We demonstrate the schema and ontology matching tool COMA++. It extends our previous prototype COMA utilizing a composite approach to combine different match algorithms [3]. COMA++ implements significant improvements and offers a comprehensive infrastructure to solve large real-world match problems. It comes with a graphical interface enabling a variety of user interactions. Using a generic data representation, COMA++ uniformly supports schemas and ontologies, e.g. the powerful standard languages W3C XML Schema and OWL. COMA++ includes new approaches for ontology matching, in particular the utilization of shared taxonomies. Furthermore, different match strategies can be applied including various forms of reusing previously determined match results and a so-called fragment-based match approach which decomposes a large match problem into smaller problems. Finally, COMA++ cannot only be used to solve match problems but also to comparatively evaluate the effectiveness of different match algorithms and strategies.

Despite the huge amount of recent research efforts on entity resolution (matching) there has not yet been a comparative evaluation on the relative effectiveness and efficiency of alternate approaches. We therefore present such an evaluation of existing implementations on challenging real-world match tasks. We consider approaches both with and without using machine learning to find suitable parameterization and combination of similarity functions. In addition to approaches from the research community we also consider a state-of-the-art commercial entity resolution implementation. Our results indicate significant quality and efficiency differences between different approaches. We also find that some challenging resolution tasks such as matching product entities from online shops are not sufficiently solved with conventional approaches based on the similarity of attribute values.

Genome-wide expression, sequence and association studies typically yield large sets of gene candidates, which must then be further analysed and interpreted. Information about these genes is increasingly being captured and organized in ontologies, such as the Gene Ontology. Relationships between the gene sets identified by experimental methods and biological knowledge can be made explicit and used in the interpretation of results. However, it is often difficult to assess the statistical significance of such analyses since many inter-dependent categories are tested simultaneously. We developed the program package FUNC that includes and expands on currently available methods to identify significant associations between gene sets and ontological annotations. Implemented are several tests in particular well suited for genome wide sequence comparisons, estimates of the family-wise error rate, the false discovery rate, a sensitive estimator of the global significance of the results and an algorithm to reduce the complexity of the results. FUNC is a versatile and useful tool for the analysis of genome-wide data. It is freely available under the GPL license and also accessible via a web service.