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Annotation with security-related metadata enables discovery of resources that meet security requirements. This paper presents the NRL Security Ontology, which complements existing ontologies in other domains that focus on annotation of functional aspects of resources. Types of security information that could be described include mechanisms, protocols, objectives, algorithms, and credentials in various levels of detail and specificity. The NRL Security Ontology is more comprehensive and better organized than existing security ontologies. It is capable of representing more types of security statements and can be applied to any electronic resource. The class hierarchy of the ontology makes it both easy to use and intuitive to extend. We applied this ontology to a Service Oriented Architecture to annotate security aspects of Web service descriptions and queries. A refined matching algorithm was developed to perform requirement-capability matchmaking that takes into account not only the ontology concepts, but also the properties of the concepts.