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NIF Data Federation

The NIF Data Federation provides the ability to drill down into individual databases and data sets and return relevant content.  This type of content, part of the so called “hidden Web,” is typically not indexed by existing web search engines.

In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Learn more about registering your resource.

NIF simultaneously queries all the federated databases and datasets through its search interface. The results are displayed under the Data Federation tab and are categorized by data type and nervous system level.  In this way, users can easily step through the content of multiple resources, all from the same interface.

Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the "Professor Icon" professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document.

NIF also has a integegrated virtual databases which combines related data indexed from multiple databases and combine them into one for easier browsing.

Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites.

 

Click to search the data in NIF.

 

NIF Integreated Databases:

  1. NIF Integrated Animal View : Indexes data from Zebrafish International Research Center, Strain reports from Rat Genome Database, Caenorhabditis Genetics Center, and International Mouse Strain Resource  
  2. NIF Integrated Brain Gene Expression View : Indexes data from Gene Expression Nervous System Atlas, Allen Mouse Brain Atlas, and Mouse Genome Institute 
  3. NIF Integrated Disease View : Indexes data from NINDS Disorder List and PubMed Health
  4. NIF Integrated Nervous System Connectivity View : Indexes data from Brain Architecture Management System , Collations of Connectivity data on the Macaque brain, BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal table of Temporal-Lobe.com and UCLA Multimodal Connectivity Database 
  5. NIF Integrated Podcasts View : Indexes data from Brain Science Podcast , Nature Podcast, NeuroPod, Science Podcast, American Journal of Psychiatry Podcast, 60-Second Mind, Science Talk, Gray Matters Radio Series, This Week in Science, Neurology Podcast, and Montreal Neurological Institute Podcast
  6. NIF Integrated Software View : Indexes data from Neuroimaging Informatics Tools and Resources Clearinghouse, Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, and Genetic Analysis Software
  7. NIF Integrated Video View : Indexes data from NIH VideoCasting and Podcasting and JoVE: Journal of Visualized Experiments 
  8. NIF Registry : Database of electronic resources that have been selected by NIF curators, or contributed by the community, as valuable tools for researchers and students in the field of neuroscience

 

The current NIF database federation consists of 100 databases:

