Table 2 Sample of Neurology and Neuroscience Databases (see additional information in Additional file 1: Table S2 for the above databases)

Allen brain map: https://portal.brain-map.org/

Varied (57 projects mouse, non-human primate & human)

Diverse dataset including imaging (eg., MRI), atlases, histology, gene, etc.

O

 + 

C

P&C

ADNI: https://adni.loni.usc.edu/

 > 1000 AD subjects

MRI, PET, biosamples, neuropsychological data, genetic data

O

 + 

C

C

LONI image & data archive: https://ida.loni.usc.edu/login.jsp

143 studies, 84864 HP subjects

MRI, EEG, PET, CT, SPECT, demographics, biospecimen, and clinical data

O*

 + 

O

P&C

Big brain project: https://bigbrain.loris.ca; https://bigbrainproject.org/

1 subject (H), full dataset over 1 TB, 7404 histological slices

Brain atlas, histology images, 3D reconstruction

F

 + 

C

C

Biomarkers for spinal muscular atrophy: https://smafoundation.org/discovery/biomarkers/

 > 100 SMA subjects at 18 sites

Primarily descriptive data but resource for potential SMA testing tools

F

 + 

C

P&C

Bipolar disorder neuroimaging database: https://sites.google.com/site/bipolardatabase/

141 studies comparing bipolar and H

Data from studies using MRI and CT scans

F

 + 

C

C

Brain architecture management system: https://bams1.org

65000 reports of rat brain connections

Brain parts, cell types, molecules

F

 + 

C

P

Brain architecture management system 2: https://bams2.bams1.org

45000 reports of connections H and animals

Brain parts, cell types, molecules

F

 + 

C

P

Brain machine interface platform (BMI PF): https://bmi.neuroinf.jp/

 > 3500 BMI-related papers, 185 BMI-related sites links

Brain atlases, reconstructed images, fMRI

F

 + 

C

P&C

Brain transcriptome database: https://www.cdtdb.neuroinf.jp/CDT/Top.jsp

Data from over 30 different gene categories

Genetic (molecular functions, cellular components, biological processes)

F

 + 

C

C

Brain/MINDS data portal: https://dataportal.brainminds.jp/

154 subjects (H), > 300 marmoset

Marmoset: MRI, brain & gene atlas, tracer injection, calcium imaging, ECoG and connectivity mapping. Human brain MRI

FUA

 + 

C

P&C

Marmoset gene atlas: https://gene-atlas.brainminds.jp/

 > 1200 genes of > 150 brain regions, 21 diseases

Atlases and gene mapping of marmoset brain

O

 + 

C

P

BrainChart: https://brainchart.shinyapps.io/brainchart/

123984 MRIs, > 100 studies, 101457 subjects

MRI scans reduced to Summary Graphs in Database

F

 + 

C

C

Brain-CODE:

https://www.braincode.ca/

1547 CP, 797 concussion, 1074 depression, 1265 epilepsy, 15959 ND, 4386 NeD & 1516 animal records

MRI, EEG, MEG, DTI, ocular data, clinical data, genomic, proteomic, demographic data

FUA

 + 

O

P&C

Brain-development.org: https://brain-development.org/

 > 2000 subjects (H)

MRI, MRA, DTI, demographic data, brain atlases

F

 + 

C

C

BrainGraph.org: https://braingraph.org/cms/

1053 H brains

Braingraphs, connectomes

F

 + 

C

C

BrainInfo: http://braininfo.rprc.washington.edu/

4 cortical views, 58 coronal sections of 3 longtailed macaque

Macaque brain atlas

F

 + 

C

P&C

BrainMap: https://brainmap.org/

Functional: 105589, Voxel-based morphometry: 115627 H

Descriptive BrainMap taxonomy and software tools

O

 + 

C

C

BrainMaps.org:

http://brainmaps.org/

 > 140 TB, "140 million megapixels of sub-micron resolution, annotated, scanned images of serial sections" of brains

