, we discuss three forms of moral reasoning (principle reasoning, consistency reasoning, and social proof) that can spur progressive changes in attitudes and behavior on a variety of issues, such as charitable giving, gay rights, and meat consumption. We conclude that moral reasoning, particularly when embedded in (...) social networks with mutual trust and respect, is integral to moral progress. (shrink)

This paper provisionally offers a way of addressing the predicament of a person who does not feel at home in her own concepts, because these concepts were once forced upon her by a colonial regime. If the goal for a person in such a circumstance is to overcome this alienation through intellectual means, then one way in which this might be accomplished would be to develop a hermeneutics that would enable her to ascertain the alienating aspects of her existing concepts. (...) To this end, I outline a hermeneutical strategy which requires that, in reading the colonizer’s textual tradition, the colonized/ex–colonized person must heuristically presuppose that her current concepts are entirely determined by this tradition unless these concepts can be shown to resist such determination on reflective–systematic grounds. (shrink)

Ayurveda is considered one of the ancient systems of knowledge in India. Various compendiums of Ayurveda i.e., Charaka, Sushruta, or Vagbhatta have enumerated an education system based on Gurukuls i.e., An Educator and their pupils. It is evident from them that a very systematized and organized form of medical education starting from selection to induction and then to effective teaching and training were given during that ancient era. The triad of education viz. Adhyayan (studying), Adhyapan (teaching) and Sambhasha (an argument (...) based on logic) is key to knowledge and the learning process as per Charaka. The selection of students and teachers was based on some set of fixed criteria necessary to be fulfilled. Induction was done prior to admission and proper disciplinary, and ethical rules were practiced. For the development of knowledge and skills in branches of Ayurveda, problems-based case discussion, identification, causes, and treatment of diseases, their principles were taught. Yogya (a set of dummy objects) was used to practice prior to the final surgery. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the (...) context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

By examining and comparing Gandhi’s statement that the Bihar earthquake of 1934 should be seen as divine punishment for the sin of untouchability with a similar claim in Kant’s writings, I argue that while Gandhi and Kant are, broadly speaking, remarkably similar in the way in which they relate morality, religion, and politics in conceptualising the categories of faith and superstition, they also seem to differ in their vocabularies and the propositional content of their respective moral psychologies. However, if we (...) are committed to dialogue across cultures, then the differences between Gandhi and Kant need not preclude reflective conversation between them. (shrink)

In this essay, I investigate one aspect of Kant’s larger theory of the transcendental self. In the Prolegomena, Kant says that the transcendental self can be represented as a feeling of existence. In contrast to the view that Kant errs in describing the transcendental self in this fashion, I show that there exists a strand in Kant’s philosophy that permits us to interpret the representation of the transcendental self as a feeling of existence—as the obscurely conscious and temporally inaccessible modification (...) of the state of the discursive subject, which is built into all the representations of such a subject. I also provide an account of how the transcendental self can be legitimately understood both as an epistemic condition for the possibility of experience as well as the representation of a non-naturalistic feeling of existence. (shrink)

Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various levels of (...) implementation representing different levels of conformity on the part of health care organizations. Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than standard guideline-based management systems. They do justice to the fact 1) that responsibilities within a health care organization are widely shared, and 2) that health care professionals may on different occasions be non-compliant with guidelines for a variety of well justified reasons. The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in its complicated implementation. (shrink)

In one of his earliest dialogues, the Soliloquia, Augustine identifies the liberal arts (disciplinae) with truth (veritas), and employs this somewhat puzzling identification as a premise in his infamous proof of the immortality of the soul (Sol. 2.24). In this paper, I examine Augustine’s argument for this peculiar identification. Augustine maintains both (1) that the constituent propositions of the liberal arts are true, and (2) that the liberal art of dialectic (disciplina disputandi) is the “truth through which all disciplines are (...) true” (Sol. 2.21). I argue that Augustine identifies the liberal arts with truth because (1) the constituent propositions of the liberal arts are learned, and (2) dialectic’s structure is essential to the liberal arts. I further suggest that the subject matter of each liberal art reflects a distinct segment of intelligible reality, that is, the realm of the intelligible Forms. (shrink)

My aim in this essay is to clarify certain issues relating to Kant’s definition of sensation. I will argue that even though sensation can occur in Kant’s system only if the subject is physiologically affected by some kind of object, Kant defines sensation non-referentially, that is, as relating entirely to the subject without reference to the affecting object. In the process, I will also demonstrate that sensation for Kant is the feeling accompanying the non-durational and obscurely conscious alteration or modification (...) in the representational state of the subject. (shrink)

