List of neuroscience databases

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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[edit]

Name 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]
Big Brain 3D reconstruction of complete brain from cell-body stained histology sections at 20 micron isotropic resolution Human Microscopic Images Healthy No [4]
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 [5]
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 Yes [6]
Braingraph.org Braingraphs computed from the Human Connectome Project data Human Macroscopic, upto 1015 nodes directed and undirected graphs in anatomically annotated GraphML format Healthy No [7]
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 [8]
BrainMaps Atlas, high resolution stained sections from brains Human, primate and non-primate (14 species in all) Neuron and Macroscopic Images Healthy No [9]
Brede Database fMRI and PET coordinate database Human Macroscopic Descriptive Healthy No [10]
Brainmuseum.org / MSU Brain Biodiversity Bank Atlas, stained sections from brains and MRI images Human and 62 other species Macroscopic Images Healthy No
Brainomics/Localizer fMRI and MRI scans, behavioral data Human Macroscopic Images, Numerical Healthy No [11]
The Cancer Imaging Archive MRI, CT, and PET imaging of cancer patients with supporting clinical data (in many cases) Human Macroscopic Images, Descriptive, Numerical Cancer No [12]
Cerebellar Development Transcriptome Database Atlas, stained sections from mouse brains showing cerebellar development and gene expression Mouse Macroscopic, Gene Images Healthy No [13]
Collaborative Research in Computational Neuroscience CRCNS.org 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 [14]
GLIMPS Project (GLucose IMaging in Parkinsonian Syndromes) http://glimpsproject.com/en/ International FDG-PET scan neurodegenerative disease database Human Macroscopic FDG-PET images Parkinson's (PD), Alzheimer's(AD), Multiple System Atrophy (MSA), Progressive Supranuclear Palsy (PSP), etc. Yes
Hippocampome Portal Circuitry, neural types, electrophysiology Adult human Neuron Cell morphology, electrophysiology, region makeup, connectivity Healthy Yes [15][16]
International Epilepsy Electrophysiology Database (IEEG.org, http://ieeg.org) EEG, metadata, imaging, annotations on data Humans and animal models of epilepsy EEG, local fields, micro-ECoG Electrophysiology Non-healthy, several healthy Yes
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
JuBrain atlas Probabilistic cytoarchitectonic 3D maps of the human brain Human Mesoscopic Structural Healthy No [17][18]
Kymata Atlas Functional atlas of the human cortex Human Macroscopic Functional Healthy No [19]
Major Depressive Disorder Neuroimaging Database Meta-analysis and database of MRI studies Human Macroscopic Descriptive, numerical Major Depressive Disorder No [20]
Mouse Brain Library Atlas, stained sections from mouse brains Mouse Macroscopic Images Healthy No [21]
Neuroelectro.org Electrophysiology of neurons Human, others Neuron Electrophysiological properties and data Healthy No [22]
Neuromorpho.org 3D models of real neurons Human, Rat, Mouse, Monkey, others Neuron Images and 3D data Healthy No [23]
NeuronDB Database of Neuron properties and classification Human Neuron Descriptive Healthy No [24]
Open Access Series of Imaging Studies (OASIS) Structural MRI images Human Macroscopic MRI datasets Healthy and Alzheimer's Disease Yes [25]
OpenFMRI Project Functional and structural MRI datasets Human Macroscopic MRI datasets Healthy No [26]
The PAIN Repository Structural, Diffusion and Functional MRI datasets Human Human Macroscopic MRI datasets and Metadata Healthy and Pain Conditions Yes [27]
SchizConnect SchizConnect is an open, public search-and-download virtual database for schizophrenia neuroimaging (MRI) images and related data. Human Macroscopic Structural, Diffusion and Functional MRI datasets, cognitive and clinical assessments Schizophrenia (+ siblings), Bipolar Disorder, Controls (+ siblings) Yes [28]
Ultrahigh resolution T1-weighted whole brain MR dataset T1-weighted MR data acquired using prospective motion correction at an ultrahigh isotropic resolution of 250 µm. Human Mesoscopic Structural MRI dataset including scanner's raw to processed data Healthy No [29]
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 [30]

Databases of Neuroscience databases[edit]

Name 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 [31]
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

Neuroscience article aggregators[edit]

Neuroscience feed at RightRelevance.[32]

See also[edit]

References[edit]

