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Open Access Data in Medicine

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Open Access Data in Medicine
Open Access Data in Medicine

The following is a comprehensive list of openly accessible datasets that can be used in different biomedical research. They are classified according to specialty. Each repository contain tens and hundreds of available open data that you can use to do your research on. Most of these repositories require a request to access datasets, but some of them you can download the dataset directly.

Oncology (Page 2)

Heart Lung Blood (Page 3)

Diabetes Digestive and Kidney diseases (Page 4)

Neurology, Neuroscience, and Mental health (Page 5)

Radiology and Ophthalmology (Page 6)

Pediatrics (Page 7)

Genetics and Proteomics (Page 8)

Pathology and Basic sciences (Page 9)

General biomedical (Page 10)

Miscellaneous (Page 11)

Oncology

These repositories include clinical studies, imaging, as well as basic investigations on cancer.

Cancer Nanotechnology Laboratory (caNanoLab): https://cananolab.nci.nih.gov/

The Cancer Imaging Archive (TCIA): http://www.cancerimagingarchive.net/

YODA project: https://yoda.yale.edu

Project Sphere: https://www.projectdatasphere.org/projectdatasphere/html/

Heart Lung Blood

Repositories for studies on cardiovascular, respiratory and pulmonology, and blood disorders.

Biologic Specimen and Data Repository Information Coordinating

Center (BioLINCC): https://biolincc.nhlbi.nih.gov/home/

National Sleep Research Resource: https://sleepdata.org/

The Cardiovascular Research Grid (CVRG): http://cvrgrid.org/

Influenza Research Database (IRD): http://www.fludb.org/brc/home.do?decorator=influenza

Medical Information Mart for Intensive Care-III (MIMIC-III): http://mimic.physionet.org/

The Malaria Atlas Project (MAP): https://map.ox.ac.uk

Diabetes Digestive and Kidney diseases

Repositories and datasets for studies on Endocrinology, Gastroenterology, and Nephrology.

NIDDK Central Repository: https://repository.niddk.nih.gov/home/

NIDDK Information Network (DKnet): https://dknet.org//

The AMP-T2D Knowledge Portal: http://www.type2diabetesgenetics.org/

Neurology, Neuroscience, and Mental health

As one of the highly investigated fields, these repositories include neurology and neuroscience dataset as well as psychology and mental health.

AMP-AD Knowledge Portal: https://www.synapse.org/ampad

National Archive of Computerized Data on Aging (NACDA): https://www.icpsr.umich.edu/icpsrweb/NACDA/index.jsp

The National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) :
https://www.niagads.org/

LONI Database: https://ida.loni.usc.edu/login.jsp?search=true

NeuroImaging Tools and Resources Collaboratory (NITRC): http://www.nitrc.org/

Neuroscience Information Framework (NIF): https://neuinfo.org//

AphasiaBank: http://aphasia.talkbank.org/

FluencyBank: http://fluency.talkbank.org/

PhysioNet: http://www.physionet.org/

OpenfMRI: https://openfmri.org/

NeuroMorpho.org: http://neuromorpho.org/index.jsp

Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR):
https://pdbp.ninds.nih.gov/

The NINDS Human Cell and Data Repository (NHCDR): https://nindsgenetics.org/

The Alzheimer’s Disease Neuroimaging Initiative (ADNI): http://adni.loni.usc.edu

Federal Interagency Traumatic Brain Injury Research (FITBIR) Informatics System:
https://fitbir.nih.gov/

SOBC Measures Repository: https://scienceofbehaviorchange.org/about/

The Patient-Reported Outcomes Measurment Informmation System (PROMIS) : http://www.healthmeasures.net/explore-measurement-systems/ promis

National Addiction & HIV Data Archive Program (NAHDAP): http://www.icpsr.umich.edu/icpsrweb/NAHDAP/index.jsp

NIDA Data Share: https://datashare.nida.nih.gov

NIMH Data Archive: https://data-archive.nimh.nih.gov/

The National Database for Clinical Trials Related to Mental Illness (NDCT):
https://data-archive.nimh.nih.gov/ndct/

Radiology and Ophthalmology

Repositories for radiology and imaging datasets as well as high quality ophthalmology and optics datasets.

