Journal
NEUROINFORMATICS
Volume 6, Issue 3, Pages 175-194Publisher
HUMANA PRESS INC
DOI: 10.1007/s12021-008-9032-z
Keywords
Neuroscience Information Framework; NIF standardized; Biomedical Informatics Research Network; Web Ontology Language
Funding
- National Institute on Drug Abuse
- National Institutes of Health
- Department of Health and Human Services [HHSN271200577531C]
- Biomedical Informatics Research Network (BIRN) [U24-RR019701, U24-RR021992, U24-RR021382, U24-RR021760]
- BIRN [U24-RR021992]
- National Center for Research Resources at the National Institutes of Health, U. S. A
- National Institutes of Health [U54 HG004028]
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A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, 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 (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF.
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