List of neuroscience databases

A number of online neuroscience databases are available which provide information regarding gene expression, neurons, macroscopic brain structure, and neurological or psychiatric disorders. Some databases contain descriptive and numerical data, some to brain function, others offer access to 'raw' imaging data, such as postmortem brain sections or 3D MRI and fMRI images. Some focus on the human brain, others on non-human.

As the number of databases that seek to disseminate information about the structure, development and function of the brain has grown, so has the need to collate these resources themselves. As a result, there now exist databases of neuroscience databases, some of which reach over 3000 entries.[1]

Neuroscience databases

Name and External Link Description Organism Level (gene, neuron, macroscopic) Data (MRI, fMRI, images, descriptive, numerical) Disorder Register to view data? Ref
Allen Brain Atlas Atlas, stained sections from brains showing development and gene expression Mouse, Human Macroscopic, Gene Images Healthy No [2]
Alzheimer's Disease Neuroimaging Initiative (ADNI) Structural MRI images Human Macroscopic MRI datasets Healthy and Alzheimer's Disease Yes [3]
BIRN fMRI and MRI data fMRI, MRI scans and atlases for human and mouse brains Mouse, Human Multilevel: brain regions, connections, neurons, gene expression patterns MRI datasets, fMRI datasets healthy, elderly No
Bipolar Disorder Neuroimaging Database Meta-analysis and database of MRI studies Human Macroscopic Descriptive, numerical Bipolar Disorder No [4]
Brain Architecture Management System Online resource for information about neural circuitry Rat, Mouse, Human Multilevel: brain regions, connections, neurons, gene expression patterns Descriptive, numerical healthy No
Brain Cloud Gene expression in the human prefrontal cortex Human Gene expression patterns Descriptive, numerical healthy No
Brain-Development.org Structural MRI images and Atlases Human Macroscopic MRI datasets Fetuses, healthy and prematurely born neonates No [5]
Braininfo Atlas, schematic atlas of Macaca fascicularis Macaque Macroscopic Schematic images Healthy Yes
Brain Machine Interface Platform Different types of data related to brain machine interface Human, Monkey Macroscopic, Neuron Images, Numerical Healthy No
BrainMap.org fMRI coordinate database Human Macroscopic Descriptive Healthy Yes [6]
BrainMaps Atlas, high resolution stained sections from brains Human, primate and non-primate (14 species in all) Neuron and Macroscopic Images Healthy No [7]
Brede Database fMRI and PET coordinate database Human Macroscopic Descriptive Healthy No [8]
Brainmuseum.org / MSU Brain Biodiversity Bank Atlas, stained sections from brains and MRI images Human and 62 other species Macroscopic Images Healthy No
Cerebellar Development Transcriptome Database Atlas, stained sections from mouse brains showing cerebellar development and gene expression Mouse Macroscopic, Gene Images Healthy No [9]
Collaborative Research in Computational Neuroscience Many kinds of neuroscience results that are relevant for modeling Human and several other species Multiscale Spike trains, LFP, MUA, MRI Healthy Yes
Database for Reaching Experiments And Models (DREAM) Reaching data. (Behavioral, generalization, adaptation, learning, spike, fMRI, uncertainty) Human and monkey Macroscopic Kinematic, Spike, fMRI Healthy Yes
The fMRI Data Center fMRI datasets from published studies Human Macroscopic fMRI datasets Healthy Yes [10]
International Neuroimaging Data-sharing Initiative (INDI) Functional connectivity data from many different groups Invertebrates (47 species in all) Macroscopic Functional connectivity Healthy, non-healthy Yes
Invertebrate Brain Platform Photos of dissections of invertebrates nervous systems Invertebrates (47 species in all) Macroscopic Photos Healthy No
Kymata Atlas Functional atlas of the human cortex. Currently in alpha testing. Human Macroscopic Functional Healthy No
Major Depressive Disorder Neuroimaging Database Meta-analysis and database of MRI studies Human Macroscopic Descriptive, numerical Major Depressive Disorder No [11]
Mouse Brain Library Atlas, stained sections from mouse brains Mouse Macroscopic Images Healthy No [12]
Neuromorpho.org 3D models of real neurons Human, Rat, Mouse, Monkey, others Neuron Images and 3D data Healthy No [13]
NeuronDB Database of Neuron properties and classification Human Neuron Descriptive Healthy No [14]
Open Access Series of Imaging Studies (OASIS) Structural MRI images Human Macroscopic MRI datasets Healthy and Alzheimer's Disease Yes [15]
OpenFMRI Project Functional and structural MRI datasets Human Macroscopic MRI datasets Healthy No [16]
UNC-Wisconsin Neurodevelopment Rhesus MRI Database Structural and Diffusion Weighted MRI images in Native and Atlas Space Macaque Macroscopic MRI datasets Healthy No
Whole Brain Atlas Atlas, Structural MRI images and PET images Human Macroscopic Images Healthy and various diseases No
Neurovault Unthresholded statistical maps from MRI and PET studies. Human Macroscopic Images Healthy and various diseases No [17]

