NeuroLex

NeuroLex
Content
Description Dynamic lexicon of neuroscience terms in a Semantic wiki
Data types
captured		 Neuroscience
Contact
Authors Maryann Martone, Stephen Larson and others
Access
Website http://neurolex.org/wiki/
Miscellaneous
License
Creative Commons Attribution 3.0 Unported License

NeuroLex is a dynamic lexicon of neuroscience concepts.[1] It is a structured as a semantic wiki, using Semantic MediaWiki. NeuroLex is supported by the Neuroscience Information Framework project.

Overview

The NeuroLex is intended 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 one uses the same terms to mean different things, one 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 one cannot compare them easily.

Utilization within the Neuroscience Information Framework

The NIF enables discovery and access to public research data and tools worldwide through an open source, networked environment. Funded by the NIH Blueprint for Neuroscience Research,[2] the NIF enables scientists and students to discover global neuroscience web resources that cut across traditional boundaries – from experimental, clinical and translational neuroscience databases, to knowledge bases, atlases, and genetic/genomic resources.

Unlike general search engines, NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, search strategies tailored to neuroscience, and access to content that is traditionally “hidden” from web search engines. The Framework is a dynamic inventory of neuroscience databases, annotated and integrated with a unified system of biomedical terminology (i.e. NeuroLex). NIF supports concept-based queries across multiple scales of biological structure and multiple levels of biological function, making it easier to search for and understand the results.

As part of the NIF, a search interface to many different sources of neuroscience information and data is provided. To make this search more effective, the NIF is constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g. stating that a neuron is a cell. This allows users 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 are used to describe data, e.g., anatomical terms, techniques, organism names.

Content

The initial entries in the NeuroLex were built from the NIFSTD ontologies which subsumed an earlier vocabulary BIRNLex. It currently contains concepts that span gross anatomy, cells of the nervous system, subcellular structures, diseases, functions and techniques. NIF is soliciting community input to add more content and correct what is there.

See also

Notes and references

  1. ↑ Initial content for this article was adapted from the NeuroLex project which is licensed under a Creative Commons Attribution License.
  2. ↑ The NIH Blueprint for Neuroscience Research is a cooperative effort among the 16 NIH Institutes, Centers and Offices that support neuroscience research. By pooling resources and expertise, the Blueprint supports the development of new tools, training opportunities, and other resources to assist neuroscientists in both basic and clinical research. Read more about the Blueprint.

Further reading

NIF was featured in the volume 6 number 3 issue in the journal Neuroinformatics in September 2008:

  1. Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME (September 2008). "The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience". Neuroinformatics. 6 (3): 175–94. doi:10.1007/s12021-008-9032-z. PMC 2743139Freely accessible. PMID 18975148. Archived from the original on February 12, 2009. 
  2. Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, Goldberg DH, Grafstein B, Grethe JS, Gupta A, Halavi M, Kennedy DN, Marenco L, Martone ME, Miller PL, Müller HM, Robert A, Shepherd GM, Sternberg PW, Van Essen DC, Williams RW (September 2008). "The neuroscience information framework: a data and knowledge environment for neuroscience". Neuroinformatics. 6 (3): 149–60. doi:10.1007/s12021-008-9024-z. PMC 2661130Freely accessible. PMID 18946742. 
  3. Gardner D, Goldberg DH, Grafstein B, Robert A, Gardner EP (September 2008). "Terminology for neuroscience data discovery: multi-tree syntax and investigator-derived semantics". Neuroinformatics. 6 (3): 161–74. doi:10.1007/s12021-008-9029-7. PMC 2663521Freely accessible. PMID 18958630. 
  4. 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 (September 2008). "Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF)". Neuroinformatics. 6 (3): 205–17. doi:10.1007/s12021-008-9033-y. PMC 2689790Freely accessible. PMID 18958629. 
  5. Halavi M, Polavaram S, Donohue DE, Hamilton G, Hoyt J, Smith KP, Ascoli GA (September 2008). "NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF". Neuroinformatics. 6 (3): 241–52. doi:10.1007/s12021-008-9030-1. PMC 2655120Freely accessible. PMID 18949582. 
  6. Marenco L, Ascoli GA, Martone ME, Shepherd GM, Miller PL (September 2008). "The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers". Neuroinformatics. 6 (3): 219–27. doi:10.1007/s12021-008-9025-y. PMC 2704600Freely accessible. PMID 18975149. 
  7. Marenco L, Li Y, Martone ME, Sternberg PW, Shepherd GM, Miller PL (September 2008). "Issues in the design of a pilot concept-based query interface for the neuroinformatics information framework". Neuroinformatics. 6 (3): 229–39. doi:10.1007/s12021-008-9035-9. PMC 2664632Freely accessible. PMID 18953674. 
  8. Müller HM, Rangarajan A, Teal TK, Sternberg PW (September 2008). "Textpresso for neuroscience: searching the full text of thousands of neuroscience research papers". Neuroinformatics. 6 (3): 195–204. doi:10.1007/s12021-008-9031-0. PMC 2666735Freely accessible. PMID 18949581. 
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