Jeffrey Grethe
Keynote speakers
- Kenji Doya
- Alon Halevy
- Astrid Prinz
- Andrew Schwartz
- Shankar Subramaniam
- Arthur Toga
Workshop speakers
- Bart ter Haar Romeny
- Uri Eden
- Klaus Linkenkaer-Hansen
- Tim Clark
- Alan Ruttenberg
- Jeffrey Grethe
- Arnd Roth
- Wulfram Gerstner
- Peter Hunter
- Markus Diesmann
- Andrey Semin
- Pietro Liò
- Albert Cardona
- Giorgio Ascoli
- Rolf Kötter
Workshop 2, Ontologies for neuroscience: Applications and advances
Jeffrey S. Grethe
Title: NeuroLex and The Neuroscience Information Framework: Building comprehensive neuroscience ontologies with and for the community
University of California at San Diego, San Diego, USA
Abstract: Informatics and new web technologies (e.g. ontologies, social networking and community wikis) are becoming increasingly important to neuroscience researchers. The sharing of research data and information pertaining to resources (i.e. tools, data, materials and people) across a research community adds tremendous value to the efforts of that community. An initiative of the NIH Blueprint for Neuroscience Research, the Neuroscience Information Framework (NIF; http://www.neuinfo.org) enables discovery and access to such public research data, contained in databases and structured web resources (e.g. queryable web services) that are sometimes referred to as the deep or hidden web, and resources through an open source dynamic inventory of neuroscience resources that are annotated and integrated with a unified system of biomedical terminology. The need for such a shared semantic framework for neuroscience has become critically important if individual researchers and automated search agents are to access and utilize the most up-to-date information. To address this need, NIF has created NeuroLex (http://www.neurolex.org), a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data.
This core component of NIF, the NIF Standard (NIFSTD; http://purl.org/nif/ontology/nif.owl) is a set of modular ontologies built from a comprehensive collection of neuroscience terminologies. Each module in NIFSTD covers a distinct orthogonal neuroscience domain such as anatomy, cells, molecules, experimental techniques, and digital resources. NIFSTD is designed to collate existing terminologies into a coherent set of interoperable modules so that neuroscientists do not have to deal with the multiplicity of terminologies currently available. Closely following the best practices of the Open Biomedical Ontologies (OBO) community, NIFSTD is standardized to the same upper level ontologies for biomedical science and promotes reuse and easy extension. In developing the NIFSTD, we strive to balance between the involvement of the neuroscience community for domain expertise and the knowledge engineering community for ontology expertise. To enable broad community contribution to NIFSTD, NeuroLex is available as a wiki that provides an easy entry point for the community. NeuroLex takes advantage of the Semantic Mediawiki open source software to provide an easily accessible interface for viewing and contributing to the lexicon. Community contribution in the develoment and refinement of this lexicon in conjunction with the consistent definition and application of these neuroscience concepts is critical for neuroscience to move forward in the areas of data integration and knowledge discovery.
Bio sketch: Dr. Jeffrey S. Grethe is co-Principal Investigator for the Neuroscience Information Framework (NIF; http://nif.nih.gov) in the Center for Research in Biological Systems (CRBS; http://crbs.ucsd.edu) at the University of California, San Diego. NIF is an open source information framework enabling neuroscientists around the world to access a rich virtual environment identifying neuroscience-relevant data and resources, to advance scientific inquiry leading to new discoveries and treatments of human neurological disorders. Unlike more general search engines, NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, provides search strategies tailored to neuroscience, and also provides access to content that is traditionally "hidden" from web search engines (i.e. the hidden or deep web). Following a B.S. in Applied Mathematics from the University of California, Irvine, he received a doctorate in neurosciences with a focus on neuroinformatics and computational modeling from the University of Southern California. After a post-doc in non-invasive human imaging (PET, MRI, fMRI) at Emory University he joined the fMRI Data Center (fMRIDC) at Dartmouth College. At the fMRIDC (http://www.fmridc.org), he was one of the core members responsible for bringing the Data Center online, the first publicly accessible repository of peer-reviewed fMRI studies. Dr. Grethe then transitioned to the BIRN Coordinating Center at the University of California, San Diego. As the Executive Director for the BIRN Coordinating Center he focused on enabling collaborative research, data sharing and discovery through the application of advanced informatics approaches. This focus continues with his work in NIF.