  1. 60-Second Mind : Podcast on the latest news in behavior and brain research
  2. Addgene : Online database of plasmids
  3. Aging Gene Database : Database of genes and interventions linked to aging
  4. Allen Brain Atlas : Gene expression data
  5. American Journal of Psychiatry Podcast : Podcast on highlights from each issue of The American Journal of Psychiatry
  6. AntibodyRegistry : A compilation of data submitted from commercial vendors NeuroMab, Labome (aka ExactAntigen) and BioCompare, as well as data submitted to the registry itself
  7. AutDB : Publicly available genetic database for autism spectrum disorders
  8. BAMS : Brain region atlas structure and hierarchy
  9. BAMS Cell : Major brain regions and which cells are contained therein
  10. BAMS Connections : Brain connectivity atlas structure and hierarchy
  11. BAMS Nested Regions : Major brain regions and their relationships
  12. BrainSpan : An atlas of the developing human brain
  13. Biocompare :  Information about antibodies and other products (searched as a part of the AntibodyRegistry)
  14. BMI Platform : Digital archive of BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics
  15. BrainInfo :  Authoritative anatomical information about brain structures, primarily monkey
  16. BrainMaps : Interactive online atlas of multiresolution scanned images with information on brain structure and function
  17. Brain Science Podcast : Poscast featuring the latest books about neuroscience as well as interviews with leading scientists from around the world
  18. Brede : Database of functional neuroimaging scientific articles with Talairach coordinates
  19. Cell: An Image Library :  Public repository of vetted and annotated images, videos, and animations of cells
  20. Cell Centered Database : Microscopy datasets from light and electron microscopy
  21. Cerebellar Platform : Digital archive of mini-reviews, papers, and mathematical models for cerebellar research
  22. CGC : Center that manages genetic stocks and information about Caenorhabditis elegans
  23. CHEBI : Freely available dictionary of molecular entities
  24. ChEMBL :  A database of bioactive drug-like small molecules
  25. ClinicalTrials.gov : Online database of both recruiting and completed clinical trials
  26. CoCoMac : Online database of tracing studies and original descriptions for monkey, mostly Macaque brain connectivity
  27. ConnectomeWIKI : Knowledge base for macro- and mesoscale brain region and brain connectivity information across species
  28. Coriell Cell Repositories : Repositories for researches that provides reagents, cells, cultures, and DNA
  29. CRCNS datasets :  Datasets available to the modeling community through the CRCNS program
  30. CTN : Clinical Trials Network (CTN) Data Share is an electronic environment that allows data from completed clinical trials to be distributed to investigators in order to promote new research, encourage further analyses, and disseminate information to the community
  31. Drugbank :  Detailed affinity, reactivity and synonym information about most drug compounds
  32. Drug Related Gene Database : Gene expression data largely from drug abuse studies
  33. ExactAntigen : Antibody provider
  34. F1000 Posters :  Open access repository of conference posters from across the life sciences and medicine
  35. Gait Dynamics in Neuro-Degenerative Disease Data Base : Records of patients with Parkinson's disease, Huntington's disease or amyotrophic lateral sclerosis 
  36. Gait in Parkinsons Disease : Measures of gait from patients with idiopathic Parkinsons Disease
  37. GAS : an alphabetic listing of software for the gene-mapping community.
  38. Gemma : Online database and software system for the meta-analysis of gene expression data
  39. GeneNetwork : Large array of linked resources and analysis tools for system genetics
  40. Gene Ontology : Standardized representation of gene and its product attributes across species and databases
  41. GENSAT :  Imaging and gene expression data from BAC transgenic mice
  42. GENSAT Retina Project : Online database of confocal stacks to freely download and view using ImageJ or the LSM Image Browser from Zeiss  
  43. GEO : Online database of microarray, next-generation sequencing, and other forms of high-throughput functional genomic data
  44. GARA : Archive of mapping, display, and analysis of 2-deoxyglucose uptake across the entire glomerular layer of the rat olfactory bulb for various odorants
  45. Grants :  Grant information on public and private foundations provided by Research Crossroads
  46. Gray Matters : Radio series on brain topics
  47. HomoloGene : Listing of homologs among the annotated genes, based on an automated detection algorithm
  48. Human Brain Atlas : Database of human brain MRI with stained sections
  49. IBVD : The Internet Brain Volume Database (IBVD) is an online database of brain neuroanatomic volumetric observations
  50. IEDB : Database on  antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species
  51. IMSR : Online database of mouse strains and stocks
  52. Journal of Comparative Neurology Antibody Database : A database of antibody used in papers that are published in the journal and their experimental design
  53. Journal of Visualized Experiments : A peer reviewed, PubMed indexed journal devoted to the publication of biological research in a video format
  54. Ki : Datasbase of Ki (affinity) values between drugs and receptors
  55. MGI :  Comprehensive collection of genomic and associated data on mouse strains
  56. MGI Transgene : MGI Transgene is a list of expression and activity data for recombinase-containing transgenes and knock-in alleles
  57. Microarray Consortium : Online database of publicly available microarray data sets
  58. MNI Podcasts : Podcasts on important issues and showcasing of expert's researches
  59. ModelDB : Database of downloadable neuroscience-related computational models
  60. MPO : Community driven ontology to provide standard terms for mammalian phenotype data
  61. Nature Podcast : A weekly podcast which features highlighted content from the week's edition of Nature
  62. NCBI Gene : Information about nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide from various species
  63. Neurodatabase : Electrophysiological data of mainly single and multiple unit activity experiments 
  64. Neurofed : Contact information for federal employees at NIH, NSF, and military institutes involved in funding neuroscience research
  65. Neurology Podcast : A weekly podcast of content from the Neurology
  66. NeuroMab :  Monoclonal antibody provider
  67. NeuroMorpho.org : Neuronal reconstructions useful for realistic 3D simulations 
  68. NeuronDB :  Cellular properties of major neuronal classes
  69. NeuroPod : Neuroscience podcast from Nature, produced in association with the Dana Foundation
  70. NIH Stem Cells : Data Tables that provide an overview of information about human and mice stem cells
  71. NIH VideoCasting and Podcasting : Videocasts and podcasts on NIH events, seminars, and lectures
  72. NHGRI: National Human Genome Research Institute (NHGRI) is a resource that maintains a list of rare genetic diseases and provides a set of answers for each disease
  73. NIH RePORTER : Online database of funded grants from NIH institutes
  74. NINDS : List of neurological diseases and disorders
  75. NITRC tool registry :  Software tools for neuroimaging
  76. NITRC Image Repository : Image Repository
  77. Novus Biologicals Antibody : Database of antibody
  78. OASIS : Database of MRI data
  79. ODE : Ontological Discovery Environment is a gene-centered database that combines diverse data sets from multiple species and experiment
    types, and allows simple and powerful data sharing publicly or across collaborative groups
  80. OdorMapDB : Database of brain activation foci within the olfactory bulb
  81. OMIM :  Comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes
  82. ORDB : a database of chemosensory receptors and associated information
  83. Physiobank : An archive of well-characterized digital recordings of physiologic signals
  84. Pubmed Health : Database of up-to-date information on diseases, conditions, injuries, drugs, supplements, treatment options, and healthy living
  85. Rat Genome Database :  Database of genetic information, including functional data, disease data, expression data and chromosome location data
  86. Research Crossroads : Database of funding, publication, clinical trial and grant data 
  87. RGD Rat Strain Reports : A comprehensive description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain source
  88. Science Podcast : Podcast on interesting stories in the journal and online
  89. Science Talk : Podcast on the latest developments in science and technology
  90. simTKCore : Simulation toolkit for biological structures
  91. SUMSDB :  Brain activation foci from published studies
  92. SynapseWeb : Portal into the 3D ultrastructure of the brain
  93. T3DB : Toxin and Toxin Target Database (T3DB) is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information
  94. This week in science : Podcasts on explaining recent scientific research and developments
  95. Temporal-lobe.com :  A table of connections in the rat hippocampus and parahippocampal region
  96. UCLA Multimodal Connectivity Database : A web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data
  97. Visiome Platform : Digital archive of mathematical models, experimental stimuli, experimental data, and analytical tools for vision science
  98. WikiPathways : An open, collaborative platform dedicated to the curation of biological pathways
  99. WormBase : An international consortium of biologists and computer scientists dedicated to provide the research community with accurate, current, accessible information on genetics, genomics, and biology of C. elegans and some related nematodes
  100. XNAT : Dataset of human MRI images, from humans of different ages, clinical dementia ratings, and handedness
  101. ZFIN : The Zebrafish Model Organism Database (ZFIN) serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data
  102. ZIRC : A central repository for wild-type and mutant strains of zebrafish (Danio rerio) and for materials and information about zebrafish research

Registering a database to the NIF

If you are a database provider and would like to make your database available through the NIF, we are happy to work with you.  The NIF data federation tools are designed to be easy to use and require minimal effort from the database provider.  Through its level 2 and level 3 tools, NIF can work with many types of data resources, regardless of underlying technology.  For more information on Resource Levels, see Registering a Resource to NIF.  If you have a data set that you would like to see registered, please email curation@neuinfo.org.

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