Databases of Neuroscience databases

Name and External Link Description Organism Level (gene, neuron, macroscopic) Data (MRI, fMRI, images, descriptive, numerical) Disorder Register to view data? Ref
Neuroscience Information Framework A meta database of neuroscience-relevant data incorporating over 100 databases. Human, Mouse, Rat, Worm Microscopic, Macroscopic Datasets Healthy and Diseased No [18]
Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) NITRC facilitates finding and comparing neuroimaging resources for functional and structural neuroimaging analyses. Human, Mouse, Rat, Worm Microscopic, Macroscopic Datasets Healthy and Diseased No

See also

References

  1. ↑ "Number of entries using search query 'database'". neuinfo.org. NIF. Retrieved 25 Jan 2015.
  2. ↑ Lein, Ed S.; Ao, Nancy; Ayres, Mikael; Bensinger, Amy; Bernard, Amy; Boe, Andrew F.; Boguski, Mark S.; Brockway, Kevin S.; Byrnes, Emi J.; Chen, Lin; Chen, Li; Chen, Tsuey-Ming; Chi Chin, Mei; Chong, Jimmy; Crook, Brian E.; Czaplinska, Aneta; Dang, Chinh N.; Datta, Suvro; Dee, Nick R.; Desaki, Aimee L.; Desta, Tsega; Diep, Ellen; Dolbeare, Tim A.; Donelan, Matthew J.; Dong, Hong-Wei; Dougherty, Jennifer G.; Duncan, Ben J.; Ebbert, Amanda J. et al. (2007). "Genome-wide atlas of gene expression in the adult mouse brain". Nature 445 (7124): 168–176. Bibcode:2007Natur.445..168L. doi:10.1038/nature05453. PMID 17151600.
  3. ↑ Jack, CR; Bernstein, MA; Fox, NC; Thompson, P; Alexander, G; Harvey, D; Borowski, B; Britson, PJ et al. (2008). "The Alzheimer's disease neuroimaging initiative (ADNI): MRI methods". Journal of Magnetic Resonance Imaging 27 (4): 685–691. doi:10.1002/jmri.21049. PMC 2544629. PMID 18302232.
  4. ↑ Kempton, M.J.; Geddes, J.R; Ettinger, U.; Williams, SC; Grasby, PM (2008). "Meta-analysis, Database, and Meta-regression of 98 Structural Imaging Studies in Bipolar Disorder". Archives of General Psychiatry 65 (9): 1017–1032. doi:10.1001/archpsyc.65.9.1017. PMID 18762588.
  5. ↑ Serag, A.; Aljabar, P.; Ball, G.; Counsell, S.J.; Boardman, J.P.; Rutherford, M.A.; Edwards, A.D.; Hajnal, J.V.; Rueckert, D. (2012). "Construction of a consistent high-definition spatio-temporal atlas of the developing brain using adaptive kernel regression". NeuroImage 59 (3): 2255–2265. doi:10.1016/j.neuroimage.2011.09.062. PMID 21985910.
  6. ↑ Laird, AR; Lancaster, JL; Fox, PT. (2005). "BrainMap: The social evolution of a functional neuroimaging database" (PDF). Neuroinformatics 3 (1): 65–78. doi:10.1385/ni:3:1:065. PMID 15897617.
  7. ↑ Mikula, S; Trotts I; Stone JM; Jones EG (2007). "Internet-enabled high-resolution brain mapping and virtual microscopy". NeuroImage 35 (1): 9–15. doi:10.1016/j.neuroimage.2006.11.053. PMC 1890021. PMID 17229579.
  8. ↑ Nielsen, F.A. (2003). The Brede database: a small database for functional neuroimaging NeuroImage 19(2), Presented at the 9th International Conference on Functional Mapping of the Human Brain, June 19--22, 2003, New York, NY.
