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.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.
Development of the NIF started in 2008, when the UC 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".Under contract HHSN271200577531C from the NIH administered by NIDAUniversity of California Press Release 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 University of California, San Diego. Together with co-principal investigators Jeffrey S. Grethe and Amarnath Gupta, Martone leads a national collaboration that includes researchers at Yale University, the California Institute of Technology, George Mason University, Harvard University, and Washington University in St. Louis.
Goals
Unlike general search engines, NIF provides much deeper access to a 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.
The NIFSTD, or NIF Standard Ontology contains many of the terms, synonyms and abbreviations useful for neuroscience, as well as dynamic categories such as defined cell classes based on various properties like neuron by neurotransmitter or by circuit role or drugs of abuse according to the National Institutes on Drug Abuse. Any term (with associated synonyms) or dynamic category (all terms with their synonyms) can be used to simultaneously query all of the data that NIF currently indexes, please find several examples below: available data about the hippocampus including synonyms data about parkinson's disease including archaic synonyms like paralysis agitans neocortical neuron a dynamic category includes all neurons that have cell soma in any part of the neocortex
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 (as of April 2013) can be found in the table below. An updated list can be found on the Data Federation page. 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 transgenic or inbred 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 April 9, 2013.
Dataset or Database Name Type
ZFIN Database, Data repository, Image collection Zebrafish International Resource Center Biomaterial supply resource, Antibody supplier, Biomaterial analysis service, Organism supplier, Material storage repository XNAT Central Database, Image collection, Data repository WormBase Database, Data repository, Data analysis service, Software resource Wired Science Blogs Blog, Narrative resource Wired Science Blog WikiPathways Wiki VMD Database, Data analysis service Visiome Platform Database, Video resource, Topical portal, Software repository, Data repository, Image UniProtKB Database, Data repository UCSF Laboratory for Visual Neuroscience Laboratory portal, Image, Video resource UCLA Multimodal Connectivity Database Data repository, Data analysis service, Database This Week In Science Podcast TheScienceJobs.com Job resource, Meeting resource, Workshop The Guardian: Science Weekly Podcast The Guardian: Science Videos Video resource The Guardian: Science Blog, Narrative resource The Daily Scan Narrative resource, Blog The Cell: An Image Library Video resource, Image, Data repository Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat Database TAIR Database, Data repository, Data analysis service, Experimental protocol T3DB Database Synapse Web Atlas, Image collection, Training material SumsDB (Surface Management System Database) and WebCaret Online Visualization Atlas, Database, Data repository, Data analysis service Simtk.org Topical portal, Software resource, Data set, Software repository SGN Database, Data repository, Data analysis service, Source code SGD Database, Data repository, Standard specification, Data analysis service SfN Brain Briefings Narrative resource SFARI Gene: AutDB Database, Data repository SciLogs Blog Scientific American Observations Blog Scientific American Guest Blog Blog Scientific American Cross-Check Blog Scientific American Bering in Mind Blog ScienceNOW Narrative resource ScienceBlogs: Medicine and Health Blog ScienceBlogs: Life Science Blog ScienceBlogs: Brain and Behavior Blog Science Talk Podcast Science Podcast Podcast, Narrative resource Science Careers Job resource, Narrative resource Sciblogs Blog Royal College of Psychiatrists Podcasts Podcast RGD Data repository, Web accessible database, Database, Data analysis service, Organism supplier RetractionWatch.com Blog Retina Project Spatially referenced dataset, Image collection ResearchCrossroads Funding resource, Data repository Research Blogging Blog, Database, Data repository Reactome Database, Data analysis service, Web service, Book QUEST Narrative resource, Community building portal, Podcast, Outreach program, Training material, Training resource, Video resource PubMed Health Database PubChem Web accessible database, Database, Service resource, Data repository, 3D spatial image Psychoactive Drug Screening Program Ki Database Database, Data repository Pseudomonas Genome Database Database, Data analysis service Protocol Online - Your labs reference book Experimental protocol PomBase Database, Data repository PolygenicBlog Blog PLoS Blogs Blog Physiobank Database PharmGKB Web accessible database, Database, Data repository, Web service, Data set PDB Database, 3D spatial image, Web service, Data analysis service, Data repository Oxford Science Blog Blog Open Access Series of Imaging Studies Atlas, Database One Mind Biospecimen Bank Listing Tissue bank, Cell repository, Brain bank, Data repository OMIM Database Olfactory Receptor DataBase Database, Data analysis service, Data repository Olfactory Bulb Odor Map DataBase (OdorMapDB) Atlas, Database Now at NEJM Blog Novus Biologicals Antibody supplier, Biomaterial manufacture, Material resource, Service resource NITRC-IR Image collection, Data repository NITRC Community building portal, Software repository NIMH Chemical Synthesis and Drug Supply Program Reagent manufacture, Reagent supplier NIH VideoCasting Video resource, Podcast, Data repository NIH Neuroscience Microarray Consortium Data analysis service, Database, Data repository NIGMS Human Genetic Cell Repository Cell repository, Biospecimen repository NIF Registry Automated Crawl Data Data set NIF Registry Database NIF Integrated Video View Video resource NIF Integrated Software View Software resource NIF Integrated Podcasts View Podcast NIF Integrated Nervous System Connectivity View Database NIF Integrated Manually Extracted Annotation Data set NIF Integrated Jobs Job resource NIF Integrated Gene-Disease Interaction Database NIF Integrated Disease View Database NIF Integrated Clinical Trials Database NIF Integrated Brain Gene Expression View Database NIF Integrated Blogs Blog, Narrative resource NIF Integrated Auto-Extracted Annotation Data set NIF Integrated Animal View Organism supplier New York Times - Well Blog New Scientist Jobs Job resource, Postdoctoral program resource Neuroskeptic Blog NeuroPod Podcast NeuronDB Database, Data analysis service NeuroMorpho.Org Data repository, Database, Image collection NeuroMab Antibody supplier Neurology Podcast Podcast Neurofed People resource neuroelectro Database Neurodatabase.org Database, Data repository NCBI Protein Database NCBI Gene Web accessible database, Database NCBI Data repository, Data analysis software Naturejobs Job resource, Narrative resource Nature Podcast Podcast Nature Network Blogs Blog Naturally Selected Blog National Institutes of Health Stem Cell Tables Data set National Institutes of Health Research Portfolio Online Reporting Tool Database National Academy of Sciences Podcasts Podcast MPO Ontology Mouse Genome Informatics Transgenes Semi structured knowledge Monster Job resource ModelDB Simulation software, Database, Data repository, Source code MNI Podcasts Podcast Mind Hacks Blog, Book MGI Database, Data repository LabSpaces Narrative resource, Blog, Community building portal, Experimental protocol Kawasaki Disease Dataset2 Data set Kawasaki Disease Dataset1 Data set Journal of Visualized Experiments Journal, Video resource, Experimental protocol Journal of Comparative Neurology Antibody database Database jobs.ac.uk Job resource JCVI CMR Database, Data analysis service IXI dataset Data set, Image collection It Takes 30 Blog, Job resource Internet Brain Volume Database Database, Web service, Data analysis service International Mouse Strain Resource Organism supplier, Data repository Indeed Job resource Immune Epitope Database and Analysis Resource Database, Data analysis service, Web service Human Brain Atlas Atlas, Video resource, Training resource HomoloGene Web accessible database, Database, Service resource