OWL Change Management Patterns

ISSN 1613-0073International audienceOntology evolution is a complex problem. In our work, we focus on issues related to change management, particularly consistency maintenance and we present in this paper, an overview of Change Management Patterns (CMP) that we have defined to model the three dimensions change, inconsistency and resolution alternative. Modelling these patterns and the links between them, helps to propose an automated process guiding and controlling change application while maintaining consistency of the evolved ontology. Change management depends closely on the ontology representation model, we focus on OWL language and we consider change impact on logical consistency as specified in OWL DL layer

Age and sex-selective predation moderate the overall impact of predators

© 2014 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society. Acknowledgements: Thanks to J. Reid, S. Redpath, A. Beckerman and an anonymous reviewer for their helpful comments on a previous version of the manuscript. This work was partly funded by a Natural Environment Research Council studentship NE/J500148/1 to SH and a grant NE/F021402/1 to XL and by Natural Research Limited. Forest Research funded all the fieldwork on goshawks, tawny owls and field voles during 1973–1996. We thank B. Little, P. Hotchin, D. Anderson and all field assistants for their help with data collection and Forest Enterprise, T. Dearnley and N. Geddes for allowing and facilitating work in Kielder Forest. In addition, we are grateful to English Nature and the BTO for kindly issuing licences annually visit goshawk nest sites. Data accessibility: All data associated with the study which have not already been given in the text are available from the Dryad Digital Repository: http://doi.org/10.5061/dryad.h1289 (Hoy et al. 2014).Peer reviewedPublisher PD

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

Guidelines for a Dynamic Ontology - Integrating Tools of Evolution and Versioning in Ontology

Ontologies are built on systems that conceptually evolve over time. In addition, techniques and languages for building ontologies evolve too. This has led to numerous studies in the field of ontology versioning and ontology evolution. This paper presents a new way to manage the lifecycle of an ontology incorporating both versioning tools and evolution process. This solution, called VersionGraph, is integrated in the source ontology since its creation in order to make it possible to evolve and to be versioned. Change management is strongly related to the model in which the ontology is represented. Therefore, we focus on the OWL language in order to take into account the impact of the changes on the logical consistency of the ontology like specified in OWL DL

Drawing OWL 2 ontologies with Eddy the editor

In this paper we introduce Eddy, a new open-source tool for the graphical editing of OWL~2 ontologies. Eddy is specifically designed for creating ontologies in Graphol, a completely visual ontology language that is equivalent to OWL~2. Thus, in Eddy ontologies are easily drawn as diagrams, rather than written as sets of formulas, as commonly happens in popular ontology design and engineering environments. This makes Eddy particularly suited for usage by people who are more familiar with diagramatic languages for conceptual modeling rather than with typical ontology formalisms, as is often required in non-academic and industrial contexts. Eddy provides intuitive functionalities for specifying Graphol diagrams, guarantees their syntactic correctness, and allows for exporting them in standard OWL 2 syntax. A user evaluation study we conducted shows that Eddy is perceived as an easy and intuitive tool for ontology specification