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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 and provides many authoritative links throughout the neuroscience portal of wikipedia.

DescriptionEdit

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.

GoalsEdit

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.

ContentEdit

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 150 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. The 'complete' list can be found in the table below.
  • 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 NIF Integrated 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. The table below was updated March 18th, 2012.
Dataset or Database Name Type
60-Second Mind Podcast
Addgene Topical portal,Material storage repository,Biomaterial supply resource
Aging Genes Database Web accessible database
Allen Mouse Brain Atlas Atlas,Database
Antibody Registry Database,Data storage repository
AutDB - An Interface to Autism Research Database,Data storage repository
BAMS Cells NIF Data Federation,Database
BAMS Connectivity Database
BAMS Nested Regions NIF Data Federation,Database
BMI (Brain Machine Interface) Platform Data storage repository,Data set,Database,Bibliography,Atlas,Software repository,Data analysis software,Image
BioGRID Web accessible database,Downloadable Database,Web service,Software resource,Data storage repository
Biocompare Database,Antibody supplier,Video
Biointeractive Training resource,Video,Podcast,Training material
Brain Science Podcast Podcast,Narrative resource
BrainInfo Atlas,Database,Topical portal
BrainMaps.org: High Resolution Brain Atlases Database,Atlas,Data analysis service,Image
BrainSpan: Exon microarray summarized to genes Expression atlas
BrainSpan: Exon microarray summarized to probe sets Expression atlas
BrainSpan: RNA-Seq exons Expression atlas
BrainSpan: RNA-Seq exons summarized to genes Expression atlas
Brede Database Database,Data analysis service
CHEBI Database,Ontology
CRCNS - Collaborative Research in Computational Neuroscience - Data sharing Data set,Data storage repository,Funding resource
Caenorhabditis Genetics Center Organism supplier,Material storage repository,Web accessible database,Standard specification
Cell Centered Database Data storage repository,Database,Image
Cerebellar Platform Database,Software repository,Data storage repository,Data analysis software
ChEMBLdb Web accessible database,Downloadable Database,Web service
Clinical Trials Network (CTN) Data Share Data set,Experimental protocol
Clinicaltrials.gov: A Service Of The National Institutes Of Health Database
CoCoMac (Collations of Connectivity Data on the Macaque Brain) Database,Data visualization software,Data storage repository,Simulation software,Bibliography,Data analysis service
Connectome Wiki Database,Ontology,Wiki,Data storage repository,Knowledge environment resource
Coriell Cell Repositories Cell repository,Biomaterial manufacture,Material storage repository,Topical portal,Database
Disorders index from the National Institute of Neurological Disorders and Stroke (NINDS) Data set
Drug Related Gene Database Database,Data storage repository
DrugBank Database
EEGbase Data storage repository,Database
ExactAntigen / Labome Database,Reagent supplier,Service resource
F1000 Posters Storage service resource,Narrative resource,Analysis service resource
GENSAT - Gene Expression Nervous System Atlas Atlas,Organism supplier,Biomaterial manufacture
GO Database,Ontology,International standard specification,Data storage repository
Gait Dynamics in Neuro-Degenerative Disease Data Base Downloadable Database,Web accessible database
Gait in Parkinsons Disease Downloadable Database
Gemma Database,Data processing software
Gene Expression Omnibus Database,Data storage repository,Service resource,Data set
Gene Weaver Web accessible database,Data analysis service,Computational hosting,Data storage repository
Genetic Analysis Software Data set,Software resource,Software repository
Glomerular Activity Response Archive Database,Image,Data analysis service
Grants.gov Funding resource,Database
Gray Matters Podcast,Narrative resource
HomoloGene Web accessible database,Downloadable Database,Service resource
Immune Epitope Database and Analysis Resource Database,Data analysis service,Web service
International Mouse Strain Resource Database,Organism supplier,Data storage repository
Internet Brain Volume Database Database
Journal of Comparative Neurology Antibody database Downloadable Database
Journal of Visualized Experiments Journal,Video,Experimental protocol
Kawasaki Disease Dataset1 Data set
MGI Database,Data storage repository
MNI Podcasts Podcast
MPO Ontology
ModelDB Simulation software,Database,Data storage repository,Source code
