A Portal to the Semantic Web of Neuroscience

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Project Description: As the need for neuroscience data integration is growing and the number of neuroscientific datasets available in RDF/OWL format is increasing, we are presently at the neuroinformatics frontier of exploring the full potential of Semantic Web technologies in enabling integrative neuroscience research (including translational research) that requires integration of diverse types of neuroscientific data provided by different sources in heterogeneous formats. As a pilot project, we have developed a prototype Web application called "Entrez Neuron" that allows the user to perform keyword searches for neuron-related information across multiple data sources (OWL ontologies) including SenseLab (NeuronDB and ModelDB) ontologies and CCDB (Cell Centered Database) ontologies. To expand this pilot application, we are prototyping a Semantic Web portal that allows semantic mashup of diverse types of data in neuroscientifically meaningful ways. To achieve this, we propose to include additional data/ontology sources and create different facets that represent user-centric aspects (or views) of ontologies. For example, "Entrez Neuron" features a "brain region/neuron" facet for organizing query results (about neurons) based on anatomical structure. Such a hierarchical structure is intuitive to neuroscientists, while benefiting from the machine use of ontologies in terms of querying, organizing, and integrating data. Additional facets that we are implementing/considering include (but not limited to) drug, disease, pathway, phenotype, gene functions, etc.

Project Members: Kei-Hoi Cheung, Matthias Samwald, Ernest Lim, Luis Marenco, Peter Masiar, Thomas Morse, Pradeep Mutalik, Huajun Chen, Perry Miller, Gordon Shepherd

Acknowledgment: We would like to thank Dr. Maryann Martone and Willy WaiHo Wong for providing the OWL ontologies of the CCDB database and assisting with their integration into Entrez Neuron. Also, we would like to thank Dr. Bryan Roth for letting us convert the PDSP database into the corresponding OWL ontology. Last but not least, we would like to thank Melliyal Annamalai and Alan Wu from Oracle Corporation for their technical assistance.