Atlases human & animals, brain connectivity graphs & 3D. Histochemical, immunocytochemical & tracer connectivity. EM, MRI, DTI. Gene database

F

O

P&C

Brainomics/Localizer: https://osf.io/vhtf6/

94 subjects (H)

fMRI, MRI, genetic, cognitive, and behavioral data

F

 + 

C

C

BRAINSPAN: https://brainspan.org/

300 distinct human brain structures

Genetic, atlas, MRI, DTI

O

 + 

C

P&C

Caltech subcortical atlas:

https://evendim.sites.caltech.edu/subcortical-atlas-new

168 subjects (H)

"Probabilistic atlases of the human amygdala and of the subcortical nuclei associated with reinforcement learning."

FUA

 + 

O

C

Cambridge centre for ageing & neuroscience: https://www.cam-can.org/

Nearly 3000 subjects

MRI, fMRI, MEG, cognitive, behavioral, demographic, and physiological data

O

 + 

O

C

Canadian open neuroscience platform:

https://braincanada.ca/funded_grants/canadian-open-neuroscience-platform/

More than 60 datasets and 75 tools

Imaging, genetic, behavioral neuroscience data, and more

O

 + 

O

P&C

Cell image library: http://www.cellimagelibrary.org/home

 > 12000 unique datasets and 30 TB of data

Images, videos, animations

F

 + 

O

P

CellML: https://www.cellml.org/

 > 900 model exposures

Computer-based mathematical models

F

C

P

Center for integrative connectomics: https://cic.ini.usc.edu/

 > 500 connectomes

Multimodal multiscale connectome & cell-type map, imaging, computational

F

 + 

C

P

Center-TBI: https://www.center-tbi.eu/

 > 4500 TBI subjects

Clinical, imaging, ICU data, and biomarker data

F

 + 

C

C

CoCoMac: http://cocomac.g-node.org/main/index.php

 > 8000 brain site

Neuroinformatics database

F

C

P

Mammalian brain collections: https://brainmuseum.org/index.html

 > 100 species of mammals including humans

Images and information from sectioned and stained brains

F

 + 

C

P&C

CNS-PF: https://cns.neuroinf.jp/index.php?ml_lang=en

47 species

Images, 3D brain gallery, brain and neurons of invertebrates

F

 + 

C

P

Connectome coordination facility: https://www.humanconnectome.org

 > 10000 subjects in 20 human connectome studies

Human connectomes

FUA

 + 

C

P&C

Baby connectome project: https://humanconnectome.org/study/lifespan-baby-connectome-project\

500 subjects (H)

MRI, clinical data, behavioral data

FUA

 + 

C

P&C

HCP YoungAdult: https://www.humanconnectome.org/study/hcp-young-adult

1200 subjects (H)

dMRI, rfMRI, tfMRI, MEG/EEG, behavioral, genetic data

F

 + 

C

P&C

HCP aging: https://www.humanconnectome.org/study/hcp-lifespan-aging

725 subjects (H)

sMRI, rfMRI, tfMRI, dMRI, ASL, demographic, and behavioral data

FUA

 + 

C

C

HCP development: https://www.humanconnectome.org/study/hcp-lifespan-development

 > 1200 subjects (H)

MRI, rfMRI, tfMRI, sMRI, fMRI, behavioral data, demographic

FUA

 + 

C

C

Collaborative research in computational neuroscience: https://crcns.org/

 > 100 datasets from rodent, feline, and primate studies

MRI, neurophysiology data

F

 + 

C

P&C

Distributed archives for neurophysiology data integration:

https://dandiarchive.org/

440 TB total data size, 233 dandisets

"Electrophysiology, optophysiology, behavioral time-series, images from immunostaining"

O

 + 

O

P&C

Data archive BRAIN initiative (DABI): https://dabi.loni.usc.edu/home

 > 430 TB

Invasive neurophysiology, EEG, single unit activity, EMG, MRI, DTI, PET, CT, clinical, demographics, behavioral, eye-tracking, movement related, etc

