NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation

Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a new recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies. It also can be customized to fit the needs of different scenarios. Ontology Recommender 2.0 combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available.Comment: 29 pages, 8 figures, 11 table

Exploiting the conceptual space in hybrid recommender systems: a semantic-based approach

Tesis doctoral inédita. Universidad Autónoma de Madrid, Escuela Politécnica Superior, octubre de 200

Ontology Ranking: Finding the Right Ontologies on the Web

Ontology search, which is the process of finding ontologies or ontological terms for users’ defined queries from an ontology collection, is an important task to facilitate ontology reuse of ontology engineering. Ontology reuse is desired to avoid the tedious process of building an ontology from scratch and to limit the design of several competing ontologies that represent similar knowledge. Since many organisations in both the private and public sectors are publishing their data in RDF, they increasingly require to find or design ontologies for data annotation and/or integration. In general, there exist multiple ontologies representing a domain, therefore, finding the best matching ontologies or their terms is required to facilitate manual or dynamic ontology selection for both ontology design and data annotation. The ranking is a crucial component in the ontology retrieval process which aims at listing the ‘relevant0 ontologies or their terms as high as possible in the search results to reduce the human intervention. Most existing ontology ranking techniques inherit one or more information retrieval ranking parameter(s). They linearly combine the values of these parameters for each ontology to compute the relevance score against a user query and rank the results in descending order of the relevance score. A significant aspect of achieving an effective ontology ranking model is to develop novel metrics and dynamic techniques that can optimise the relevance score of the most relevant ontology for a user query. In this thesis, we present extensive research in ontology retrieval and ranking, where several research gaps in the existing literature are identified and addressed. First, we begin the thesis with a review of the literature and propose a taxonomy of Semantic Web data (i.e., ontologies and linked data) retrieval approaches. That allows us to identify potential research directions in the field. In the remainder of the thesis, we address several of the identified shortcomings in the ontology retrieval domain. We develop a framework for the empirical and comparative evaluation of different ontology ranking solutions, which has not been studied in the literature so far. Second, we propose an effective relationship-based concept retrieval framework and a concept ranking model through the use of learning to rank approach which addresses the limitation of the existing linear ranking models. Third, we propose RecOn, a framework that helps users in finding the best matching ontologies to a multi-keyword query. There the relevance score of an ontology to the query is computed by formulating and solving the ontology recommendation problem as a linear and an optimisation problem. Finally, the thesis also reports on an extensive comparative evaluation of our proposed solutions with several other state-of-the-art techniques using real-world ontologies. This thesis will be useful for researchers and practitioners interested in ontology search, for methods and performance benchmark on ranking approaches to ontology search