Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research.
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 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.
Samwald
Matthias
M
Digital Enterprise Research Institute, National University of Ireland Galway, IDA Business Park, Lower Dangan, Galway, Ireland. samwald@gmx.at
Lim
Ernest
E
Masiar
Peter
P
Marenco
Luis
L
Chen
Huajun
H
Morse
Thomas
T
Mutalik
Pradeep
P
Shepherd
Gordon
G
Miller
Perry
P
Cheung
Kei-Hoi
KH
D035843:Biomedical Research; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D007256:Information Systems; D020407:Internet; D009488:Neurosciences; D012660:Semantics; D018875:Vocabulary, Controlled