Extending an ontology alignment system with BioPortal: a preliminary analysis

Ontology alignment (OA) systems developed over the past decade produced alignments by using lexical, structural and logical similarity measures between concepts in two different ontologies. To improve the OA process, string-based matchers were extended to look up synonyms for source and target concepts in background or external knowledge sources such as general purpose lexicons, for example, WordNet.3 Other OA systems such as SAMBO [8] and ASMOV [6] applied this approach but with specialized background knowledge, i.e. the UMLS Metathesaurus,4 for the anatomy track of the Ontology Alignment Evaluation Initiative5 (OAEI). Then a composition-based approach was proposed to use background knowledge sources such as Uberon6 and the Foundational Model of Anatomy7 (FMA) as intermediate ontologies [5] for the anatomy track. Here source concepts and target concepts are first mapped to the intermediate background ontology. If source and target concepts map to an exact match in the intermediate ontology, a mapping can be made between them. Other OA systems also followed with a composition-based approach using Uberon [1, 2]. One issue on the use of background knowledge sources is determining the best knowledge source on which to use these various alignment techniques. Previous OA systems using specialized knowledge sources have pre-selected specific biomedical ontologies such as Uberon for the anatomy track. As a coordinated community effort, BIOPORTAL [3, 4] provides access to more than 370 biomedical ontologies, synonyms, and mappings between ontology entities via a set of REST services.8 By tapping into this resource, an OA system has access to the full range of these ontologies, including Uberon and many of the ontologies integrated in the UMLS Metathesaurus. Since BioPortal has not been exploited in the context of the OAEI, this paper examines two practical uses of BIOPORTAL as a generalized yet also specialized background knowledge source for the biomedical domain. We provide a preliminary investigation of the results of these two uses of BIOPORTAL in the OAEI’s anatomy track using the LogMap system [7].