This medium ITR project will develop a framework to facilitate science research and education on the semantic web, and will implement and evaluate prototype tools and applications for use in the biocomplexity and biodiversity domains. These capabilities include the ability to collaborate and convey meaning through the automatic and semi-automatic semantic annotation of web documents; to improve information retrieval using background knowledge and inference; and to extract and fuse information from multiple, heterogeneous sources in response to a query. A testbed for prototyping these capabilities will be the web portal of the National Biological Information Infrastructure (www.nbii.org/). The framework will include specifications for ontologies, protocols, agents, and tools for authoring, automated ingest, and annotation. These tools will leverage collaboratively constructed ontologies to bring diverse communities together and enable community construction of scientific knowledge. Additional domain-independent, general purpose ontologies will be developed to enable metadata about the contents and structure of databases and other knowledge repositories to be expressed in emerging knowledge markup languages such as RDF and OWL. This will enable agents to both access and index the hidden web, and will also support the data mining of diverse and distributed databases.
