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The Neuroscience Information Framework is a repertory of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources.

Contents

Description

The Neuroscience Information Framework (NIF) is an initiative of the NIH Blueprint for Neuroscience Research, which was established in 2004 by the National Institutes of Health.[1]

Development of the NIF started in 2008, when the University of California, San Diego School of Medicine obtained an NIH contract to create and maintain "a dynamic inventory of web-based neurosciences data, resources, and tools that scientists and students can access via any computer connected to the Internet".[2][3] The project is headed by Maryann Martone, co-director of the National Center for Microscopy and Imaging Research (NCMIR), part of the multi-disciplinary Center for Research in Biological Systems (CRBS), headquartered at UC San Diego. Together with co-principal investigators Jeffrey S. Grethe and Amarnath Gupta, Martone will lead a national collaboration that includes researchers at Yale University, the California Institute of Technology, George Mason University, and Washington University.

Goals

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 NIF 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. NIF will also provide a registry through which resources providers can disclose availability of resources relevant to neuroscience research. NIF is not intended to be a warehouse or repository itself, but a means for disclosing and locating resources elsewhere available via the web.

Content

Listed resources include databases, software tools, experimental reagents and tools, knowledge bases and portals, and other entities identified by the neuroscience research community. Although NIF continues to be developed, the latest version can be accessed at www.neuinfo.org. NIH has released several program announcements that encourage resource providers to register their resource with NIF.[4]

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. The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience. Neuroinformatics. 2008 Sep;6(3):175-94. Epub 2008 Oct 31. PMID: 18975148 PDF
  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. The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience. Neuroinformatics. 2008 Sep;6(3):149-60. Epub 2008 Oct 23. PMID: 18946742 PDF
  3. Gardner D, Goldberg DH, Grafstein B, Robert A, Gardner EP. Terminology for Neuroscience Data Discovery: Multi-tree Syntax and Investigator-Derived Semantics. Neuroinformatics. 2008 Sep;6(3):161-74. Epub 2008 Oct 29. PMID: 18958630 PDF
  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. 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 PDF
  5. Halavi M, Polavaram S, Donohue DE, Hamilton G, Hoyt J, Smith KP, Ascoli GA. NeuroMorpho.Org Implementation of Digital Neuroscience: Dense Coverage and Integration with the NIF. Neuroinformatics. 2008 Sep;6(3):241-52. Epub 2008 Oct 24. PMID: 18949582 PDF
  6. Marenco L, Ascoli GA, Martone ME, Shepherd GM, Miller PL. The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers. Neuroinformatics. 2008 Sep;6(3):219-27. Epub 2008 Oct 31. PMID: 18975149 PDF
  7. Marenco L, Li Y, Martone ME, Sternberg PW, Shepherd GM, Miller PL. Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework. Neuroinformatics. 2008 Sep;6(3):229-39. Epub 2008 Oct 25. PMID: 18953674 PDF
  8. Müller HM, Rangarajan A, Teal TK, Sternberg PW. Textpresso for Neuroscience: Searching the Full Text of Thousands of Neuroscience Research Papers. Neuroinformatics. 2008 Sep;6(3):195-204. Epub 2008 Oct 24. PMID: 18949581 PDF

More information on related publications can be found on the NIF publications page.

External links

Notes and references

  1. ^ The NIH Blueprint for Neuroscience Research supports the development of new tools, training opportunities, and other resources to assist neuroscientists in both basic and clinical research.
  2. ^ Under contract HHSN271200577531C from the NIH administered by NIDA
  3. ^ University of California Press Release
  4. ^ http://www.neuinfo.org/program_announcements.shtml
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