Ludger Jansen

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.

Aristoteles unterscheidet zwischen zwei Arten, das Wort „dynaton" zu gebrauchen. Die erste dieser beiden Verwendungsweisen dient zur Zuschreibung von Vermögen (dynaton kata dynamin), die zweite entspricht unserer Verwendung des logisch-alethischen Modaloperators „Es ist möglich, dass" (dynaton ou kata dynamin). Ich argumentiere dafür, dass wichtige Unterschiede zwischen Vermögensprädikationen und Modalaussagen bestehen. Ich nenne mehrere Gründe dafür, dass Vermögensprädikationen keine Modalaussagen sind, zeige aber auch, dass Vermögensprädikationen zwei modale Elemente haben: Sie implizieren erstens nichttriviale Modalaussagen, weil es keine Vermögen für Unmögliches gibt. Und sie implizieren zweitens nichttriviale Aussagen über kontrafaktische Situationen, weil sie Aussagen über kausale Rollen sind.

BACKGROUND The need for detailed description and modeling of cells drives the continuous generation of large and diverse datasets. Unfortunately, there exists no systematic and comprehensive way to organize these datasets and their information. CELDA (Cell: Expression, Localization, Development, Anatomy) is a novel ontology for the association of primary experimental data and derived knowledge to various types of cells of organisms. RESULTS CELDA is a structure that can help to categorize cell types based on species, anatomical localization, subcellular structures, developmental stages and origin. It targets cells in vitro as well as in vivo. Instead of developing a novel ontology from scratch, we carefully designed CELDA in such a way that existing ontologies were integrated as much as possible, and only minimal extensions were performed to cover those classes and areas not present in any existing model. Currently, ten existing ontologies and models are linked to CELDA through the top-level ontology BioTop. Together with 15.439 newly created classes, CELDA contains more than 196.000 classes and 233.670 relationship axioms. CELDA is primarily used as a representational framework for modeling, analyzing and comparing cells within and across species in CellFinder, a web based data repository on cells (http://cellfinder.org). CONCLUSIONS CELDA can semantically link diverse types of information about cell types. It has been integrated within the research platform CellFinder, where it exemplarily relates cell types from liver and kidney during development on the one hand and anatomical locations in humans on the other, integrating information on all spatial and temporal stages. CELDA is available from the CellFinder website: http://cellfinder.org/about/ontology.

Es gibt Staaten und Fußballmannschaften, Fakultäten und Punkbands. Und mansollte meinen, daß diese Entitäten etwas gemeinsam haben, daß sie zu ein und derselben ontologischen Kategorie gehören. Und daß sie sich unterscheiden von Elektronen, Tischen, Grizzlybären, einem Zehn-Euro-Schein, dem neuen Präsidenten, der Amtseinführung des neuen Präsidenten und der Tatsache, daß ich einen Vortrag halte. Mein Ziel ist es, zu zeigen, daß die Kategorie, die alle Beispiele der ersten Gruppe umfaßt, aber keines der zweiten Gruppe, die Kategorie der vereinten Pluralpersonen ist. Um diese These stark zu machen, muß ich zunächst eine Reihe ontologischer Unterscheidungen diskutieren. Zunächst werde ich die Begriffe des Statusobjekts und des Pluralobjekts einführen, zwei relativ neue ontologische Kategorien. Sodann werde ich die traditionellen Kategorien der Substanz und der Person diskutieren, wobei ich mit Hilfe der zuvor eingeführten Begriffe des Statusobjekts und des Pluralobjekts verschiedene Arten von Personen unterscheiden werde. Die natürlichen Personen bilden nur eine dieser Arten, wenn auch die Art von Personen, zu der wir selber als Individuen gehören. Nach diesen Vorarbeiten stehen die Hilfsmittel bereit, die zu Beginn angeführten Beispiele zu kategorisieren.

Statements about the behavior of biological entities, e.g. about the interaction between two proteins, abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that is necessary to take into account in the practice of biomedical ontology engineering. Several concurring formalizations are proposed. Emphasis is laid on the discussion of biological dispositions.

Objectives: Medical decision support and other intelligent applications in the life sciences depend on increasing amounts of digital information. Knowledge bases as well as formal ontologies are being used to organize biomedical knowledge and data. However, these two kinds of artefacts are not always clearly distinguished. Whereas the popular RDF(S) standard provides an intuitive triple-based representation, it is semantically weak. Description logics based ontology languages like OWL-DL carry a clear-cut semantics, but they are computationally expensive, and they are often misinterpreted to encode all kinds of statements, including those which are not ontological. Method: We distinguish four kinds of statements needed to comprehensively represent domain knowledge: universal statements, terminological statements, statements about particulars and contingent statements. We argue that the task of formal ontologies is solely to represent universal statements, while the non-ontological kinds of statements can nevertheless be connected with ontological representations. To illustrate these four types of representations, we use a running example from parasitology. Results: We finally formulate recommendations for semantically adequate ontologies that can efficiently be used as a stable framework for more context-dependent biomedical knowledge representation and reasoning applications like clinical decision support systems.