COllaborative Informatics and Neuroimaging Suite (COINS) https://portal.mrn.org/micis/index.php?subsite=dx

The Cancer Imaging Archive (TCIA) http://www.cancerimagingarchive.net/ (Collections)

Alzheimer’s Disease Neuroimaging Initiative (ADNI) http://adni.loni.ucla.edu/

The Open Access Series of Imaging Studies (OASIS) http://www.oasis-brains.org/

Breast Cancer Digital Repository http://bcdr.inegi.up.pt/

DDSM: Digital Database for Screening Mammography http://marathon.csee.usf.edu/Mammography/Database.html

The Mammographic Image Analysis Society (MIAS) mini-database http://peipa.essex.ac.uk/info/mias.html

Mammography Image Databases 100 or more images of mammograms with ground truth. Additional images available by request, and links to several other mammography databases are provided http://marathon.csee.usf.edu/Mammography/Database.html

Coherent X-ray Imaging Data Bank (CXIDB): http://www.cxidb.org

The SICAS Medical Image Repository: https://www.smir.ch

Image Data Resource (IDR): http://idr.openmicroscopy.org/about/

The Cancer Imaging Archive (TCIA): http://www.cancerimagingarchive.net/

LONI Database:
https://ida.loni.usc.edu/login.jsp?search=true
NeuroImaging Tools and Resources Collaboratory (NITRC): http:// www.nitrc.org/

OpenfMRI: https://openfmri.org/

EyeGENE®: https://eyegene.nih.gov/

National Eye Institute (NEI) Data Commons: https://neicommons.nei.nih.gov/#/

A global review of publicly available datasets for ophthalmological imaging: https://www.sciencedirect.com/science/article/pii/S2589750020302405#!

Pediatrics

Repositories for studies on children and neonates.

Biospecimen Repository Access and Data Sharing (BRADS): https://brads.nichd.nih.gov/Home/

Kids First: https://commonfund.nih.gov/kidsfirst

Child Language Data Exchange System (CHILDES): https://childes.talkbank.org

National Children’s Study (NCS) Archive: https://ncsarchive.s-3.net/bioshare/

Genetics and Proteomics

In addition to the human genome project data, these repositories contain data from genes to proteins.

Epigenomics: https://www.encodeproject.org/

exRNA Atlas: https://exrna.org/

The Genotype-Tissue Expression (GTEx): https://gtexportal.org/home/

The Human Microbiome Project (HMP) DACC: https://hmpdacc.org/

Illuminating Druggable Genome: https://pharos.nih.gov/

The Library of Integrated Network-Based Cellular Signatures : http://www.lincsproject.org/

Metabolomics Workbench (MetWB): http://www.metabolomicsworkbench.org/

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

The Universal Protein Resource (UniProt): http://www.uniprot.org/

Immune Epitope Database and Analysis Resource (IEDB): http://www.iedb.org/

Data and Specimen Hub (DASH): https://dash.nichd.nih.gov/

NIDA Center for Genetics Studies: https://nidagenetics.org/

Nuclear Receptor Signaling Atlas (NURSA): https://www.nursa.org/nursa/index.jsf

Database of Interacting Proteins (DIP): http://dip.doe-mbi.ucla.edu/dip/Main.cgi

Protein Data Bank (PDB): http://www.rcsb.org/pdb/home/home.do

Biological General Repository for Interaction Datasets (BioGRID): https://www.nlm.nih.gov/NIHbmic/ nih_data_sharing_repositories.html

NIMH Repository and Genomics Resources (NRGR): https://www.nimhgenetics.org/

database of Genotypes and Phenotypes (dbGaP): https://www.ncbi.nlm.nih.gov/gap

dbSNP: https://www.ncbi.nlm.nih.gov/snp

dbVar: https://www.ncbi.nlm.nih.gov/dbvar/

GenBank: https://www.ncbi.nlm.nih.gov/genbank/

Gene Expression Omnibus (GEO): https://www.ncbi.nlm.nih.gov/geo/

Sequence Read Archive (SRA): https://www.ncbi.nlm.nih.gov/sra

Pathology and Basic sciences

Include datasets on immunology, biochemistry, microbiology among other basic sciences.

