Ontology-based data integration

About: Ontology-based data integration is a research topic. Over the lifetime, 11065 publications have been published within this topic receiving 216888 citations.

Disease Ontology: a backbone for disease semantic integration

Abstract: The Disease Ontology (DO) database (http://disease-ontology.org) represents a comprehensive knowledge base of 8043 inherited, developmental and acquired human diseases (DO version 3, revision 2510). The DO web browser has been designed for speed, efficiency and robustness through the use of a graph database. Full-text contextual searching functionality using Lucene allows the querying of name, synonym, definition, DOID and cross-reference (xrefs) with complex Boolean search strings. The DO semantically integrates disease and medical vocabularies through extensive cross mapping and integration of MeSH, ICD, NCI's thesaurus, SNOMED CT and OMIM disease-specific terms and identifiers. The DO is utilized for disease annotation by major biomedical databases (e.g. Array Express, NIF, IEDB), as a standard representation of human disease in biomedical ontologies (e.g. IDO, Cell line ontology, NIFSTD ontology, Experimental Factor Ontology, Influenza Ontology), and as an ontological cross mappings resource between DO, MeSH and OMIM (e.g. GeneWiki). The DO project (http://diseaseontology.sf.net) has been incorporated into open source tools (e.g. Gene Answers, FunDO) to connect gene and disease biomedical data through the lens of human disease. The next iteration of the DO web browser will integrate DO's extended relations and logical definition representation along with these biomedical resource cross-mappings.

Measuring Similarity between Ontologies

Abstract: Ontologies now play an important role for many knowledge-intensive applications for which they provide a source of precisely defined terms However, with their wide-spread usage there come problems concerning their proliferation Ontology engineers or users frequently have a core ontology that they use, eg, for browsing or querying data, but they need to extend it with, adapt it to, or compare it with the large set of other ontologies For the task of detecting and retrieving relevant ontologies, one needs means for measuring the similarity between ontologies We present a set of ontology similarity measures and a multiple-phase empirical evaluation

The PROMPT suite: interactive tools for ontology merging and mapping

Abstract: Researchers in the ontology-design field have developed the content for ontologies in many domain areas. This distributed nature of ontology development has led to a large number of ontologies covering overlapping domains. In order for these ontologies to be reused, they first need to be merged or aligned to one another. We developed a suite of tools for managing multiple ontologies. These suite provides users with a uniform framework for comparing, aligning, and merging ontologies, maintaining versions, translating between different formalisms. Two of the tools in the suite support semi-automatic ontology merging: IPROMPT is an interactive ontology-merging tool that guides the user through the merging process, presenting him with suggestions for next steps and identifying inconsistencies and potential problems. ANCHORPROMPT uses a graph structure of ontologies to find correlation between concepts and to provide additional information for IPROMPT.

Methodologies, tools and languages for building ontologies: where is their meeting point?

Abstract: In this paper we review and compare the main methodologies, tools and languages for building ontologies that have been reported in the literature, as well as the main relationships among them. Ontology technology is nowadays mature enough: many methodologies, tools and languages are already available. The future work in this field should be driven towards the creation of a common integrated workbench for ontology developers to facilitate ontology development, exchange, evaluation, evolution and management, to provide methodological support for these tasks, and translations to and from different ontology languages. This workbench should not be created from scratch, but instead integrating the technology components that are currently available.

Ontology Mapping: The State of the Art

Abstract: Ontology mapping is seen as a solution provider in today's landscape of ontology research. As the number of ontologies that are made publicly available and accessible on the Web increases steadily, so does the need for applications to use them. A single ontology is no longer enough to support the tasks envisaged by a distributed environment like the Semantic Web. Multiple ontologies need to be accessed from several applications. Mapping could provide a common layer from which several ontologies could be accessed and hence could exchange information in semantically sound manners. Developing such mapping has beeb the focus of a variety of works originating from diverse communities over a number of years. In this article we comprehensively review and present these works. We also provide insights on the pragmatics of ontology mapping and elaborate on a theoretical approach for defining ontology mapping.