O

 + 

O

P&C

DevelopmentalBrainDisorderGeneDatabase: https://dbd.geisingeradmi.org/

7204 cases, 704 genes

Genotypic and phenotypic data

O

 + 

C

C

Drug design data resource: https://drugdesigndata.org/

Datasets in MS Excel and HTML

Experimental datasets for diverse protein–ligand interactions

F

 + 

C

P

EBRAINS: https://ebrains.eu/

128 Projects, 943 datasets, 221 models

Knowledge graphs, atlases, simulations, brain modelling, neuromorphic computer, neurorobotics, medical data analytics

O

 + 

O

P&C

EEGbase: http://eeg2.kiv.zcu.cz:8080/home-page?0

 > 350 EEGs across 39 different scenarios (H)

EEG/ERP

F

O

C

ENCODE: https://www.encodeproject.org/

H: 1063878 cCREs, 1518 cells. Mo: 313838 cCREs, 169 cells

Functional genomics, characterization, terminology, elements from genome

O

 + 

O

P&C

ENIGMA: https://enigma.ini.usc.edu/

 > 12,800

MRI, DTI, fMRI, genetic data

O

 + 

O

C

Ensembl: https://useast.ensembl.org/index.html

 > 500000 genomes

Comparative genomics from multiple species (eg. Human, mouse, etc.)

O

 + 

C

P

Fruit fly brain observatory: https://www.fruitflybrain.org/#/brainmapsviz

7 Fruit Fly Connectomes

7 different adult and larva datasets

O

 + 

C

P

Gene expression nervous system atlas: http://www.gensat.org/

Undefined

Gene expression atlas and select brain slice images

O

 + 

C

P

Gene expression omnibus: https://www.ncbi.nlm.nih.gov/geo/

101940 datasets

"Gene-specific information from microarray and sequencing studies"

F

 + 

O

P

GeneNetwork:

https://genenetwork.org/

Unknown [25 years of legacy genetic data sets]

"Data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes"

O

 + 

O

P&C

Genetics Alzheimer’s disease data storage site: https://www.niagads.org/

263.5 million annotated genetic variants

Genotype & phenotype inform from 56 summary statistics from AD/ADRD GWAS

O

 + 

O

C

G-NODE open data: https://gin.g-node.org/

 > 270 study data sets

Electrophysiology, behavioral, biospecimens, stimulation, imaging, modeling

O

O

P&C

Hippocampome portal: https://hippocampome.org/php/index.php

527802 datapoints, 46004 pieces of evidence

Cell morphology, electrophysiology, region makeup, connectivity

O

 + 

C

P

Human connectome project: http://www.developingconnectome.org/

783 neonatal subjects (886 datasets)

MRI, rs-fMRI, demographics, clinical, neurodevelopmental, genetics

FUA

 + 

C

P&C

Global Alzheimer’s AssociationInteractiveNetwork: https://www.gaain.org/

480629 subjects (HP)

MRI, fMRI, DTI, clinical data, biospecimen, genetic data

O

 + 

C

C

Human brain transcriptome: https://hbatlas.org/

1340 tissue samples, genotyping data for 2.5 million markers

Transcriptome data and associated metadata

FUA

 + 

C

C

INCF knowledgespace: https://knowledge-space.org/

Unknown

Anatomy, expression, models, morphology, physiology, links to data sets

F

 + 

O

P&C

International epilepsy electrophysiology database: https://www.ieeg.org/

 > 3000 datasets

Electrophysiology data, MRI, PET, clinical data

O

 + 

O

P&C

Invertebrate brain platform: https://invbrain.neuroinf.jp/modules/htmldocs/IVBPF/Top/index.html