Like the doctrine of the categories in general, Aristotle’s category of the relative fulfils disparate functions: On the one hand, the category of the pros ti fulfils a dialectic or logical function that aims at the avoidance of fallacies. On the other hand, the category respects the peculiar mode of being of the relative. Taking these two different functions into consideration helps with the interpretation of Aristotle’s two definitions of the relative and his treatment of the properties of the relative in Cat. 7, with the question whether corresponding relatives are of equal priority or ontologically independent, with the genus-species problem , and with the categorical classification of potency and act

There are group-actions, and if actions are intentional, there should also be group-intentions. Who has got these intentions? The groups? This seems to be the natural answer. But then: Groups do not have a mind or brain of there own to form any mental attitude. Different kinds of individualistic analyses of group-intentions have been suggested in the literature. On the one hand there are suggestions to reduce group intentions to a complex of different Iattitudes. John Searle, on the other hand, suggests a special social kind of attitudes, namely we-intentions. We-intentions are being had by individual persons, though they have the form “We intend to do such-and-such”. However, because of the fallibility of Searlian we-intentions and the possibility of ignorance this concept is of no help: We-intentions are neither necessary nor sufficient for group-intentions. In this respect, Margaret Gilbert’s approach is much more successful, though it covers only a special case, namely small-scale informal groups. I suggest a generalised solution in order to cover also large-scale and formal groups.

Tun und Können erläutert und diskutiert den Gründungstext der Modalontologie: das neunte Buch der Metaphysik des Aristoteles. Aristoteles' Thesen und Argumente werden zum ersten Mal in Gänze mit formalen analytischen Mitteln rekonstruiert und auf ihre Kohärenz und Gültigkeit geprüft. Erstmals verwendet der Autor dazu eine adverbiale Analyse von Ausdrücken des Könnens und des Vermögens als Prädikatmodifikatoren. Das Buch zeigt, dass Aristoteles' Theorie der Vermögen nicht nur eine konsistente, sondern auch eine leistungsfähige Analyse von Dispositionen und Dispositionsprädikaten bietet. Die Neuausgabe wurde vollständig durchgesehen und um weiterführende Anhänge ergänzt. Der Inhalt: Können, Tun und Möglichkeit. Eine Einführung • Die kausale Dimension von Vermögen • Die ontologische Dimension von Vermögen• Eine notwendige Bedingung für Vermögen • Hindernisse und Verwirklichung • Prioritätsfragen • Aristotle’s Theory of Dispositions • Das Problem des Neuen • Planners, Deciders, Performers

BACKGROUND In biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. This paper investigates two important subrelations of has_proper_part, viz. the relation has_grain, which relates a collective entity to its multiply occurring uniform parts (e.g., water molecules in a portion of water), and the relation has_component, which relates a compound to its constituents (e.g., molecules to the atoms they consist of). METHOD We distinguish between four kinds of complex entities and characterize them in first order logic. We then discuss whether similar characterizations could be given in description logics, and finally apply the results to mixtures. RESULTS At first sight, collectives and compounds seem to be disjoint categories. Their disjointness, however, relies on agreement about what are uniform entities, and thus on the granularity of description. For instance, the distinction between isomeric subtypes of a molecule can be important in one use case but might be neglected in another one. We demonstrate that, as implemented in the BioTop domain upper level ontology, equivalence or subsumption between different descriptions of same or similar entities cannot be achieved. Using OWL-DL, we propose a new design pattern that avoids primitive subrelations at the expense of more complex descriptions and thus supports the needed inferences.

In 'Metaphysics IX.6' (1048b 18-35) Aristotle presents a test to distinguish between "kinesis" and "energeia," based on relations between the perfective and the imperfective aspect of the verb. This passage has been interpreted as drawing a linguistic distinction between classes of verbs (e.g., stative verbs) by means of a linguistic criterion (Ackrill, Graham). But such an interpretation is in conflict with the text. Aristotle's test must, therefore, be understood as a metaphysical criterion between items in the world (rather than lingual items) by means of a metaphysical criterion, exploiting properties of these items. These items are events, and 'Metaphysics IX.6' exhibits Aristotle's awareness to certain topics discussed in modern event ontology.

BACKGROUND Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current biomedical and cell-biological research. Nevertheless, the large body of published knowledge in this area is underused, as most results are only represented in natural language, impeding their finding, comparison, aggregation, and usage. Scientific understanding of the complex molecular mechanisms underlying cell transitions could be improved by making essential pieces of knowledge available in a formal (and thus computable) manner. RESULTS We describe the outline of two ontologies for cell phenotypes and for cellular mechanisms which together enable the representation of data curated from the literature or obtained by bioinformatics analyses and thus for building a knowledge base on mechanisms involved in cellular reprogramming. In particular, we discuss how comprehensive ontologies of cell phenotypes and of changes in mechanisms can be designed using the entity-quality (EQ) model. CONCLUSIONS We show that the principles for building cellular ontologies published in this work allow deeper insights into the relations between the continuants (cell phenotypes) and the occurrents (cell mechanism changes) involved in cellular reprogramming, although implementation remains for future work. Further, our design principles lead to ontologies that allow the meaningful application of similarity searches in the spaces of cell phenotypes and of mechanisms, and, especially, of changes of mechanisms during cellular transitions.

Wether the chicken or the egg came first, is not only a mind-boggling but a substantial question. Its answer depends on the biological background theory one assumes. I review recent work on the topic (by Teichmann, Sorensen, Waller and Raatzsch) and resolve some of the disputes between these authors by borrowing from Aristotle the distinction between chicken-producing eggs. I then introduce the concept of a quasi-species to make explicit the vagueness involved in species-terms and prove 13 different priority-claims within a Darwinian framework.

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.