Relations in biomedical ontologies To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.
Summary. The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using the latter to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by crossreferencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized by other ontologies for cross-product generation. Necessity of a Common Anatomy Reference OntologyGenomes are modified over evolutionary time to produce a diversity of anatomical forms. Understanding the relationship between a genome and its phenotypic outcome requires an integrative approach that synthesizes knowledge derived from the study of biological entities at various levels of granularity, encompassing gene structure and function, development, phylogenetic relationships, and ecology.Many model organism databases collect large amounts of data on the relationship between genetic/genomic variation and morphological phenotypes in databases. Model organism databases standardize the description of morphological phenotypes and gene expression patterns by using types from anatomy ontologies that are specific to their focus species of interest. These ontologies have allowed the model organism databases to group phenotypic and gene expression data pertaining to partic- * Melissa Haendel, Fabian Neuhaus, and David Osumi-Sutherland contributed equally to this chapter.
Abstract. There is a diversity of ontology languages in use, among them OWL, RDF, OBO, Common Logic, and F-logic. Related languages such as UML class diagrams, entity-relationship diagrams and object role modelling provide bridges from ontology modelling to applications, e.g. in software engineering and databases. Another diversity appears at the level of ontology modularity and relations among ontologies. There is ontology matching and alignment, module extraction, interpolation, ontologies linked by bridges, interpretation and refinement, and combination of ontologies. The Distributed Ontology, Modelling and Specification Language (DOL) aims at providing a unified meta language for handling this diversity. In particular, DOL provides constructs for (1) "as-is" use of ontologies formulated in a specific ontology language, (2) ontologies formalised in heterogeneous logics, (3) modular ontologies, and (4) links between ontologies. This paper sketches the design of the DOL language. DOL will be submitted as a proposal within the OntoIOp (Ontology Integration and Interoperability) standardisation activity of the Object Management Group (OMG).
Executive summary ProblemCurrently, there is no agreed on methodology for development of ontologies, and there is no consensus on how ontologies should be evaluated. Consequently, evaluation techniques and tools are not widely utilized in the development of ontologies. This can lead to ontologies of poor quality and is an obstacle to the successful deployment of ontologies as a technology. ApproachThe goal of the Ontology Summit 2013 was to create guidance for ontology developers and users on how to evaluate ontologies. Over a period of four months a variety of approaches were discussed by participants, who represented a broad spectrum of ontology, software, and system developers and users. We explored how established best practices in systems engineering and in software engineering can be utilized in ontology development. ResultsThis document focuses on the evaluation of five aspects of the quality of ontologies: intelligibility, fidelity, craftsmanship, fitness, and deployability. A model for the ontology life cycle is presented, and F. Neuhaus et al. / Communiquéevaluation criteria are presented in the context of the phases of the life cycle. We discuss the availability of tools and the document ends with observations and recommendations. Given the current level of maturity of ontology as an engineering discipline, any results on how to best build and evaluate ontologies have to be considered as preliminary. However, the results achieved a broad consensus across the range of backgrounds, application foci, specialties and experience found in the Ontology Summit community. RecommendationsFor more reliable success in ontology development and use, ontology evaluation should be incorporated across all phases of the ontology life cycle. Evaluation should be conducted against carefully identified requirements; these requirements depend on the intended use of the ontology and its operational environment. For this reason, we recommend the development of integrated ontology development and management environments that support the tracking of requirements for, and the evaluation of, ontologies across all phases of their development and use. Purpose of this documentThe purpose of this document is to advance the understanding and adoption of ontology evaluation practices. Our focus is on the critical relationships between usage requirements, the life cycle of an ontology, evaluation, and the quality of the result.This document is rooted in the 2013 Ontology Summit. Over four months, Summit participants prepared and presented materials, shared references, suggested resources, discussed issues and materials by email list, and met virtually each week for presentations and discussions. This Summit had the focal topic "Ontology Evaluation across the Ontology Lifecycle". This document represents a synthesis of a subset of ideas presented, discussed, and developed over the course of these four months, and reflects the contributions of the Summit's participants and the consensus of the Summit community.The intended audience for th...
Image schemas are recognised as a fundamental ingredient in human cognition and creative thought. They have been studied extensively in areas such as cognitive linguistics. With the goal of exploring their potential role in computational creative systems, we here study the viability of the idea to formalise image schemas as a set of interlinked theories. We discuss in particular a selection of image schemas related to the notion of 'path', and show how they can be mapped to a formalised family of microtheories reflecting the different aspects of path following. Finally, we illustrate the potential of this approach in the area of concept invention, namely by providing several examples illustrating in detail in what way formalised image schema families support the computational modelling of conceptual blending.
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