15,365 research outputs found
Instance-Based Matching of Large Life Science Ontologies
Ontologies are heavily used in life sciences so that there is increasing value to match different ontologies in order to determine related conceptual categories. We propose a simple yet powerful methodology for instance-based ontology matching which utilizes the associations between molecular-biological objects and ontologies. The approach can build on many existing ontology associations for instance objects like sequences and proteins and thus makes heavy use of available domain knowledge. Furthermore, the approach is flexible and extensible since each instance source with associations to the ontologies of interest can contribute to the ontology mapping. We study several approaches to determine the instance-based similarity of ontology categories. We perform an extensive experimental evaluation to use protein associations for different species to match between subontologies of the Gene Ontology and OMIM. We also provide a comparison with metadata-based ontology matching
How do Ontology Mappings Change in the Life Sciences?
Mappings between related ontologies are increasingly used to support data
integration and analysis tasks. Changes in the ontologies also require the
adaptation of ontology mappings. So far the evolution of ontology mappings has
received little attention albeit ontologies change continuously especially in
the life sciences. We therefore analyze how mappings between popular life
science ontologies evolve for different match algorithms. We also evaluate
which semantic ontology changes primarily affect the mappings. We further
investigate alternatives to predict or estimate the degree of future mapping
changes based on previous ontology and mapping transitions.Comment: Keywords: mapping evolution, ontology matching, ontology evolutio
MultiFarm: A benchmark for multilingual ontology matching
In this paper we present the MultiFarm dataset, which has been designed as a benchmark for multilingual
ontology matching. The MultiFarm dataset is composed of a set of ontologies translated in different
languages and the corresponding alignments between these ontologies. It is based on the OntoFarm dataset, which has been used successfully for several years in the Ontology Alignment Evaluation Initiative (OAEI). By translating the ontologies of the OntoFarm dataset into eight different languages – Chinese, Czech, Dutch, French, German, Portuguese, Russian, and Spanish – we created a comprehensive set of realistic test cases. Based on these test cases, it is possible to evaluate and compare the performance of matching approaches with a special focus on multilingualism
Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-based Modules
Large ontologies still pose serious challenges to state-of-the-art ontology alignment systems. In this paper we present an approach that combines a neural embedding model and logic-based modules to accurately divide an input ontology matching task into smaller and more tractable matching (sub)tasks. We have conducted a comprehensive evaluation using the datasets of the Ontology Alignment Evaluation Initiative. The results are encouraging and suggest that the proposed method is adequate in practice and can be integrated within the workflow of systems unable to cope with very large ontologies
Lightweight Ontologies
Ontologies are explicit specifications of conceptualizations. They are often thought of as directed graphs whose nodes represent concepts and whose edges represent relations between concepts. The notion of concept is understood as defined in Knowledge Representation, i.e., as a set of objects or individuals. This set is called the concept extension or the concept interpretation. Concepts are often lexically defined, i.e., they have natural language names which are used to describe the concept extensions (e.g., concept mother denotes the set of all female parents). Therefore, when ontologies are visualized, their nodes are often shown with corresponding natural language concept names. The backbone structure of the ontology graph is a taxonomy in which the relations are “is-a”, whereas the remaining structure of the graph supplies auxiliary information about the modeled domain and may include relations like “part-of”, “located-in”, “is-parent-of”, and many others
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