NeuroLex and The Neuroscience Information Framework: Building comprehensive neuroscience ontologies with and for the community
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1
University of California at San Diego, United States
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.
Conference:
Neuroinformatics 2009, Pilsen, Czechia, 6 Sep - 8 Sep, 2009.
Presentation Type:
Oral Presentation
Topic:
Workshop 2- Ontologies for neuroscience: applications and advances
Citation:
Grethe
JS
(2019). NeuroLex and The Neuroscience Information Framework: Building comprehensive neuroscience ontologies with and for the community.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2009.
doi: 10.3389/conf.neuro.11.2009.08.140
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Received:
30 Jun 2009;
Published Online:
09 May 2019.
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Correspondence:
Jeffrey S Grethe, University of California at San Diego, San Diego, United States, jgrethe@ucsd.edu