NeuroLex - A dynamic lexicon of neuroscience terms

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 The NeuroLex project, supported by the Neuroscience Information Framework project, is a dynamic lexicon of neuroscience terms. Unlike an encyclopedia, a lexicon provides the meaning of a term, and not all there is to know about it.

The NeuroLex is being constructed to help improve the way that neuroscientists communicate about their data, so that information systems like the NIF can find data more easily and provide more powerful means of integrating data that occur across distributed resources. One of the big roadblocks to data integration in neuroscience is the inconsistent use of terminology in databases and other resources like the literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources. For example, if three databases have information about what genes are expressed in cortex, but they all use different definitions of cerebral cortex, then we cannot compare them easily.

As part of the NIF, we provide a simple search interface to many different sources of neuroscience information and data. To make this search more effective, we are constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g., neuron is a cell. These categories provide the means to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that we use to describe our data, e.g., anatomical terms, techniques, organism names. Because wikis provide an easy interface for communities to contribute their knowledge, we started the NeuroLex.

Authors

Stephen Larson
Jeffrey S. Grethe
Amarnath Gupta
Maryann E. Martone

Associated Institutions

University of California San Diego

Resource URL
Application Domains
  • Biology
  • Clinical
  • Clinical records
  • Domain independent
  • Genomics
  • Literature
  • Metabolomics
  • Proteomics
Other Resource Type
Software Subtype
Programming Languages
Operating Systems
Included Components
Dataset Subtype
  • Human annotated
  • Machine annotated
  • Structured data
  • Unstructured data
Data Model Subtype
Online Resource Subtype
  • Registry / repository
Knowledge Base Subtype
  • Controlled vocabulary
  • Guidelines
  • Ontology
  • Standards
Intended User Types
  • Clinician
  • Clinical researcher
  • Informatics researcher
  • NLP researcher or developer
  • Software developer
Citations

Gupta A, Bug W, Marenco L, Qian X, Condit C, Rangarajan A, Müller HM, Miller PL, Sanders B, Grethe JS, Astakhov V, Shepherd G, Sternberg PW, Martone ME. Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF). Neuroinformatics. 2008 Sep;6(3):205-17. Epub 2008 Oct 29. PMID: 18958629; PMCID: PMC2689790

Available Documentation
  • API
  • Screenshots
  • Text/pictures
  • Tutorial
  • Video
  • Video demonstration
  • Web page/HTML documentation
Licensing Type
Open source