This is a curated list of computational biology datasets that have been pre-processed for machine learning. This list is a work in progress.
Genotyping
| The Cancer Genome Atlas | Variety of Cancer Data, most cancer types have 100-1000 samples |
| NIH GDC | Cancer, many types of genomic data |
| UK Biobank | |
| European Genome-Phenome Archive | |
| METABRIC | The genomic profiles (somatic mutations, copy number alterations, and gene expression) of 2509 breast cancers |
| HapMap | |
| 23andMe | 2280 public domain curated genotypes |
| Mice | SNPs, 2000+ samples, 4 generations, might be possible to learn a family structure |
| Arabidopsis | SNPs, 100+ phenotypes |
Promoter-Enhancer Pairs
| TargetFinder | ~100,000 DNA-DNA interaction pairs |
Gene/Protein Expression
| GEO | Main place for NCBI data |
| ENCODE | Variety of assays to identify functional elements |
| ArrayExpress | DNA sequencing, gene/protein expression, epigenetics |
| Cytometry Continuous | Flow cytometry data of 11 proteins+phospholipids, discretized and cleaned data available offline |
| Transcription Factor Binding | ChIP-Seq data on 12 TFs |
| GTEx | Landmark study for EQTL analysis |
| PharmacoGenomics DB | |
| ProteomeXChange |
Single-cell Data
| Single-cell Expression Atlas |
Regulatory Networks
| TRRUST | Manually curated database of human transcriptional regulatory network |
| Yeast Network | 23-million yeast 2-hybrid experiments to investigate genetic interactions |
| Perturb-Seq | Integrated model of perturbations, single cell phenotypes, and epistatic interactions |
| KEGG Metabolic Regulatory Network (Undirected) | 65554 instances, 29 attributes each |
| KEGG Metabolic Regulatory Network (Directed) | 53414 instance, 24 attributes each |
Images
| The Cancer Imaging Archive | Extracts the images from the TCGA data |
| Multiple Myeloma DREAM Challenge | Challenge to identify Multiple Myeloma Patients |
| Breast Cancer Wisconsin (Diagnostic) Data Set | Predict whether the cancer is benign or malignant |
| DDSM | Mammogram Database |
| Kaggle Soft Tissue Sarcomas | Preprocessed subset of the TCIA study “Soft Tissue Sarcoma” |
| Kaggle Cervical Cancer Screening | Classify cervix type from images |
| CMELYON17 | Pathology challenge – automated detection and classification of breast cancer metastases in whole-slide images of histological lymph node sections |
| Grand Challenges | Datasets from biomedical image analysis competitions |
fMRI
| ENGIMA Cerebellum | Goal: Examine the relationships between regional atrophy and motor and cognitive dysfunction |
| Seizure Prediction | Goal: Classify EEG time series into pre-seizure vs. interictal (i.e., not preceding a seizure). |
Electronic Medical Records
| MIMIC | 59,000 EHRs |
| UCI Diabetes | 130 US hospital data for 1999-2008 |
| i2b2 | Clinical notes only, designed for NLP tasks |
| PhysioNet | |
| Metadata Acquired from Clinical Case Reports (MACCRs) | 3,100 curated clinical case reports spanning 15 disease groups and more than 750 reports of rare diseases |
| eICU | 200k EHRs |
Radiographs
| CheXPert | 200k chest radiographs, Competition and leaderboard associated |
| MIMIC-CXR | ~400k chest x-rays, 14 labels |
| PadChest | 160k chest x-rays, 174 different findings |
Protein-Protein Interactions
| HINT (High-quality INTeractomes) | curated compilation of high-quality protein-protein interactions from 8 interactome resources |
Longitudinal Studies
| National Population Health Survey | Longitudinal Survey that collects health information via surveys every two years. |
Protein Structure
| ProteinNet | Standardized dataset for learning protein structure. Includes sequences, structures, alignments, PSSMs, and standardized train/test/valid splits. |
Natural Language Data
| BioASQ | Abstracts of medical articles (from PubMed); ontologies of medical concepts. |
| Cases | Articles from medical case studies |
| UPMC Pathology | UPMC Pathology case studies |
If you have any recommendations for additional data sets, please email: msvogt2@illinois.edu