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.

 

The current NIF database federation consists of 58 databases:

1. Addgene: Online database of plasmids to sell and distribute
2. Aging Gene Database: Database of genes and interventions linked to aging
3. Allen Brain Atlas: Gene expression data
4. AntibodyTable: A compilation of data submitted from most antibody vendors to Labome (aka ExactAntigen) and BioCompare
5. BAMS: Brain region atlas structure and hierarchy
6. BAMS Connections: Brain connectivity atlas structure and hierarchy
7. BMI Platform: Digital archive of BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics
8. Brain Gene Expression: A view into three very large databases that all contain data about gene expression in brain regions
9. BrainInfo:  General information about brain structures
10. BrainMaps: Interactive online atlas of multiresolution scanned images with information on brain structure and function
11. Brede: Database of functional neuroimaging scientific articles with Talairach coordinates
12. Cell Centered Database: Microscopy datasets from light and electron microscopy
13. Cerebellar Platform: Digital archive of mini-reviews, papers, and mathematical models for cerebellar research
14. Chemoreceptors: ORDB database of chemosensory receptors and associated information
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. Drugbank:  Information on drugs
20. DrugDependentGene Database: Online database of resources relevant to drug abuse research
21. ExactAntigen: Antibody provider
22. GAS: an alphabetic listing of software for the gene-mapping community.
23. Gemma: Online database and software system for the meta-analysis of gene expression data
24. GeneNetwork: Large array of linked resources and analysis tools for system genetics
25. GENSAT:  Imaging and gene expression data from BAC transgenic mice
26. GENSAT Retina Project: Online database of confocal stacks to freely download and view using ImageJ or the LSM Image Browser from Zeiss  
27. Grants:  Grant information on public and private foundations provided by Research Crossroads
28. HomoloGene: Online system for automated detection of homologs among the annotated genes
29. IBVD: Online database of brain neuroanatomic volumetric observations
30. IMSR: Online database of mouse strains and stocks
31. Ki: Datasbase of Ki (affinity) values and related papers
32. MGI:  Comprehensive collection of genomic and associated data on mouse strains
33. MichiganAtlas: Human brain atlas with matching cell stained and MRI sections
34. Microarray Consortium: Online database of publicly available microarray data sets
35. ModelDB: Database of downloadable neuroscience-related models
36. Nervous System Connectivity: A view into 4 major connectivity databases including CoCoMac, BAMS, temporal-lobe.com and ConnectomeWIKI
37. Neurodatabase: Electrophysiological data of mainly single and multiple unit activity experiments 
38. Neurofed: Contact information for federal employees at NIH, NSF, and military institutes involved in funding neuroscience research
39. NeuroMab:  Monoclonal antibody provider
40. NeuroMorpho.org: Neuronal reconstructions
41. NeuronDB:  Cellular properties of major neuronal classes
42. 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
43. NIH RePORTER: Online database of funded grants from NIH institutes
44. NINDS: List of neurological diseases and disorders
45. NITRC tool registry:  Software tools for neuroimaging
46. OASIS/XNAT: Set of human MRI images of different ages, clinical dementia ratings, and handedness
47. OdorMapDB: Database of brain activation foci within the olfactory bulb
48. ORDB: a database of chemosensory receptors and associated information
49. Rat Genome Database:  Database of genetic information, including functional data, disease data, expression data and chromosome location data
50. 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
51. SUMSDB:  Brain activation foci from published studies
52. T3DB: Toxin and Toxin Target Database (T3DB) is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information
53. Temporal-lobe.com:  A hippocampal parahippocampal table together with references that provides a fully searchable knowledgebase of connections in the rat
54. Visiome Platform: Digital archive of mathematical models, experimental stimuli, experimental data, and analytical tools for vision science
55. WikiPathways: An open, collaborative platform dedicated to the curation of biological pathways
56. 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
57. XNAT: Dataset of human MRI images, from humans of different ages, clinical dementia ratings, and handedness available from XNAT central
58. ZFIN: A zebrafish model organism database that includes transgenic fish but not wild-types.

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.