A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

Ontology patterns for the representation of quality changes of cells in time

Background: Cell tracking experiments, based on time-lapse microscopy, have become an important tool in biomedical research. The goal is the reconstruction of cell migration patterns, shape and state changes, and, comprehensive genealogical information from these data. This information can be used to develop process models of cellular dynamics. However, so far there has been no structured, standardized way of annotating and storing the tracking results, which is critical for comparative analysis and data integration. The key requirement to be satisfied by an ontology is the representation of a cell’s change over time. Unfortunately, popular ontology languages, such as Web Ontology Language (OWL), have limitations for the representation of temporal information. The current paper addresses the fundamental problem of modeling changes of qualities over time in biomedical ontologies specified in OWL. Results: The presented analysis is a result of the lessons learned during the development of an ontology, intended for the annotation of cell tracking experiments. We present, discuss and evaluate various representation patterns for specifying cell changes in time. In particular, we discuss two patterns of temporally changing information: n-ary relation reification and 4d fluents.These representation schemes are formalized within the ontology language OWL and are aimed at the support for annotation of cell tracking experiments. We analyze the performance of each pattern with respect to standard criteria used in software engineering and data modeling, i.e. simplicity, scalability, extensibility and adequacy. We further discuss benefits, drawbacks, and the underlying design choices of each approach. Conclusions: We demonstrate that patterns perform differently depending on the temporal distribution of modeled information. The optimal model can be constructed by combining two competitive approaches. Thus, we demonstrate that both reification and 4d fluents patterns can work hand in hand in a single ontology. Additionally, we have found that 4d fluents can be reconstructed by two patterns well known in the computer science community, i.e. state modeling and actor-role pattern

A Mono- and Multi-objective Approach for Recommending Software Refactoring

Les systèmes logiciels sont devenus de plus en plus répondus et importants dans notre société. Ainsi, il y a un besoin constant de logiciels de haute qualité. Pour améliorer la qualité de logiciels, l’une des techniques les plus utilisées est le refactoring qui sert à améliorer la structure d'un programme tout en préservant son comportement externe. Le refactoring promet, s'il est appliqué convenablement, à améliorer la compréhensibilité, la maintenabilité et l'extensibilité du logiciel tout en améliorant la productivité des programmeurs. En général, le refactoring pourra s’appliquer au niveau de spécification, conception ou code. Cette thèse porte sur l'automatisation de processus de recommandation de refactoring, au niveau code, s’appliquant en deux étapes principales: 1) la détection des fragments de code qui devraient être améliorés (e.g., les défauts de conception), et 2) l'identification des solutions de refactoring à appliquer. Pour la première étape, nous traduisons des régularités qui peuvent être trouvés dans des exemples de défauts de conception. Nous utilisons un algorithme génétique pour générer automatiquement des règles de détection à partir des exemples de défauts. Pour la deuxième étape, nous introduisons une approche se basant sur une recherche heuristique. Le processus consiste à trouver la séquence optimale d'opérations de refactoring permettant d'améliorer la qualité du logiciel en minimisant le nombre de défauts tout en priorisant les instances les plus critiques. De plus, nous explorons d'autres objectifs à optimiser: le nombre de changements requis pour appliquer la solution de refactoring, la préservation de la sémantique, et la consistance avec l’historique de changements. Ainsi, réduire le nombre de changements permets de garder autant que possible avec la conception initiale. La préservation de la sémantique assure que le programme restructuré est sémantiquement cohérent. De plus, nous utilisons l'historique de changement pour suggérer de nouveaux refactorings dans des contextes similaires. En outre, nous introduisons une approche multi-objective pour améliorer les attributs de qualité du logiciel (la flexibilité, la maintenabilité, etc.), fixer les « mauvaises » pratiques de conception (défauts de conception), tout en introduisant les « bonnes » pratiques de conception (patrons de conception).Software systems have become prevalent and important in our society. There is a constant need for high-quality software. Hence, to improve software quality, one of the most-used techniques is the refactoring which improves design structure while preserving the external behavior. Refactoring has promised, if applied well, to improve software readability, maintainability and extendibility while increasing the speed at which programmers can write and maintain their code. In general, refactoring can be performed in various levels such as the requirement, design, or code level. In this thesis, we mainly focus on the source code level where automated refactoring recommendation can be performed through two main steps: 1) detection of code fragments that need to be improved/fixed (e.g., code-smells), and 2) identification of refactoring solutions to achieve this goal. For the code-smells identification step, we translate regularities that can be found in such code-smell examples into detection rules. To this end, we use genetic programming to automatically generate detection rules from examples of code-smells. For the refactoring identification step, a search-based approach is used. The process aims at finding the optimal sequence of refactoring operations that improve software quality by minimizing the number of detected code-smells while prioritizing the most critical ones. In addition, we explore other objectives to optimize using a multi-objective approach: the code changes needed to apply refactorings, semantics preservation, and the consistency with development change history. Hence, reducing code changes allows us to keep as much as possible the initial design. On the other hand, semantics preservation insures that the refactored program is semantically coherent, and that it models correctly the domain-semantics. Indeed, we use knowledge from historical code change to suggest new refactorings in similar contexts. Furthermore, we introduce a novel multi-objective approach to improve software quality attributes (i.e., flexibility, maintainability, etc.), fix “bad” design practices (i.e., code-smells) while promoting “good” design practices (i.e., design patterns)