Unknown

Images of invertebrate brain and nervous system

F

 + 

C

P

IonChannelGenealogy: https://ionchannelmodels.org/

4815 models with 3706 quantitative ion channel data

Ion channel electrophysiology from diverse species, locations & neurons

O

 + 

O

P

Japan monkey centre primate brain imaging repository

http://www.j-monkey.jp/BIR/index_e.html

16 datasets

High-resolution MRI of non-human primates

F

 + 

C

P

JuBrain atlas: https://julich-brain-atlas.de/

Maps of > 200 regions

Brain atlases. Integrating big brain dataset, and EBRAINS data

O

 + 

C

C

Kymata atlas: https://kymata.org/

 > 50 functions mathematical describing brain functions

Functional atlas of brain (eg. binary detection of skin vibration)

O

 + 

C

C

Major depressive disorder neuroimaging database

https://sites.google.com/site/depressiondatabase/

225 studies in (HP) subjects

Descriptive and numerical information of the studies which have investigated brain structure using MRI and CT scans

F

 + 

C

C

MSU brain biodiversity bank: https://brains.anatomy.msu.edu/

27 brain atlases from humans, sheep, dolphin, and axolotls

Brain images and atlases

O

C

P

National institute of mental health data archive (NDA)

https://nda.nih.gov/

2396 collections of data from NIH studies

Virtual container for data and other information related to a project/grant. Clinical, phenotypical, neurosignal recordings, omics

O

 + 

O

P&C

National database for autism research: https://nda.nih.gov/

As of 2013, 90000 participants

Data from genetic validation, imaging, and genomics tools

O

 + 

O

P&C

National database for clinical trials related to mental illness: https://nda.nih.gov/

Unknown

Molecular, genetic, behavioral, social, and environmental interaction data

O

 + 

O

P&C

NeuroData

https://neurodata.io/

 > 100 datasets

Neuroimaging datasets, electron microscopy, cleared lightsheet microscopy, array tomography, sMRI, fMRI. Brain atlas of the zebrafish. Connectomes

F

 + 

C

P&C

Neuroelectro.org

http://neuroelectro.org/

 > 2300 electrophysiology assessments from ~ 100 distinct neurons and > 300 publications

Electrophysiological properties and data of diverse neuron types

F

C

P

Neuroimaging tools and resources collaboratory: https://www.nitrc.org/

 > 17 Imaging Studies (1000’s patients) & compatible software

MRI, CT, PET, neuroinformatics software and data from 17 + studies

O

 + 

C

P&C

1000 functional connectomes https://www.nitrc.org/projects/fcon_1000/

1288 subjects, 1200 R-fMRI from 33 sites

fMRI, demographics

F

 + 

C

C

International neuroimaging data-sharing initiative (INDI)

5 + studies, > 7000 subjects (HP)

rs-fMRI, MRI, DTI, software, demographics, behavioral data

O

 + 

O

C

Southwest university adult lifespan dataset (SALD)

494 subjects (H)

sMRI, rs-fMRI, behavioral data, basic phenotypic data

F

 + 

C

C

Autism brain imaging data exchange (ABIDE)

1060 ASD and 1166 (H)

rs-fMRI, MRI, anatomical and phenotypic data

F

 + 

C

C

Consortium for reliability and reproducibility (CoRR)

“1629 subjects (H), 3357 anatomical scans, 5093 resting functional scans, 1302 diffusion scans, 300 CBF & ASL scans”

rs-fMRI and diffusion imaging data

FUA

 + 

C

C

Addiction connectome preprocessed initiative (ACPI)

158 subjects, 128 anatomical scans, 185 resting functional scans

rs-fMRI

FUA

 + 

C

C

Preprocessed connectomes:

http://preprocessed-connectomes-project.org/index.html

11 repositories

MRI

F

 + 

C

C

NeuroML database: https://neuroml-db.org/

Annotated computational models

Neuronal morphology, ion channel dynamics, synaptic mechanisms, etc

O

 + 

C

P

Neuromorpho.org: https://neuromorpho.org/

241034 cells

Atlases and 3D data

O

 + 

C

P&C

Neuroscience gateway portal: https://www.nsgportal.org/overview.html

Provides NSF-funded HPC resources for modelling

Can model EEG, MRI, fMRI data, and more

O

C

C

Neuroscience information framework: https://neuinfo.org/

Can deep search across over 150 separate platforms

Brain atlases, genomics, clinical, experimental, knowledge databases

O

 + 

C

P&C

NeuroVault: https://neurovault.org/

 > 6500 studies

"Statistical maps, parcellations & atlases produced by MRI & PET studies."

