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...mance; and harnessing the power and scalability of database systems to represent ontologies [6]. Solutions to scaling ontology alignment are only starting to emerge. In fact, scalability continues to be one of the grand challenges of ontology construction and use [6] and scaling ontology alignment in particular remains a research area [5]. Some early attempts at scaling ontology alignment include initial elimination of candidates prior to alignment. Typically, light-weight string-based matching has been applied to handle the task of candidate elimination in largescale ontology alignment [19], [9]. The problem with these approaches is that they are comparing lexical qualities of ontological classes instead of semantic qualities. Thus, this approach risks reduced accuracy, in particular, reduced recall. Some of the more successful approaches that use string-based matching to eliminate candidates perform alignment using domain-specific knowledge sources [19], [9]. Use of domain-specific knowledge sources, however, precludes these solutions from performing successful ontology alignment in other domains. At the Ontology Matching workshop in 2008, Paulheim proposed two approaches to enhance...

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...eption in the biomedical domain is the Gene Ontology (Ashburner, et al., 2000), for which the gene products annotated to Gene Ontology terms can be considered instances of the corresponding classes. (=-=Kirsten, et al., 2007-=-) have aligned GO terms across the three hierarchies of GO through the genes products to which they are co-annotated. To our knowledge, our work is the first attempt to align pharmacologic classes wit...

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...ations between concepts from ontologies of our interest (see Section 5 for details). In contrast, SURD shows much better coverage for biomedical ontologies. Instance-based methods (Doan et al., 2004; =-=Kirsten et al., 2007-=-) have been used for finding equivalence relationships between ontologies. However, these techniques cannot be widely applied due to the difficulties in finding common sets of instances shared by onto...

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...ne exception in the biomedical domain is the Gene Ontology (GO) (Ashburner, et al., 2000), for which the gene products annotated to GO terms can be considered instances of the corresponding classes. (=-=Kirsten, et al., 2007-=-) have aligned GO terms across the three hierarchies of GO through the gene products to which they are co-annotated. To our knowledge, our work is the first attempt to align pharmacologic classes with...

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... from another direction based on the divide-and-conquer strategy. In addition, there exist some domain-specific approaches that address matching large ontologies in particular areas (e.g., in biology =-=[34,63]-=- and geography [9]). Usually, they utilize certain light-weight methods to gain initial candidates and use domain knowledge to infer alignments. AOAS [63] is a representative tool that is heavily spec...

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..., Molecular Functions and Biological Processes, and was determined by an instance-based match technique which derives the similarity of two concepts from their associations to the same instances (see =-=[KTR07]-=- for details). Both correspondences have a relatively high similarity value of 0.95 in the last mapping version but significantly differ in their history. The first correspondence (GO:0051016-GO:00037...