The consistent representation of scientific knowledge : investigations into the ontology of karyotypes and mitochondria

PhD ThesisOntologies are widely used in life sciences to model scienti c knowledge. The engineering of these ontologies is well-studied and there are a variety of methodologies and techniques, some of which have been re-purposed from software engineering methodologies and techniques. However, due to the complex nature of bio-ontologies, they are not resistant to errors and mistakes. This is especially true for more expressive and/or larger ontologies. In order to improve on this issue, we explore a variety of software engineering techniques that were re-purposed in order to aid ontology engineering. This exploration is driven by the construction of two light-weight ontologies, The Mitochondrial Disease Ontology and The Karyotype Ontology. These ontologies have speci c and useful computational goals, as well as providing exemplars for our methodology. This thesis discusses the modelling decisions undertaken as well as the overall success of each ontological model. Due to the added knowledge capture steps required for the mitochondrial knowledge, The Karyotype Ontology is further developed than The Mitochondrial Disease Ontology. Speci cally, this thesis explores the use of a pattern-driven and programmatic approach to bio-medical ontology engineering. During the engineering of our biomedical ontologies, we found many of the components of each model were similar in logical and textual de nitions. This was especially true for The Karyotype Ontology. In software engineering a common technique to avoid replication is to abstract through the use of patterns. Therefore we utilised localised patterns to model these highly repetitive models. There are a variety of possible tools for the encoding of these patterns, but we found ontology development using Graphical User Interface (GUI) tools to be time-consuming due to the necessity of manual GUI interaction when the ontology needed updating. With the development of Tawny- OWL, a programmatic tool for ontology construction, we are able to overcome this issue, with the added bene t of using a single syntax to express both simple and - i - patternised parts of the ontology. Lastly, we brie y discuss how other methodologies and tools from software engineering, namely unit tests, di ng, version control and Continuous Integration (CI) were re-purposed and how they aided the engineering of our two domain ontologies. Together, this knowledge increases our understanding in ontology engineering techniques. By re-purposing software engineering methodologies, we have aided construction, quality and maintainability of two novel ontologies, and have demonstrated their applicability more generally

A framework for analyzing changes in health care lexicons and nomenclatures

Ontologies play a crucial role in current web-based biomedical applications for capturing contextual knowledge in the domain of life sciences. Many of the so-called bio-ontologies and controlled vocabularies are known to be seriously defective from both terminological and ontological perspectives, and do not sufficiently comply with the standards to be considered formai ontologies. Therefore, they are continuously evolving in order to fix the problems and provide valid knowledge. Moreover, many problems in ontology evolution often originate from incomplete knowledge about the given domain. As our knowledge improves, the related definitions in the ontologies will be altered. This problem is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations, and the overreliance on human factors. Also most of the current approaches have been focused on changes within the internal structure of ontologies, and interactions with other existing ontologies have been widely neglected. In this research, alter revealing and classifying some of the common alterations in a number of popular biomedical ontologies, we present a novel agent-based framework, RLR (Represent, Legitimate, and Reproduce), to semi-automatically manage the evolution of bio-ontologies, with emphasis on the FungalWeb Ontology, with minimal human intervention. RLR assists and guides ontology engineers through the change management process in general, and aids in tracking and representing the changes, particularly through the use of category theory. Category theory has been used as a mathematical vehicle for modeling changes in ontologies and representing agents' interactions, independent of any specific choice of ontology language or particular implementation. We have also employed rule-based hierarchical graph transformation techniques to propose a more specific semantics for analyzing ontological changes and transformations between different versions of an ontology, as well as tracking the effects of a change in different levels of abstractions. Thus, the RLR framework enables one to manage changes in ontologies, not as standalone artifacts in isolation, but in contact with other ontologies in an openly distributed semantic web environment. The emphasis upon the generality and abstractness makes RLR more feasible in the multi-disciplinary domain of biomedical Ontology change management

