Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research

Matthias Samwald, Ernest Lim, Peter Masiar, Luis Marenco, Huajun Chen, Thomas Morse, Pradeep Mutalik, Gordon Shepherd, Perry Miller, Kei-Hoi Cheung
2009 Studies in Health Technology and Informatics  
The amount of biomedical data available in Semantic Web formats has been rapidly growing in recent years. While these formats are machine-friendly, user-friendly web interfaces allowing easy querying of these data are typically lacking. We present "Entrez Neuron", a pilot neuron-centric interface that allows for keyword-based queries against a coherent repository of OWL ontologies. These ontologies describe neuronal structures, physiology, mathematical models and microscopy images. The returned
more » ... query results are organized hierarchically according to brain architecture. Where possible, the application makes use of entities from the Open Biomedical Ontologies (OBO) and the 'HCLS knowledgebase' developed by the W3C Interest Group for Health Care and Life Science. It makes use of the emerging RDFa standard to embed ontology fragments and semantic annotations within its HTML-based user interface. The application and underlying ontologies demonstrate how Semantic Web technologies can be used for information integration within a curated information repository and between curated information repositories. It also demonstrates how information integration can be accomplished on the client side, through simple copying and pasting of portions of documents that contain RDFa markup.
pmid:19745321 pmcid:PMC3753668 fatcat:l5m7xkexb5farewthnwcacmw6m