Ontology engineering is mainly done by domain experts who are specialists in their domain but have, if at all, limited knowledge in logics, computer science, or analytic philosophy. The literature on formal ontologies and biomedical ontologies is neither suited nor intended to serve as an educational resource that would help domain experts to become good ontologists. Existing educational resources focus rather on ontology tools and languages than on good practice. The purpose of the GoodOD guideline is to pave the road (...) for domain experts who want (or need) to become ontology engineers. It pursues the openly pragmatic approach that ontology engineers only need to know ontology theory to the extent which supports the (measurable) outcome of their work. The GoodOD Guideline builds upon given philosophical and methodological principles as well as preexisting tools and resources. In particular (pragmatic) scientific realism, first order logics and its subset OWL-DL (description logics), set theory, an upper-level ontology with high-level categories and a canonic set of relations, constraints which limit the freedom of choice when building coordinate expressions, the ontology editor Protégé 4, a complete DL reasoner, such as HermIT, ontology design patterns, and naming conventions. -/- Given these precepts the guideline contains all the knowledge to be acquired by a user to be able to solve ontology engineering problems in a foreseeable and non-arbitrary way. The didactic concept is to convey the skills not only by theory but also by practical examples. (shrink)

Background -/- Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in (...) the respective approaches, we investigate whether the Action ODP can be embedded into BioTop. We demonstrate that this requires re-interpreting the meaning of classes of the NeOn Action ODP in the light of the precepts of realist ontologies. -/- Results -/- As a result, the re-design required clarifying the ontological commitment of the ODP classes by assigning them to top-level categories. Thus, ambiguous definitions are avoided. Classes of real entities are clearly distinguished from classes of information artifacts. The proposed approach avoids the commitment to the existence of unclear future entities which underlies the NeOn Action ODP. Our re-design is parsimonious in the sense that existing BioTop content proved to be largely sufficient to define the different types of actions and plans. -/- Conclusions -/- The proposed model demonstrates that an expressive upper-level ontology provides enough resources and expressivity to represent even complex ODPs, here shown with the different flavors of Action as proposed in the NeOn ODP. The advantage of ODP inclusion into a top-level ontology is the given predetermined dependency of each class, an existing backbone structure and well-defined relations. Our comparison shows that the use of some ODPs is more likely to cause problems for ontology developers, rather than to guide them. Besides the structural properties, the explanation of classification results were particularly hard to grasp for 'self-sufficient' ODPs as compared with implemented and 'embedded' upper-level structures which, for example in the case of BioTop, offer a detailed description of classes and relations in an axiomatic network. This ensures unambiguous interpretation and provides more concise constraints to leverage on in the ontology engineering process. (shrink)

Background: In order to improve ontology quality, tool- and language-related tutorials are not sufficient. Care must be taken to provide optimized curricula for teaching the representational language in the context of a semantically rich upper level ontology. The constraints provided by rigid top and upper level models assure that the ontologies built are not only logically consistent but also adequately represent the domain of discourse and align to explicitly outlined ontological principles. Finally such a curriculum must take into account the (...) pre-existing skills and knowledge of the target audience. -/- Objective: To develop a well-structured curriculum aligned to the particular requirements of life science professionals, in order to enable them to create logically sound, domain adequate and predicable ontologies using the Web Ontology Language (OWL) in Protégè. -/- Methods: Content selection for the curriculum was based on the literature, pre-existing tutorials, and a guideline for good ontology development (i.e ontology design enhancing domain adequacy, sustainability and interoperability) that drew on the authors previous experiences with large ontology development projects. Learning objectives were formulated according to a needs assessment of the targeted learners, who were students trained in life sciences with basic knowledge and practical skills in computer science. As instructional format we choose an approach with a high amount of practical exercises. The curriculum was first implemented with 24 Students and 7 lecturers/ tutors over 5 full days. The curriculum was evaluated by gathering the participants feedback via a questionnaire. -/- Results: Curricular development produced 16 modules of approximately 2 hours each, which covered basic principles of Applied Ontology, description logic syntax and semantics, as well as best design practices outlined in ontology design patterns and variants of the BioTop upper ontology. An opinion survey based on questionnaires indicated that the participants took advantage from the teaching strategies applied, as they indicated good knowledge gain and acknowledged the relevance of the modules. The difficulty was rated slightly lower. -/- Conclusion: The development of teaching material for principled ontology design and best practices is of crucial importance in order to enhance the quality of biomedical ontologies. Here, we present a curriculum for a week long workshop, leveraging on current educational principles, focusing on interactive hands-on exercises, group interactions, and problem-oriented learning. Whereas evaluation clearly showed the success of this approach, in particular regarding student’s satisfaction, the objective measurement of traceable effects on the quality of the generated ontology, although of much higher interest, has just started. (shrink)

