Semantic Infrastructure to Enable Collaboration in Ontology Development

In many scientific disciplines, and in biomedicine in particular, researchers rely on ontologies to enable them to annotate and integrate their data. These ontologies are living and constantly evolving artifacts and the ontology authors must rely on their user community to ensure that the coverage of the ontologies is sufficient for annotations and other tasks for which users deploy the ontologies. We have developed a distributed collaborative mechanism to enable users to provide feedback to ontology authors, to request new terms, and to use provisional terms in their applications. The ontology authors can use the same infrastructure to explore this feedback in their ontology-editing environment, to update the ontology, to record their decisions on the users ' requests, and to publish both the updated ontology and the information on how they acted on the requested changes. Specifically, we present the Notes ontology that we use to represent the different types of user feedback and change requests, the service-oriented Notes API to access the information that conforms to this ontology, and the two ontology editing and publishing environments, WebProtégé and NCBO BioPortal, that use this API to provide services for their users