Bioinformatics This article introduces a measurement ontology for applications to Semantic Web applications, specifically for emerging domains such as microarray analysis. The Semantic Web is the next generation Web of structured data that are automatically shared by software agents, which apply definitions and constraints organized in ontologies to correctly process data from disparate sources. One facet needed to develop Semantic Web ontologies of emerging domains is creating ontologies of concepts that are common to these domains. These general “common-sense” ontologies can be used as building blocks to develop more domain-specific ontologies. However most measurement ontologies concentrate on representing units of measurement and quantities, and not on other measurement concepts such as sampling, mean values, and evaluations of quality based on measurements. In this article, we elaborate on a measurement ontology that represents all these concepts. We present the generality of the ontology, and describe how it is developed, used for analysis and validated.