OBJECTIVE: (a) To measure the effect of a guideline-based training on the performance of ontology developers compared with the performance after unspecific training by a competency question based evaluation; and (b) to provide empirical evidence for the applicability of competency questions in formal ontology evaluation in general. BACKGROUND: A close connection between ontology development and ontology evaluation as quality management procedure can been attained with the use of competency questions. Competency questions are often used as a semi-formal specification of requirements (...) for an ontology under development. Hence they can also be used as evaluation instruments, in order to check how far an ontology fulfills these requirements. METHODS: A randomized controlled trial was conducted with two groups of 12 students each. The intervention consisted in a differential guideline-based training on ontology development vs. unspecific training. After a group-specific training focusing on three topics per group, performance of students was assessed with 12 exercises (2 exercises per topic), in which the students had to apply their skills. Different types of competency questions were elaborated for the analysis of the students' ontologies. We used the proportion of correct answers as a measure of ontology quality. RESULTS: On single topic level, the performance of ontology developers increased after guideline-based training for two out of the six topics: it increased from a proportion of 0.46 to 0.63 for the topic Process \& Participation and from 0.44 to 0.53 for the topic Collective Material Entity. In regression analysis, a positive correlation was shown between the performance of students on untrained topics and the performance after specific guideline-based training. Moreover, in multiple regression analysis an overall effect of specific training of 0.09 was calculated (p < 0.1). CONCLUSION: The results show an effect of a specific guideline-based training on the performance of ontology developers compared to the performance after unspecific training by an increase of about 10 \% on the rate of correct competency questions. In addition, this study has shown the general applicability of competency questions in a formal ontology evaluation scenario. However, the study also shows that the training of ontology developers and their performance evaluation is a tedious task. The resulting performance of ontology developers is more dependent on the a priori individual competencies than on the specific acquired skills after training. (shrink)

"La géocritique de Nietzsche permet de comprendre sa pensée grâce aux pays, régions et villes du monde qui comptent pour lui. Outre la France, l'Allemagne et l'Europe, son regard englobe des espaces extra-européens, l'Inde, la Chine et l'Islam. Des données d'actualité l'intéressent autant que les strates historiques, parmi les paysages naturels, la Haute Engadine n'enchante pas moins que la Méditerranée et le désert. Nietzsche fait découvrir les lieux par l'intermédiaire des personnages qui les habitent ou incarnent. Ils peuvent être écrivains, (...) musiciens, peintres, figures mythologiques ou poétiques, fondateurs de religions, hommes d'Etat, etc. Le côte à côte d'observations anthropologiques, esthétiques et philosophiques ainsi que le lien entre espaces et cultures font apparaître, dans un langage souvent imagé, les concepts-clés, à savoir le surhomme, la volonté de puissance et l'éternel retour du même. La démarche nietzschéenne révèle des contrastes et se caractérise par le désir de dépasser les frontières pour accéder à l'interculturalité. Ouvrant des horizons nouveaux, elle reflète aussi l'héritage des Lumières et du classicisme allemand." -- [4ème de couverture]. (shrink)

"Aie le courage de te servir de ton propre entendement!" écrit Immanuel Kant comme réponse à la question de savoir "Qu'est-ce que les Lumières? (Aufklärung)". Ce volume présente quelques exemples de la mise en pratique de son appel du XVIIIe au XXe siècle à travers des thématiques variées : "Les Lumières et leurs ombres", "L'éternel féminin dans l'espace de l'Eros", "La mort de Dieu", "Weimar à l'épreuve", "Antidotes contre la barbarie", "Humour et humanisme". Les auteurs étudiés ont en commun l'expérience (...) de l'exil ou de l'errance, et dans leurs vies la France a joué un rôle non négligeable. Il s'agit de Friedrich Schlegel, Friedrich Nietzsche, Raoul Hausmann, Ernst Cassirer, Lion Feuchtwanger, Max Horkheimer et Theodor W Adorno. Parmi leurs sources d'inspiration figure la philosophie des Lumières mais aussi l'héritage du judaïsme. Le choix des auteurs et des thématiques est certes sélectif et subjectif, mais il fait apparaître quelques reflets des Lumières dans la pensée allemande. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

