Neuroscience Information Framework

Neuroscience portal

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

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

NIF content can be thought of as a Catalog (NIF Registry) and deep database search (NIF Data Federation)

• The NIF Catalog has the largest listing of NIH-funded, neuroscience-relevant resources, including scientific databases, software tools, experimental reagents and tools, knowledge bases and portals, and other entities identified by the neuroscience research community.

A listing of current resources can be found at www.neuinfo.org/registry

• The NIF Data Federation searches deep database content of over 100 databases including: various NCBI databases (PubMed, Gensat, Entrez Gene, Homologene, GEO) as well as many large and small databases that have something to do with neuroscience including Gemma (microarray data from the nervous system), CCDB & CIL (images of neurons and astrocytes, mainly), GeneNetwork, AgingGenesDB, XNAT, 1000 Functional Connectomes and many more.

• In addition many databases that have very similar types of data have been integrated into 'virtual databases', which combine many databases into one table. For example, the AntibodyRegistry combines data from 200+ vendors, the BrainGeneExpression combines gene expression data from Gensat, Alan Brain, and Mouse Genome Informatics, the Connectivity view combines six databases that have statements about nervous system connectivity, the Integrated Animal view combines data about experimental animal catalogs available to researchers from worms, zebrafish, mice and rats. We add more of these as data are registered, so check back to this page to see the current contents.

• For an exhaustive and up to date list of Databases and Datasets registered to NIF please check this page www.neurolex.org.

External links

• Neuroscience Information Framework (NIF) website
• NIF NeuroLex - The Neuroscience Lexicon
• Neuroscience Information Framework News & Announcements
• Neuroscience Information Framework Facebook Page
• Neuroscience Information Framework Mendeley Group

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