In this paper current author proposes a need for studying intricate differences between psychological aspects, factors, cognitions, affect, behaviour and related dynamics. It can be promoted as a separate branch within the domain of Psychology as Intricacy Psychology. Case history taking for the new Intervention Meditation of current author is proposed in line with capturing such intricacies of the client. The current also proposes to study the intricacies belonging to ‘Self’ as an important factor within his new Intervention Meditation approach. (...) View of Self in line with current author’s new Intervention Meditation is also outlined. This paper is at the initial stage of the series of papers planned to develop his new Intervention Meditation approach which is entirely different from all other meditations in vogue. (shrink)

Samuel Scheffler has argued that people value tradition for its own sake because they view it as accumulated experience, and as playing an important role in forming their personal integrity, structuring their lives, and providing them with a sense of belonging. These reasons, according to Scheffler, are de facto justifications that people offer for choosing to act on purely traditional grounds. In this essay, I argue that these de facto reasons must be supplemented if they are to be seen as (...) de jure rational grounds for valuing tradition for its own sake. Such a supplementation would open up the possibility of articulating a coherent theory of moderate cosmopolitanism. (shrink)

An important part of the Unified Medical Language System (UMLS) is its Semantic Network, consisting of 134 Semantic Types connected to each other by edges formed by one or more of 54 distinct Relation Types. This Network is however for many purposes overcomplex, and various groups have thus made attempts at simplification. Here we take this work further by simplifying the relations which involve the three Semantic Types – Diagnostic Procedure, Laboratory Procedure and Therapeutic or Preventive Procedure. We define operators (...) which can be used to generate terms instantiating types from this selected set when applied to terms designating certain other Semantic Types, including almost all the terms specifying clinical tasks. Usage of such operators thus provides a useful and economical way of specifying clinical tasks. The operators allow us to define a mapping between those types within the UMLS which do not represent clinical tasks and those which do. This mapping then provides a basis for an ontology of clinical tasks that can be used in the formulation of computer-interpretable clinical guideline models. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

Digitisation of research data is widely increasing all around the world because it needs more and development of enormous digital technologies. Data curation services are starting to offer many libraries. Research data curation is the collective invaluable and reusable information of the researchers. Collected data preservation is more important. The majority of the higher education institutes preserved the research data for their students and researchers. It is stored for a long time using various formats. It is called research data preservation. (...) Without proper research data management plan and implementation cannot curate the research data. The aim of the study is to identify the Asian Library and Information Science (LIS) faculties’ experiences in the research data preservation and curation during their research. Data management, curation and preservation all are interlinked. For reuse of the research data; data curation is an essential role. For this research, we adopted a survey method and an online questionnaire was shared with 1400 LIS professionals, belonging to the Asian region but the completed study respondents are 125 university faculties from various Asian countries. The study findings are 76.8 per cent generated statistical data followed by 58.4 per cent textual files. By far, the most preferable data analysis tool is Microsoft Excel 82.4 per cent. Moreover, the result shows that generated data is mostly stored by personal computers and laptop hard disks. This study concludes LIS faculties having adequate skills and knowledge on data curation and preservation even though they are expecting more services from their academic institute …. (shrink)

Wild Wise Weird: The Kingfisher Story Collection is an imaginative anthology that blends whimsical, wise, and strange tales. Filled with adventures, life lessons, and unique insights, it offers engaging and thought-provoking stories for readers of all ages. Perfect for fans of fantasy and the surreal, this collection captivates and inspires.

1. Over the last 50 years or so, and especially over the last few decades, the U.S. and many other societies have undergone a large, rapid, and broad decline in anti-gay attitudes. The magnitude, s...

Individuals come across extreme Uncertainty situations, feeling rounded–up 360 degrees, as if trapped inside Chakra Vyuha (wheel form strategy). For uncertainty is often related to future, the concept of Future Time perspective (FTP) is relied upon for attaining positive states. But FTP is a critical factor which works both positively and negatively depending on other factors intervening. For politicians and businessmen such states of being trapped in Chakra Vyuha, can mean end of their political life or business life. In the (...) current paper, the author describes the introspection of a Subject while he attempted to alter his Future Time perspective. This introspective report further gave clue for Merged Time Perspective or Seamless Time Horizon instead of FTP and also that Regulatory Focus and Resistance To Change need to be combined, coalesced and treated on a single continuum. Current author also has proposed a therapy outline to help businessmen and politicians to come out of devastating situations in which they feel rounded – up by opponents 360 degrees. (shrink)

In this paper, a new Intervention Meditation approach is outlined by the current author. To overcome lack of clarity in defining meditation, a new universal Operational definition of meditation is proposed with elaborative explanation. The new meditation approach has multitude of deeper concepts from Bhagavad Gita and modern psychology and the expert / Guru of the proposed method must be a qualified and experienced before getting trained on this approach specifically. This paper elevates meditation from a casual approach level to (...) a separate systematic branch of psychology level. (shrink)