Mouse Genome Informatics Transgenes Semi structured knowledge
NCBI Gene Web accessible database,Downloadable Database
NIF Integrated Animal View Database,Organism supplier
NIF Integrated Brain Gene Expression View Database
NIF Integrated Disease View Database
NIF Integrated Nervous System Connectivity View Database
NIF Integrated Podcasts View Database,Podcast
NIF Integrated Software View Database,Software resource
NIF Integrated Video View Database,Video
NIGMS Human Genetic Cell Repository Cell repository,Material storage repository
NIH Neuroscience Microarray Consortium Biomaterial analysis service,Database,Data storage repository
NIH VideoCasting Video,Podcast,Data storage repository
NITRC - Neuroimaging Informatics Tools and Resources Clearinghouse Community building portal,Database,Software resource,Software repository
NITRC-IR Web accessible database,Image,Data storage repository
National Academy of Sciences Podcasts Podcast
National Institutes of Health Research Portfolio Online Reporting Tool Web accessible database
National Institutes of Health Stem Cell Tables Data set
Nature Podcast Podcast
NeuroMab Antibody supplier
NeuroMorpho.Org Data storage repository,Database,Image
NeuroPod Podcast
Neurodatabase.org Web accessible database,Downloadable Database,Data storage repository,Source code
Neurofed People resource
Neurology Podcast Podcast
Neuron database Database
Novus Biologicals Antibody supplier,Database,Biomaterial manufacture,Material resource,Service resource
OMIM Database
Olfactory Bulb Odor Map DataBase (OdorMapDB) Atlas,Database
Olfactory Receptor DataBase Database,Data analysis service,Data storage repository
One Mind Biospecimen Bank Listing Database,Biomaterial supply resource,Tissue bank,Cell repository,Brain bank,Data storage repository
Physiobank Database
Psychoactive Drug Screening Program Ki Database Database,Data storage repository
PubChem Web accessible database,Downloadable Database,Service resource,Data storage repository,3D spatial image
PubMed Health Database
RGD Data storage repository,Web accessible database,Downloadable Database,Data analysis service
ResearchCrossroads Database,Data storage repository
RetractionWatch.com Bibliographic database,Blog
Science Podcast Podcast,Narrative resource
Science Talk Podcast
SfN Brain Briefings Narrative resource
SimTKCore Simulation software,Software toolkit,Source code
Simtk.org Topical portal,Software resource,Data set,Software repository
SumsDB (Surface Management System Database) and WebCaret Online Visualization Atlas,Database,Data storage repository,Data analysis service
Synapse Web Atlas,Image,Database,Experimental protocol,Bibliography,Training material
Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat Database
The American Journal of Psychiatry Podcast Podcast
The Brain Architecture Management System Database,Ontology,Data storage repository
The Cell: An Image Library Web accessible database,Video,Image,Data storage repository
The Gene Ontology Consortium: AmiGO Software application,Database
The GeneNetwork / WebQTL Database,Data analysis service,Source code
The Human Brain Atlas Atlas,Video,Training material
The NINDS Repository Biomaterial supply resource,Cell repository,Material storage repository,Data resource
The Open Access Series of Imaging Studies Atlas,Database
The Retina Project from GENSAT Spatially referenced dataset,Image
This Week In Science Podcast
Toxin, Toxin-Target Database Database
UCLA Multimodal Connectivity Database Data storage repository,Data analysis service,Data set,Image,Computational hosting
Visiome Platform Database,Video,Topical portal,Software repository,Data storage repository,Image
WikiPathways Database,Knowledge environment resource,Image,Wiki,Web service
WormBase Web accessible database,Downloadable Database,Data storage repository,Data analysis service,Software resource
XNAT Central Database,Image,Data storage repository
ZFIN Web accessible database,Downloadable Database,Data storage repository,Image
Zebrafish International Resource Center Biomaterial supply resource,Antibody supplier,Service resource


Data Via Web ServicesEdit

When data is made public via NIF, it also becomes immediately available via web services. Currently, the data can be queried and pulled as an XML feed and several other sites are now pulling NIF data via services, including DOMEO and Eagle i. Developers can learn how to access data by viewing the WADL file available at http://neuinfo.org/developers

External linksEdit


Notes and referencesEdit

  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
This page uses Creative Commons Licensed content from Wikipedia (view authors).

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