Schober et al. describe two studies on how survey interview respondents misunderstand interview questions. After answering a survey, participants are given standardized definitions of the questions they have just answered. Even apparently simple questions such as “Have you smoked more than 100 cigarettes?” are interpreted very differently by participants. Moreover, clarifying the meaning of the definitions with the interviewer does not always help resolve the miscommunication.

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

This study described the relationships between academic class and student moral sensitivity and reasoning and between curriculum design components for ethics education and student moral sensitivity and reasoning. The data were collected from freshman (n = 506) and senior students (n = 440) in eight baccalaureate nursing programs in South Korea by survey; the survey consisted of the Korean Moral Sensitivity Questionnaire and the Korean Defining Issues Test. The results showed that moral sensitivity scores in patient-oriented care and conflict were (...) higher in senior students than in freshman students. Furthermore, more hours of ethics content were associated with higher principled thinking scores of senior students. Nursing education in South Korea may have an impact on developing student moral sensitivity. Planned ethics content in nursing curricula is necessary to improve moral sensitivity and moral reasoning of students. (shrink)

Childhood overweight and obesity, especially among migrant children, are current health problems in several European countries. In the present study the prevalence of overweight and obesity among migrant children from Turkey and the former Yugoslavia was documented and compared with that of Austrian children in Vienna. Anthropometric data from 1786 children were collected at the ages of 6, 10 and 15 years. Body mass was estimated by means of the body mass index and percentile curves were used to determine weight (...) status. The prevalence of overweight and obesity was found to be significantly higher among migrant children. Children and adolescents from the former Yugoslavia and Turkish girls exhibited especially high rates of overweight and obesity. Biosocial and cultural factors are discussed as causes of these observations. (shrink)

Die Generation der deutschen Spätaufklärung galt nach ihrer Selbstinterpretation als Vertreter einer neuen Zeit, in der das Bürgertum - die Klasse, mit der sie paktierten, - den künftigen Lauf der Geschichte zu bestimmen habe. Ihre Monatsschrift war das Medium einer Vermittlung zwischen Theorie und Praxis. Indem die Aufklärer das reaktionäre Potential des absolutistischen Staates unterschätzten und den Willen ihres bürgerlichen Publikums zum Selbstdenken überschätz- ten, büssten sie ihre Führungsrolle ein. Staat und Gesellschaft wehrlos ausgeliefert, hat die Generation der Spätaufklärung Aktualität (...) als Paradigma einer gescheiterten Intelligenzschicht. (shrink)

In recent years cultural definitions of »gender« have had extraordinary institutional success. This paper analyses visual worlds that have been motivated by constructivist gender concepts that often display a pronounced symmetry. It relates them to competing images which present difference as scandal, as a mirrored form of the self, or as figurations, and which politicize a-symmetrical forms. The study looks into the social condition of publicity that is constituted by such »picture acts«.

Conversational partners' representations may be less aligned than they appear even when interlocutors believe they have successfully understood each other, as data from a series of experiments on surveys about facts and behaviors suggest. Although the goal of a mechanistic psychology of dialogue is laudable, the ultimate model is likely to require far greater specification of individual and contextual variability.

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)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

This work presents the concepts of translation and conservative translation between logics. By using algebraic semantics we introduce several conservative translations involving the classical propositional calculus and the many-valued calculi of Post and Lukasiewicz.

RésuméLa croyance que l'on est (ou pas) dans un état de douleur est singulière en ceci qu'elle semble pouvoir être qualifiée d'infaillibilité ou d'incorrigibilité logique, de même que le cogito. Mais comment se peut-il que l'existence d'une croyance (vraie) et l'existence du fait qui est l'objet de cette croyance puisssent constituer la même existence? Je propose ici une réponse à cette question. Parfois, une croyance peut être un désir.