Biology

The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data.

Automatic Non-rigid Histological Image Registration (ANHIR) consists of 2D histological microscopy images.

The American Gut project is the largest crowdsourced citizen science project to date. Fecal, oral, skin, and other body site samples collected from thousands of participants represent the largest human microbiome cohort in existence. Detailed health and lifestyle and diet data associated with each…

There are WSIs of 1058 patients, part of tumor regions are annotated in WSIs. Except for the WSIs, we have also provided the clinical data of each patient, which includes age, tumor size, tumor type, ER, PR, HER2, HER2 expression, histological grading, surgical, Ki67, molecular subtype, number of…

The Broad Bioimage Benchmark Collection (BBBC) is a collection of freely downloadable microscopy image sets. In addition to the images themselves, each set includes a description of the biological application and some type of "ground truth" (expected results).

CIMA dataset includes images of 2D histological microscopy tissue slices.

A large-scale dataset of microscopy images. Contains 890,737 total grayscale images. 894 classes (approx. 1000 images per class). Images belong to 40 openly-available datasets from Recursion, Image Data Resource, Broad Bioimage Benchmark Collection, Kaggle and the Cell Image Library.

Which SNP markers are present on consumer DNA genotyping arrays. 70 clinically discussed markers checked against the 5 published Illumina arrays that consumer chips are built on, plus 9 consumer products, giving 980 rows of marker x platform -> present / absent / unknown. Built only from public…

ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community.

The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

The Encyclopedia of DNA Elements (ENCODE) Consortium is an ongoing international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements…

EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure.

GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.

GO annotation files

The Harvard Medical School (HMS) LINCS Center is funded by NIH grant U54 HL127365 and is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. The overall goals of this program are to collect and disseminate data and analytical tools needed to understand how human…

A group of scientists at Stanford University have collaborated on a large study to understand genetic diversity in human populations. We analyzed genomic DNA from 1,043 individuals from around the world, determining their genotypes at more than 650,000 SNP loci, with the Illumina BeadStation…

The ICOS PSP benchmarks repository contains an adjustable real-world family of benchmarks suitable for testing the scalability of classification/regression methods. When we test a machine learning method we usually choose a test suite containing datasets with a broad set of characteristics, as we…

All JCB data was moved to Biostudies

KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput…

The NCBI Taxonomy database is a curated set of names and classifications for all of the organisms that are represented in GenBank. When new sequences are submitted to GenBank, the submission is checked for new organism names, which are then classified and added to the Taxonomy database. As of April…

The GDC Data Portal is a robust data-driven platform that allows users to search and download cancer data for analysis using modern web technologies.

The goal of palmerpenguins is to provide a great dataset for data exploration & visualization, as an alternative to iris.

Protein-Protein Interactions Catalog

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

The purpose of the Psychiatric Genomics Consortium (PGC) is to unite investigators around the world to conduct meta- and mega-analyses of genome-wide genomic data for psychiatric disorders.

PubChem is the world's largest collection of freely accessible chemical information. Search chemicals by name, molecular formula, structure, and other identifiers. Find chemical and physical properties, biological activities, safety and toxicity information, patents, literature citations and more.

COREMINE™ is a family of tools developed by the Norwegian bioinformatics company PubGene using the company’s patented text mining algorithms, as well as big biomedical data integration and analysis pipeline.

COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer.

The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies including Illumina, 454, IonTorrent, Complete Genomics, PacBio and OxfordNanopores. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a…

Analysis of 7.1 million RNA/DNA sequencing datasets to discover the total biodiversity of RNA viruses.

Systems Science of Biological Dynamics database (SSBD:database) provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, gene expression nuclei, etc. Quantitative biological data and microscopy image are…

The Catalogue of Life is a quality-assured checklist of more than 1.8 million species known to science.

The Personal Genome Project, initiated in 2005, is a vision and coalition of projects across the world dedicated to creating public genome, health, and trait data. Sharing data is critical to scientific progress, but has been hampered by traditional research practices. The PGP approach is to invite…

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.

Community-maintained species observation database with 180M+ observations across 370K+ taxa. Includes location, date, species ID, and photos. CC0/CC-BY licensed with open API.

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).