A Better Ape covers the evolution of morality from the birth of our ape family through the evolution of human species and all the way up to the development of modern societies. In this summary, we highlight several main elements of this account: the co-evolution of morality with intelligence and complex sociality; the role of social institutions and religious morality in the cultural evolution of behaviorally modern humans in prehistory; the increasing complexity of the moral mind through biological evolution in (...) apes, gene-culture co-evolution in various human species, cultural evolution in Homo sapiens, and rational-cultural evolution in recent centuries; and, finally, a cultural evolutionary model of progressive and regressive moral change on which a key factor driving moral progress is social and democratic integration. (shrink)

The present investigation was undertaken to investigate the acute toxicity of cadmium, a heavy metal widely detected in the aquatic environment due to natural effects and anthropogenic activities, in freshwater teleost, Channa punctata (Bloch). The experiments for the bioassay were performed in semi-static test condition according to the standard guidelines. The behavioural changes in the fish were observed for all tested concentrations of the metal. The data obtained for bioassay were analyzed for median lethal concentrations (LC ) of the metal (...) by SPSS computer software. The LC 50 50 values, estimated by SPSS, with 95% confidence level were found to be:20.589 (18.326-23.221), 17.133 (14.840- 19.734), 11.815 (9.696 – 13.850) mg/L and 9.908 (7.635-12381) mg/L for cadmium chloride at 24, 48, 72 and 96 h exposure, respectively. (shrink)

Kant interpreters have contrasting views on what Kant takes to be the basis for human dignity. Several commentators have argued that human dignity can be traced back to some feature of human beings. Others contend that humans in themselves lack dignity, but dignity can be attributed to them because the moral law demands respect for humanity. I argue, alternatively, that human dignity in Kant’s system can be seen to be grounded in the reciprocal relationship between the dignity of the moral (...) law and the dignity inherent in the human constitution. The latter includes the dignity of personhood, construed as rational inner purposiveness, and the dignity of giving oneself the law and striving to follow it. (shrink)

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the (...) way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins. (shrink)

Kant interpreters are divided on the question of whether determinate cognition plays a role in the harmony of the faculties in aesthetic judgement. I provide a ‘non-cognitive’ interpretation that allows Kant’s statements regarding judgements of natural beauty to cohere such that determinate cognition need not be taken to perform any role in such judgements. I argue that, in aesthetic harmony, judgement privileges the free activity of the imagination over the cognizing function of the understanding for the purpose of unifying the (...) object, although the free imagination cannot violate the obscure concepts and principles of ordinary common sense. (shrink)

Kant claims that the transcendental self can be represented as a “feeling of existence” (Gefühl eines Daseins). Some interpreters take this claim to be inconsistent with Kant’s larger theory of self-consciousness. I consider the extent to which two eighteenth-century philosophy texts that Kant knew well - Tetens’ Philosophische Versuche über die menschliche Natur und ihre Entwickelung and Feder’s Logik und Metaphysik - can contribute to our understanding of Gefühl eines Daseins. I point to some continuities between Kant’s characterization of “Gefühl” (...) in Gefühl eines Daseins, and Tetens’ and Feder’s conceptualizations of Selbstgefühl. I show that Gefühl eines Daseins is prima facie consistent with Feder’s clear “I” (or Selbstgefühl) and Tetens’ clear Selbstgefühl; and both Gefühl eines Daseins and clear Selbstgefühl relate to higher cognition. Finally, I discuss whether the notion of Selbstgefühl is compatible with key aspects of Kant’s conceptualization of the self - the transcendental-empirical distinction, and the atemporality of the self. (shrink)

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. (...) For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration. (shrink)

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

This chapter discusses contemporary scientific research on the role of reason and emotion in moral judgment. The literature suggests that moral judgment is influenced by both reasoning and emotion separately, but there is also emerging evidence of the interaction between the two. While there are clear implications for the rationalism-sentimentalism debate, we conclude that important questions remain open about how central emotion is to moral judgment. We also suggest ways in which moral philosophy is not only guided by empirical research (...) but continues to guide it. (shrink)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

Causal models of agents have been used to analyse the safety aspects of machine learning systems. But identifying agents is non-trivial -- often the causal model is just assumed by the modeler without much justification -- and modelling failures can lead to mistakes in the safety analysis. This paper proposes the first formal causal definition of agents -- roughly that agents are systems that would adapt their policy if their actions influenced the world in a different way. From this we (...) derive the first causal discovery algorithm for discovering agents from empirical data, and give algorithms for translating between causal models and game-theoretic influence diagrams. We demonstrate our approach by resolving some previous confusions caused by incorrect causal modelling of agents. (shrink)