Immune Tolerance Network (ITN) TrialShare shares : https://www.itntrialshare.org/login/home/login.view? returnUrl=%2Fproject%2Fhome%2Fstart.view%3F

Pathosystems Resource Integration Center (PATRIC): https://www.patricbrc.org/

The Immunology Database and Analysis Portal (ImmPort): http://www.immport.org/immport-open/public/home/home

VectorBase: https://www.vectorbase.org/

Virus Pathogen Research (ViPR): http://www.viprbrc.org/

Chemical Effects in Biological Systems (CEBS): https://manticore.niehs.nih.gov/cebssearch/

Cell Image Library: http://www.cellimagelibrary.org/pages/about

Transporter Classification Database (TCDB): http://www.tcdb.org/

PubChem: https://pubchem.ncbi.nlm.nih.gov/

The International Society for Digital Imaging of the Skin (ISDIS): https://isdis.net/home

The Histology Image Dataset (histologyDS) http://www.informed.unal.edu.co/histologyDS

The Cancer Genome Atlas (TCGA) http://cancergenome.nih.gov/ https://tcga-data.nci.nih.gov/tcga/

International Cancer Genome Consortium http://icgc.org, (Data portal) http://dcc.icgc.org/

Stanford Tissue Microarray Database (TMA) http://tma.im

MITOS dataset http://ipal.cnrs.fr/ICPR2012/

Cancer Image Database (caIMAGE) http://cancerim ages.nci.nih.gov/caIMAGE/

DPA’s Whole Slide Imaging Repository https://digitalpathologyassociation.org/whole-slide-imaging-repository

Atlas of bleast Histology http://www.webmicroscope.net/atlases/breast/brcatlas_start.asp

ITK Analysis of Large Histology Datasets http://www.na-mic.org/Wiki/index.php/ITK_Analysis_of_Large_Histology_Datasets

Histology Photo Album http://www.histology-world.com/photoalbum/thumbnails.php?album=52

Slide Library of Virtual pathology, University of Leeds http://www.virtualpathology.leeds.ac.uk/

Tissue Acquisition and Banking Services (TABS) of the NYU Experimental Pathology Core Facilities http://pathology.med.nyu.edu/research/core-laboratories/tissue-banking

Aperio Images http://images2.aperio.com/

HAPS Histology Image Database http://hapshistology.wikifoundry.com/

General biomedical

Whole country dataset as well as general biomedical repositories.

The Network Data Exchange (NDEx):

http://www.ndexbio.org/#/

ClinicalTrials.gov: https://clinicaltrials.gov/

Clinical Practice Research Datalink: https://cprd.com/home

The UK Data Service: https://beta.ukdataservice.ac.uk/datacatalogue/studies/#!? Search=&Page=1&Rows=10&Sort=0&DateFrom=1753&DateTo=20 19

Health data UK: https://data.gov.uk/search?filters%5Btopic%5D=Health

Health data USA: https://healthdata.gov/content/about

ClinicalStudyDataRequest.com (CSDR): https://clinicalstudydatarequest.com/Default.aspx

Data Sharing for Demographic Research (DSDR): http://www.icpsr.umich.edu/icpsrweb/content/DSDR/index.html

Archive of Data on Disability to Enable Policy (ADDEP): https://www.icpsr.umich.edu/icpsrweb/content/addep/index.html

Miscellaneous

Repositories that accept dataset from individuals, where it include dataset from almost all disciplines.

http://datadryad.org

https://figshare.com https://dataverse.harvard.edu https://zenodo.org https://data.mendeley.com

Last updated on Feb, 2023