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Welcome to the SAMBO web site.

Many biomedical ontologies have been developed, each with their own focus, that cover different aspects in biology (see e.g. OBO). These ontologies often contain overlapping information. In applications using multiple ontologies it is therefore of interest to be able to merge these ontologies. For instance, companies may want to use community standard ontologies and use them together with company-specific ontologies. Applications may need to use ontologies from different areas or from different views on one area. Ontology builders may want to use already existing ontologies as the basis for the creation of new ontologies by extending the existing ontologies or by combining knowledge from different smaller ontologies. In each of these cases it is important to know the relationships between the terms in the different ontologies. We say that we align two ontologies when we define the relations between terms in the different ontologies. We merge two ontologies when we, based on the alignment relations between the ontologies, create a new ontology containing the knowledge included in the source ontologies.

SAMBO is a system that assists a user in aligning and merging two ontologies in OWL format. The user performs an alignment process with the help of alignment suggestions proposed by the system. The system carries out the actual merging and derives the logical consequences of the merge operations. Regarding the generation of the suggestions we implemented several strategies, including (combinations of) linguistic matching algorithms, structure-based strategies and algorithms based on machine learning. SAMBO also provides a number of reasoning services, such as checking whether the new ontology is consistent, whether there are cycles in the new ontology and whether there are unsatisfiable concepts.

When refering to SAMBO, please cite:
Lambrix P, Tan H, `SAMBO - A System for Aligning and Merging Biomedical Ontologies', Journal of Web Semantics, Special issue on Semantic Web for the Life Sciences, 4(3):196-206, 2006.