  9. ↑ Sato, A; Sekine, Y; Saruta, C; Nishibe, H; Morita, N; Sato, Y; Sadakata, T; Shinoda, Y et al. (2008). "Cerebellar development transcriptome database (CDT-DB): profiling of spatio-temporal gene expression during the postnatal development of mouse cerebellum". Neural Networks 21 (8): 1056–69. doi:10.1016/j.neunet.2008.05.004. PMID 18603407.
  10. ↑ Van Horn JD, Grethe JS, Kostelec P, Woodward JB, Aslam JA, Rus D, Rockmore D, Gazzaniga MS (2001) The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studiesPhilos Trans R Soc Lond B Biol Sci Aug 29;356(1412):1323-39
  11. ↑ Kempton MJ, Salvador Z, Munafò MR, Geddes JR, Simmons A, Frangou S, Williams SC.; Salvador; Munafò; Geddes; Simmons; Frangou; Williams (2011). "Structural Neuroimaging Studies in Major Depressive Disorder: Meta-analysis and Comparison With Bipolar Disorder". Arch Gen Psychiatry 68 (7): 675–90. doi:10.1001/archgenpsychiatry.2011.60. PMID 21727252. see also MRI database at www.depressiondatabase.org
  12. ↑ Rosen GD, Williams AG, Capra JA, Connolly MT, Cruz B, Lu L, Airey DC, Kulkarni K, Williams RW (2000) The Mouse Brain Library @ www.mbl.org. Int Mouse Genome Conference 14: 166. www.mbl.org.
  13. ↑ Ascoli GA, Donohue DE, Halavi M. (2007). NeuroMorpho.Org: a central resource for neuronal morphologiesJ Neurosci., 27(35):9247-51 .
  14. ↑ Mirsky, Jason S.; Nadkarni, Prakash M.; Healy, Matthew D.; Miller, Perry L.; Shepherd, Gordon M. (1998). "Database tools for integrating and searching membrane property data correlated with neuronal morphology". Journal of Neuroscience Methods 82 (1): 105–21. doi:10.1016/S0165-0270(98)00049-1. PMID 10223520.
  15. ↑ Marcus, DS; Wang, TH; Parker, J; Csernansky, JG; Morris, JC; Buckner, RL (Sep 2007). "Open Access Series of Imaging Studies (OASIS): cross-sectional MRI data in young, middle aged, nondemented, and demented older adults". J Cogn Neurosci 19 (9): 1498–507. doi:10.1162/jocn.2007.19.9.1498. PMID 17714011.
  16. ↑ Poldrack, RA; Barch, DM; Mitchell, JP; Wager, TD; Wagner, AD; Devlin, JT; Cumba, C; Koyejo, O; Milham, MP (Jul 2013). "Toward open sharing of task-based fMRI data: the OpenfMRI project". Frontiers in Neuroinformatics 7 (12): 12. doi:10.3389/fninf.2013.00012. PMC 3703526. PMID 23847528.
  17. ↑ Gorgolewski, KJ; Varoquaux, G; Rivera, G; Schwartz, Y; Ghosh, SS; Maumet, M; Nichols, T. E.; Poldrack, RA; Poline, J-B; Yarkoni, T; Margulies, DS (Oct 2014). "NeuroVault.org: A web-based repository for collecting and sharing unthresholded statistical maps of the human brain". BioRXiv. doi:10.1101/010348.
  18. ↑ Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, Goldberg DH, Grafstein B, Grethe JS; Akil; Ascoli; Bowden; Bug; Donohue; Goldberg; Grafstein; Grethe; Gupta; Halavi; Kennedy; Marenco; Martone; Miller; Müller; Robert; Shepherd; Sternberg; Van Essen; Williams (September 2008). "The neuroscience information framework: a data and knowledge environment for neuroscience". Neuroinformatics 6 (3): 149–60. doi:10.1007/s12021-008-9024-z. PMC 2661130. PMID 18946742.