Domain ontologies are now commonly used to enable heterogeneous information resources, such as knowledge-based systems, to communicate with each other. In this article, we present a classification of ontological mismatches, which represent various ways in which knowledge haring can be impeded by different decisions made by the developers of different resources. We address some of the ways in which the complexity of biological knowledge will inevitably lead to such mismatches arising across different resources. As ontological mismatches an limit the potential for knowledge sharing, we assess the potential for the resolution of these problems.
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