  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. PMID 17151600. doi:10.1038/nature05453. 
  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. PMC 2544629Freely accessible. PMID 18302232. doi:10.1002/jmri.21049. 
  4. ^ Amunts K, Lepage C, Borgeat L, Mohlberg H, Dickscheid T, Rousseau MÉ, Bludau S, Bazin PL, Lewis LB, Oros-Peusquens AM, Shah NJ, Lippert T, Zilles K, Evans AC (2013). "BigBrain: an ultrahigh-resolution 3D human brain model". Science. 340 (6139): 1472–5. PMID 23788795. doi:10.1126/science.1235381. 
  5. ^ 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. PMID 18762588. doi:10.1001/archpsyc.65.9.1017. 
  6. ^ 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. PMID 21985910. doi:10.1016/j.neuroimage.2011.09.062. 
  7. ^ Szalkai, Balázs; Kerepesi, Csaba; Varga, Balint; Grolmusz, Vince (2017). "Parameterizable consensus connectomes from the Human Connectome Project: the Budapest Reference Connectome Server v3.0". Cognitive Neurodynamics. 11 (1): 113–116. PMC 5264751Freely accessible. PMID 28174617. doi:10.1007/s11571-016-9407-z. 
  8. ^ Laird AR, Lancaster JL, Fox P (2005). "BrainMap: The social evolution of a functional neuroimaging database" (PDF). Neuroinformatics. 3 (1): 65–78. PMID 15897617. doi:10.1385/ni:3:1:065. 
  9. ^ Mikula, S; Trotts I; Stone JM; Jones EG (2007). "Internet-enabled high-resolution brain mapping and virtual microscopy". NeuroImage. 35 (1): 9–15. PMC 1890021Freely accessible. PMID 17229579. doi:10.1016/j.neuroimage.2006.11.053. 
  10. ^ 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.
  11. ^ Papadopoulos Orfanos D, Michel V, Schwartz Y, Pinel P, Moreno A, Le Bihan D, Frouin V (October 2015). "The Brainomics/Localizer database". NeuroImage. PMID 26455807. doi:10.1016/j.neuroimage.2015.09.052. 
  12. ^ Clark, K; Vendt, B; Smith, K; Freymann, J; Kirby, J; Koppel, P; Moore, S; Phillips, S; Maffitt, D; Pringle, M; Tarbox, L; Prior, F (2013). "The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository". J Digit Imaging. 26: 1045–57. PMC 3824915Freely accessible. PMID 23884657. doi:10.1007/s10278-013-9622-7. 
  13. ^ 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. PMID 18603407. doi:10.1016/j.neunet.2008.05.004. 
  14. ^ 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
  15. ^ "Hippocampome". hippocampome.org. Retrieved 10 August 2016. 
  16. ^ Wheeler, Diek W; White, Charise M; Rees, Christopher L; Komendantov, Alexander O; Hamilton, David J; Ascoli, Giorgio A (24 September 2015). "Hippocampome.org: a knowledge base of neuron types in the rodent hippocampus". eLife. 4: e09960. PMC 4629441Freely accessible. PMID 26402459. doi:10.7554/eLife.09960. 
  17. ^ Amunts K, Zilles K (2015). "Architectonic Mapping of the Human Brain beyond Brodmann". Neuron. 88 (6): 1086–107. PMID 26687219. doi:10.1016/j.neuron.2015.12.001. 
  18. ^ Zilles K, Amunts K (2010). "Centenary of Brodmann's map--conception and fate". Nature Reviews. Neuroscience. 11 (2): 139–45. PMID 20046193. doi:10.1038/nrn2776. 
  19. ^ "The Kymata Atlas Homepage". The Kymata Atlas. University of Cambridge. Retrieved 11 December 2015. 
  20. ^ 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. PMID 21727252. doi:10.1001/archgenpsychiatry.2011.60.  see also MRI database at www.depressiondatabase.org
  21. ^ 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.
  22. ^ Tripathy, Shreejoy; Gerkin, Richard. "NeuroElectro". www.neuroelectro.org. Retrieved 10 August 2016. 
  23. ^ Ascoli GA, Donohue DE, Halavi M. (2007). NeuroMorpho.Org: a central resource for neuronal morphologiesJ Neurosci., 27(35):9247-51 .
  24. ^ 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. PMID 10223520. doi:10.1016/S0165-0270(98)00049-1. 
  25. ^ 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. PMID 17714011. doi:10.1162/jocn.2007.19.9.1498. 
  26. ^ 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. PMC 3703526Freely accessible. PMID 23847528. doi:10.3389/fninf.2013.00012. 
  27. ^ Labus J, Naliboff B, Kilpatrick L, Liu C, Ashe-McNalley C, Dos Santos I, Alaverdyan M, Woodworth D, Gupta A, Ellingson B, Tillisch K, Mayer E (2016). "Pain and Interoception Imaging Network: A multimodal, multisite, brain-imaging repository for chronic somatic and visceral pain disorders". NeuroImage. 124 (Pt B): 1232–1237. PMC 4627849Freely accessible. PMID 25902408. doi:10.1016/j.neuroimage.2015.04.018. 
  28. ^ Wang L, Alpert K, Calhoun V, Cobia D, Keator D, King M, Kogan A, Landis D, Tallis M, Turner M, Potkin S, Turner J, Ambite J (2016). "SchizConnect: Mediating neuroimaging databases on schizophrenia and related disorders for large-scale integration.". NeuroImage. 124 (Pt B): 1155–1167. PMC 4651768Freely accessible. PMID 26142271. doi:10.1016/j.neuroimage.2015.06.065. 
  29. ^ Lüsebrink, F.; Sciarra, A.; Mattern, H.; Yakupov, R.; Speck, O. (2017). "T1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm.". Scientific Data. 4 (170032). PMC 5349250Freely accessible. PMID 28291265. doi:10.1038/sdata.2017.32. 
  30. ^ Gorgolewski KJ, Varoquaux G, Rivera G, Schwartz Y, Ghosh SS, Maumet M, Nichols TE, Poldrack RA, Poline J, 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. 
  31. ^ 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. PMC 2661130Freely accessible. PMID 18946742. doi:10.1007/s12021-008-9024-z. 
  32. ^ "Right Relevance : Neuroscience". www.rightrelevance.com. Right Relevance. Retrieved 10 August 2016.