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The field of biomedicine has embraced the Semantic Web probably more than any other field. As a result, there is a large number of biomedical on-tologies covering overlapping areas of the field. We have developed BioPortal— an open community-based repository of biomedical ontologies. We analyzed on-tologies and terminologies in BioPortal and the Unified(More)
Creating mappings between concepts in different ontologies is a critical step in facilitating data integration. In recent years, researchers have developed many elaborate algorithms that use graph structure, background knowledge, machine learning and other techniques to generate mappings between ontologies. We compared the performance of these advanced(More)
BACKGROUND Ontologies in biomedicine facilitate information integration, data exchange, search and query of biomedical data, and other critical knowledge-intensive tasks. The OBO Foundry is a collaborative effort to establish a set of principles for ontology development with the eventual goal of creating a set of interoperable reference ontologies in the(More)
When three or more ontologies have been aligned, longer chains of mapped concepts start to appear. In this paper, we empirically study the nature of these composite mappings, focusing on chains of (near) equivalence links of length two. We ask human experts to evaluate samples of composite map-pings, taken from large real life data sets. Based on these(More)
The problem of ontology modularization is an active area of research in the Semantic Web community. With the emergence and wider use of very large ontologies, in particular in fields such as biomedicine, more and more application developers need to extract meaningful modules of these ontologies to use in their applications. Researchers have also noted that(More)
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