In the case of AI, automated systems are making increasingly complex decisions with significant ethical implications, raising questions about who is responsible for decisions made by AI and how to ensure that these decisions align with society's ethical and moral values, both in India and the West. Jonathan Haidt has conducted research on moral and ethical decision-making. Today, solving problems like decision-making in autonomous vehicles can draw on the literature of the trolley dilemma in that it illustrates the complexity of (...) ethical decisions faced in emergency situations, as well as the moral implications of the decisions made. However, a series of moral principles must be understood and cited to avoid insufficient mechanistic explanations. Here we present a compilation of ethical positions both in India and the West. (shrink)

How can we make moral progress on factory farming? Part of the answer lies in human moral psychology. Meat consumption remains high, despite increased awareness of its negative impact on animal welfare. Weakness of will is part of the explanation: acceptance of the ethical arguments doesn’t always motivate changes in dietary habits. However, we draw on scientific evidence to argue that many consumers aren’t fully convinced that they morally ought to reduce their meat consumption. We then identify two key psychological (...) mechanisms—motivated reasoning and social proof—that lead people to resist the ethical reasons. Finally, we show how to harness these psychological mechanisms to encourage reductions in meat consumption. A central lesson for moral progress generally is that durable social change requires socially-embedded reasoning. (shrink)

The present article traces the development of the concept of social justice through different philosophical traditions. The notion and philosophy of 'Justice' is the core of socio-legal and political streams and ethics. The idea of justice is applied not just to individual engagements but to broader aspects such as public policies and laws of the land. Justice is often used in the context of 'righteousness' and as a 'virtue'. Still, it is not easy to define and completely clarify the concept (...) of justice. We can analyse it by employing specific terms, which acquaint us with the best possible understanding of justice. A single definition would not suffice to fulfil our aim of the study. Therefore, in this essay, the author delineates how philosophers and thinkers have theorised 'Justice' throughout ancient, medieval and modern times. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in the (...) WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and (...) formal ontological principles as a first step towards finding answers to this question. (shrink)

Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...) worth investigating whether, by overcoming some of its weaknesses from the point of view of formal-ontological principles, we might not be able to enhance a version of GO which can come even closer to serving the needs of the various communities of biomedical researchers and practitioners. It is accepted that clinical and bioinformatics need to find common ground if the results of data-intensive biomedical research are to be harvested to the full. It is also widely accepted that no single method will be sufficient to create the needed common framework. We believe that the principles-based approach to life-science data integration and knowledge representation must be one of the methods applied. Indeed in dealing with the ontological representation of carcinomas, and specifically of colon carcinomas, we have established that, had GO (and related biomedical ontologies) followed some of the basic formal-ontological principles we have identified (Smith et al. 2004, Ceusters et al. 2004), then the effort required to navigate successfully between clinical and bioinformatics systems would have been reduced. We point here to the sources of ontologically-related errors in GO, and also provide arguments as to why and how such errors need to be resolved. (shrink)

It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different purposes and the (...) separate data-structures which they employ are not conducive to the needed data integration. When we attempt to classify the entities in the domain of proteins, we find ourselves faced with a number of cross-cutting principles of classification. Our question here is: how can we bring together these separate taxonomies in order to describe protein functions? Our proposed answer is: via a careful top-level ontological analysis of the relevant principles of classification, combined with a new framework for the simultaneous manipulation of classifications constructed for different purposes. (shrink)

Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED (...) CT classes with respect to these principles. Our major results are: 31% of these classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with the phenomenon of multiple inheritance. The advantages and limitations of our approach are also discussed. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a (...) way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population. (shrink)

Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...) such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

Outcomes research in healthcare has been a topic much addressed in recent years. Efforts in this direction have been supplemented by work in the areas of guidelines for clinical practice and computer-interpretable workflow and careflow models.In what follows we present the outlines of a framework for understanding the relations between organizations, guidelines, individual patients and patient-related functions. The derived framework provides a means to extract the knowledge contained in the guideline text at different granularities, in ways that can help us (...) to assign tasks within the healthcare organization and to assess clinical performance in realizing the guideline. It does this in a way that preserves the flexibility of the organization in the adoption of the guidelines. (shrink)

There is an unexamined use of words and language in writing and speaking. Philosophy always stresses on argumentation that carries meaning. Wittgenstein even draws pictures of language to relate it to its idea, usage and meaning. This paper, therefore, intends to highlight the relevance of use theory of meaning in Wittgenstein’s philosophy.