O

 + 

O

C

NIDA data share website: https://datashare.nida.nih.gov/

Around 78 studies

Substance Abuse Disorder clinical trial data

O

 + 

O

P&C

NIDDK central repository

https://repository.niddk.nih.gov/home/

136 studies with data, 91 studies with biospecimens

NIDDK-sponsored study data including clinical data, biospecimens and associated databases. MRI, CT

O

 + 

O

P&C

NIH NeuroBioBank (NBB): https://neurobiobank.nih.gov/

6 biorepositories of diseased subjects

Human post-mortem brain tissue and related biospecimens

O

 + 

C

P&C

NIH roadmap epigenomics mapping consortium https://egg2.wustl.edu/roadmap/web_portal/

Data from 127 different tissues and both adult and embryonic cell types

"High-quality, genome-wide maps of several key histone modifications, chromatin accessibility, DNA methylation and mRNA expression"

F

C

P&C

NURSA: https://www.nursa.org/nursa/index.jsf

527 transcriptomic & 21 non-transcriptomic datasets

Transcriptomic, non-transcriptomic, molecular, cell line data, and more

F

 + 

C

P

Open access series of imaging studies: https://www.oasis-brains.org/

 > 3000 H and AD subjects

MRI, PET, clinical data, cognitive data, biomarker data

F

 + 

C

C

Open MEG archive (OMEGA) https://www.mcgill.ca/bic/neuroinformatics/omega

3 studies, 161 H, 127 PD & 7 chronic pain subjects, about 900 resting-state MEG

MEG, T1 MRI, multimodal electrophysiological data, demographics data, questionnaire information

FUA

 + 

C

C

OPEN SCIENCE—repository for research data and publications of OVGU: http://open-science.ub.ovgu.de/xmlui/

Data from 73 publications

Neuro data includes structural MRI, microstructure MRI, fMRI

O

 + 

C

P&C

OpenSource Brain: https://www.opensourcebrain.org/

Unknown

Computational models of neural systems. NeuroML and PyNN

O

C

P

OpenfMRI: http://openfmri.org/

3372 subjects, 3372 datasets

Functional and structural MRI, EEG

F

 + 

O

C

OpenNEURO: https://openneuro.org/

29450 participants, 770 public datasets

MRI, PET, MEG, EEG, iEEG

O

 + 

O

C

Pain and interoception imaging network (PAIN) https://www.painrepository.org/repositories/

 > 1500 scans, CBP, FM, migraine, IBS, Vlvd, IBD and H subjects

MRI, demographic, behavioral data

O

 + 

O

C

Parkinson’s disease biomarkers program (PDBP): https://pdbp.ninds.nih.gov/

 > 2000 Parkinsonian, > 250 Lewy body

Biospecimen, imaging, clinical

O

 + 

O

C

Parkinson’s progression markers initiative: https://www.ppmi-info.org/

1758 subjects (902 PD, 619 Prodromal, 237 H)

Clinical, imaging, ‘omics, genetic, sensor, biospecimen

O

 + 

C

C

PeptideAtlas: http://www.peptideatlas.org/

1600 samples

"Compendium of peptides in a large set of tandem mass spectrometry proteomics experiments"

O

 + 

O

P

PhysioBank: https://archive.physionet.org/physiobank/

Over 75 databases

"Digital recordings of physiologic signals" and related clinical data

F

 + 

O

C

PhysioNet gait in aging and disease database https://physionet.org/content/gaitdb/1.0.0/

