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Many ontologies have been developed, each with their own focus, that cover different aspects in their domains (see e.g. in biology and medicine OBO). These ontologies often contain overlapping information. In applications using multiple ontologies it is therefore of interest to be able to align 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 matching strategies, including (combinations of) linguistic matching algorithms, structure-based strategies and algorithms based on machine learning. We also implemented novel filtering strategies. 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. A simple version of SAMBO was integrated in the RepOSE environment and this combination allows for debugging, completing and aligning ontologies. SAMBO was one of the best systems at the Ontology Evaluation Aligment Initiative in 2007-2008.

One of the major challenges in ontology alignment is how to include the user in the alignment process, and this at different stages of the process, such as generation of suggestions and validation. Since 2008 we focused developing a new version of SAMBO that deals with this issue. In addition to the functionality of SAMBO, our session-based SAMBO supports interruptable sessions for computation and user validation of the suggestions, implements preprocessing to reduce the search space for the generation of suggestions, implements recommendation algorithms for recommending the settings for the matching, combination and filtering algorithms, and supports the use of previous validation results in preprocessing, matching and filtering. We also provided requirements for user support in ontology alignment systems.

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When refering to SAMBO, please cite:
Lambrix P, Tan H, SAMBO - A System for Aligning and Merging Biomedical Ontologies, Journal of Web Semantics 4(3):196-206, 2006.

When refering to session-based SAMBO, please cite:
Lambrix P, Kaliyaperumal R, A Session-based Ontology Alignment Approach enabling User Involvement, Semantic Web Journal 8(2):225-251, 2017.
Lambrix P, Kaliyaperumal R, A Session-based Approach for Aligning Large Ontologies, Tenth Extended Semantic Web Conference - ESWC 2013, LNCS 7882, 46-60, 2013.