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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" showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document.

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

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. [Full record]

2. NIF Integrated Brain Gene Expression View : Indexes data from Gene Expression Nervous System Atlas, Allen Mouse Brain Atlas, and Mouse Genome Institute. [Full record]

3. NIF Integrated Disease View : Indexes data from NINDS Disorder List and PubMed Health. [Full record]

4. NIF Integrated Nervous System Connectivity View : Indexes data from Brain Architecture Management System (BAMS), Collations of Connectivity data on the Macaque brain (CoCoMac), BrainMaps, Connectome Wiki, the Hippocampal-Parahippocampal table of Temporal-Lobe.com, UCLA Multimodal Connectivity Database, and Avian Brain Circuitry Database. [Full record]

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, This Week in Science, Neurology Podcast, Montreal Neurological Institute (MNI) Podcast, Biointeractive, National Academy of Sciences Podcast, BrainPod, Science Talk, Royal College of Psychiatrists Podcasts (AKA- Let Wisdom Guide), The Guardian: Science Weekly, All in the Mind. [Full record]

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. [Full record]

7. NIF Integrated Video View : Indexes data from NIH VideoCasting and Podcasting, JoVE: Journal of Visualized Experiments, The Guardian: Science Videos, and Biointeractive. [Full record]

8. NIF Integrated Jobs : Indexes data from Naturejobs, Monster, Indeed, Hays, jobs.ac.uk, New Scientist Jobs, Science Careers, Access-ScienceJobs.co.uk, TheScienceJobs.com, ScienceBlogs: Jobs, and It Takes 30. [Full record]

9. NIF Integrated Blogs : Indexes data from Nature Network Blogs, Wired Science Blogs, The Guardian: Science, It Takes 30, Scientific American Cross-Check, Scientific American Bering in Mind, Research Blogging, CENtral Science, ScienceBlogs: Medicine and Health, ScienceBlogs: Brain and Behavior, ScienceBlogs: Life Science, Scientific American Guest Blog, Scientific American Observations, LabSpaces, PLoS Blogs, Daring Nucleic Adventures - genegeek, H2SO4Hurts - Brian Krueger PhD, Sciblogs, New York Times - Well, RetractionWatch.com, Wired Science, and Genomes Unzipped. [Full record]

 

The NIF's Data Federation consists of the following 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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