Datasets

The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the pub

Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve

BindingDB is the first public database of protein-small molecule affinity data.

PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records.

ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.

RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases.

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be b

The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype.

The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation.

The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.

The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information.

The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

Images and other data from the JUMP Cell Painting Consortium

Benchmark datasets, data loaders, and evaluators for graph machine learning

Foster the development of impactful AI models in drug discovery.

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

cz-benchmarks is a package for standardized evaluation and comparison of machine learning models for biological applications.

Formalizing and benchmarking open problems in single-cell genomics

CZ CELLxGENE Discover Census

Benchmarking DNA Language Models on Biologically Meaningful Tasks