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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.
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 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 Services[]
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 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[]
- ↑ 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.
- ↑ Under contract HHSN271200577531C from the NIH administered by NIDA
- ↑ University of California Press Release
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