15 H and PD subjects

Electrophysiological recordings, clinical data

F

 + 

C

C

Pig imaging group: https://pigmri.illinois.edu/

15 pigs

MRI

F

 + 

C

P

Primate cell type database: https://primatedatabase.com/

106 patch clamp recordings

Images, morphology, 3D reconstructions, electrophysiological data

F

 + 

C

P

ProteomeXchange: http://www.proteomexchange.org/

24923 datasets

Proteomics repository

O

 + 

O

P&C

PTSD MRI database and meta-analysis https://sites.google.com/site/ptsdmri/

89 studies

Descriptive, numerical

F

 + 

C

C

Scalable brain atlas: https://scalablebrainatlas.incf.org/

20 brain atlases

Brain regions and reference images in 2D and 3D

F

C

P&C

SchizConnect: http://schizconnect.org/

1392 Subjects

Structural and functional MRI, clinical data, cognitive data

O

 + 

C

C

ORDB (Olfactory Receptor Database) https://senselab.med.yale.edu/ORDB/

12 databases with over 20,000 entries in total

Chemosensory receptor data, tissue, sequencing, nomenclature data, etc

O

 + 

C

P

NeuronDB: https://senselab.med.yale.edu/neurondb

83 neurons

Descriptive data

F

 + 

C

P&C

ModelDB: https://senselab.med.yale.edu/ModelDB/

1770 models

Computational neuroscience models (text files)

O

 + 

O

P

OdorMapDB: https://senselab.med.yale.edu/odormapdb/

68 entries

Maps of the olfactory bulb, descriptions, imaging (fMRI)

F

 + 

C

P

SimTK: https://simtk.org/

1649 projects

High quality simulation tools, models

O

StudyForrest: https://www.studyforrest.org/

36 subjects (H)

fMRI, structural brain scans, eye tracking data, clinical data

F

 + 

C

C

SynapseWeb: https://synapseweb.clm.utexas.edu/

1 atlas, shared data from 6 publications

3D brain ultrastructure, high resolution images of CNS cells

 + 

C

P

The ABCD study: https://abcdstudy.org/

Nearly 12000 youth

Structural, task functional and resting state functional imaging, clinical data

O

 + 

C

C

The cancer imaging archive https://www.cancerimagingarchive.net/

 > 3000 cancer subjects

MRI, CT, PT, SC, digital histopathology

O

 + 

O

P&C

The mouse brain library (MBL): https://www.mbl.org/

800 brain images, > 8000 numerical data

Atlases, numerical data

F

 + 

C

P

The federal interagency traumatic brain injury research (FITBIR) informatics system: https://fitbir.nih.gov

170 studies, 86985 subjects, 5276289 record (2352 forms with data)

MRI, CT, blood biospecimens, clinical data

O

 + 

C

C

UK biobank: https://www.ukbiobank.ac.uk/

500000 subjects (HP)

Varied biomedical data

O

 + 

P&C

UNC-wisconsin neurodevelopment rhesus database https://data.kitware.com/#collection/54b582c38d777f4362aa9cb3

 > 150 neonate macaque brain scans across 32 subjects, 34 rhesus monkeys (healthy infants and juveniles)

Structural and diffusion MRI

FUA

 + 

C

P

USC multimodal connectivity database (USC-MCD) http://umcd.humanconnectomeproject.org/

2354 records

Connectivity matrices from de-identified neuroimaging data

O

 + 

O

C

VISTA: https://genome.lbl.gov/vista/index.shtml

3315 in vivo tested elements, 1694 elements with enhancer activity

Genetic data from mice and humans

F

O

P&C

Whole brain atlas: https://www.med.harvard.edu/aanlib/

 > 30 imaging-based atlas of (HP)

Brain atlas from structural MRI, PET, CT, SPECT

F

C

C

WORMATLAS

https://www.wormatlas.org/

Unknown

Gene expression, mutant phenotypes, genome and proteome data, educational resources, neural connectivity and neural circuits

O

 + 

C

P

XNAT central: https://central.xnat.org/

506 projects, 7139 subjects, 16567 imaging sessions

MRI, fMRI, PET, CT

O

O

P&C