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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.

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.

 

The current NIF database federation consists of 63 databases:

  1. Addgene: Online database of plasmids
  2. Aging Gene Database: Database of genes and interventions linked to aging
  3. Allen Brain Atlas: Gene expression data
  4. AntibodyRegistry: A compilation of data submitted from commercial vendors NeuroMab, Labome (aka ExactAntigen) and BioCompare, as well as data submitted to the registry itself
  5. BAMS: Brain region atlas structure and hierarchy
  6. BAMS Connections: Brain connectivity atlas structure and hierarchy
  7. Biocompare:  Information about antibodies and other products (searched as a part of the AntibodyRegistry)
  8. BMI Platform: Digital archive of BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics
  9. Brain Gene Expression: Data about gene expression in brain regions from the following databases: Allen Brain Atlas, Mouse Genome Informatics, and GENSAT
  10. BrainInfo:  Authoritative anatomical information about brain structures, primarily monkey
  11. BrainMaps: Interactive online atlas of multiresolution scanned images with information on brain structure and function
  12. Brede: Database of functional neuroimaging scientific articles with Talairach coordinates
  13. Cell Centered Database: Microscopy datasets from light and electron microscopy
  14. Cerebellar Platform: Digital archive of mini-reviews, papers, and mathematical models for cerebellar research
  15. ClinicalTrials.gov: Online database of both recruiting and completed clinical trials
  16. CoCoMac: Online database of tracing studies and original descriptions for monkey, mostly Macaque brain connectivity
  17. ConnectomeWIKI: Knowledge base for macro- and mesoscale brain region and brain connectivity information across species
  18. CRCNS datasets:  Datasets available to the modeling community through the CRCNS program
  19. 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
  20. Drugbank:  Detailed affinity, reactivity and synonym information about most drug compounds
  21. Drug Related Gene Database: Gene expression data largely from drug abuse studies
  22. ExactAntigen: Antibody provider
  23. GAS: an alphabetic listing of software for the gene-mapping community.
  24. Gemma: Online database and software system for the meta-analysis of gene expression data
  25. GeneNetwork: Large array of linked resources and analysis tools for system genetics
  26. GENSAT:  Imaging and gene expression data from BAC transgenic mice
  27. GENSAT Retina Project: Online database of confocal stacks to freely download and view using ImageJ or the LSM Image Browser from Zeiss  
  28. Grants:  Grant information on public and private foundations provided by Research Crossroads
  29. HomoloGene: Listing of homologs among the annotated genes, based on an automated detection algorithm
  30. IBVD: The Internet Brain Volume Database (IBVD) is an online database of brain neuroanatomic volumetric observations
  31. IMSR: Online database of mouse strains and stocks
  32. Ki: Datasbase of Ki (affinity) values between drugs and receptors
  33. MGI:  Comprehensive collection of genomic and associated data on mouse strains
  34. MGI Transgene: MGI Transgene is a list of expression and activity data for recombinase-containing transgenes and knock-in alleles
  35. MichiganAtlas: Human brain atlas with matching cell stained and MRI sections
  36. Microarray Consortium: Online database of publicly available microarray data sets
  37. ModelDB: Database of downloadable neuroscience-related computational models
  38. Nervous System Connectivity: rain region level connectivity information from the following databases: CoCoMac, BAMS, temporal-lobe.com and ConnectomeWIKI 
  39. Neurodatabase: Electrophysiological data of mainly single and multiple unit activity experiments 
  40. Neurofed: Contact information for federal employees at NIH, NSF, and military institutes involved in funding neuroscience research
  41. NeuroMab:  Monoclonal antibody provider
  42. NeuroMorpho.org: Neuronal reconstructions useful for realistic 3D simulations 
  43. NeuronDB:  Cellular properties of major neuronal classes
  44. 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
  45. 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
  46. NIH RePORTER: Online database of funded grants from NIH institutes
  47. NINDS: List of neurological diseases and disorders
  48. NITRC tool registry:  Software tools for neuroimaging
  49. 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
  50. OdorMapDB: Database of brain activation foci within the olfactory bulb
  51. ORDB: a database of chemosensory receptors and associated information
  52. Rat Genome Database:  Database of genetic information, including functional data, disease data, expression data and chromosome location data
  53. 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
  54. Stem Cell Information: Tables of information about stem cells that have been derived from mice and humans
  55. SUMSDB:  Brain activation foci from published studies
  56. T3DB: Toxin and Toxin Target Database (T3DB) is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information
  57. Temporal-lobe.com:  A table of connections in the rat hippocampus and parahippocampal region
  58. Visiome Platform: Digital archive of mathematical models, experimental stimuli, experimental data, and analytical tools for vision science
  59. WikiPathways: An open, collaborative platform dedicated to the curation of biological pathways
  60. 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
  61. XNAT: Dataset of human MRI images, from humans of different ages, clinical dementia ratings, and handedness
  62. ZFIN: The Zebrafish Model Organism Database (ZFIN) serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data
  63. 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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