Domain Specific Language for Magnetic Measurements at CERN

CERN, the European Organization for Nuclear Research, is one of the world’s largest and most respected centres for scientific research. Founded in 1954, the CERN Laboratory sits astride the Franco–Swiss border near Geneva. It was one of Europe’s first joint ventures and now has 20 Member States. Its main purpose is fundamental research in partcle physics, namely investigating what the Universe is made of and how it works. At CERN, the design and realization of the new particle accelerator, the Large Hadron Collider (LHC), has required a remarkable technological effort in many areas of engineering. In particular, the tests of LHC superconducting magnets disclosed new horizons to magnetic measurements. At CERN, the objectively large R&D effort of the Technolgy Department/Magnets, Superconductors and Cryostats (TE/MSC) group identified areas where further work is required in order to assist the LHC commissioning and start-up, to provide continuity in the instrumentation for the LHC magnets maintenance, and to achieve more accurate magnet models for the LHC exploitation. In view of future projects, a wide range of software requirements has been recently satisfied by the Flexible Framework for Magnetic Measurements (FFMM), designed also for integrating more performing flexible hardware. FFMM software applications control several devices, such as encoder boards, digital integrators, motor controllers, transducers. In addition, they synchronize and coordinate different measurement tasks and actions

24th International Conference on Information Modelling and Knowledge Bases

In the last three decades information modelling and knowledge bases have become essentially important subjects not only in academic communities related to information systems and computer science but also in the business area where information technology is applied. The series of European – Japanese Conference on Information Modelling and Knowledge Bases (EJC) originally started as a co-operation initiative between Japan and Finland in 1982. The practical operations were then organised by professor Ohsuga in Japan and professors Hannu Kangassalo and Hannu Jaakkola in Finland (Nordic countries). Geographical scope has expanded to cover Europe and also other countries. Workshop characteristic - discussion, enough time for presentations and limited number of participants (50) / papers (30) - is typical for the conference. Suggested topics include, but are not limited to: 1. Conceptual modelling: Modelling and specification languages; Domain-specific conceptual modelling; Concepts, concept theories and ontologies; Conceptual modelling of large and heterogeneous systems; Conceptual modelling of spatial, temporal and biological data; Methods for developing, validating and communicating conceptual models. 2. Knowledge and information modelling and discovery: Knowledge discovery, knowledge representation and knowledge management; Advanced data mining and analysis methods; Conceptions of knowledge and information; Modelling information requirements; Intelligent information systems; Information recognition and information modelling. 3. Linguistic modelling: Models of HCI; Information delivery to users; Intelligent informal querying; Linguistic foundation of information and knowledge; Fuzzy linguistic models; Philosophical and linguistic foundations of conceptual models. 4. Cross-cultural communication and social computing: Cross-cultural support systems; Integration, evolution and migration of systems; Collaborative societies; Multicultural web-based software systems; Intercultural collaboration and support systems; Social computing, behavioral modeling and prediction. 5. Environmental modelling and engineering: Environmental information systems (architecture); Spatial, temporal and observational information systems; Large-scale environmental systems; Collaborative knowledge base systems; Agent concepts and conceptualisation; Hazard prediction, prevention and steering systems. 6. Multimedia data modelling and systems: Modelling multimedia information and knowledge; Contentbased multimedia data management; Content-based multimedia retrieval; Privacy and context enhancing technologies; Semantics and pragmatics of multimedia data; Metadata for multimedia information systems. Overall we received 56 submissions. After careful evaluation, 16 papers have been selected as long paper, 17 papers as short papers, 5 papers as position papers, and 3 papers for presentation of perspective challenges. We thank all colleagues for their support of this issue of the EJC conference, especially the program committee, the organising committee, and the programme coordination team. The long and the short papers presented in the conference are revised after the conference and published in the Series of “Frontiers in Artificial Intelligence” by IOS Press (Amsterdam). The books “Information Modelling and Knowledge Bases” are edited by the Editing Committee of the conference. We believe that the conference will be productive and fruitful in the advance of research and application of information modelling and knowledge bases. Bernhard Thalheim Hannu Jaakkola Yasushi Kiyok