1000 Genomes Project internationalgenome.org

Reference panel of human genetic variation from 2,504 individuals across 26 populations.

DeepDSC ieeexplore-ieee-org.ezp2.lib.umn.edu

Autoencoder + fully connected NN.

Therapeutic Target Database idrblab.net

Drug-target, target-disease, and drug-disease datasets.

ICD10 icd.who.int

International Classification of Diseases, 10th revision.

Human Cell Atlas humancellatlas.org

Open global atlas of all cells in the human body.

BioMedLM huggingface.co

2.7B parameter GPT-2-style language model trained exclusively on biomedical literature from PubMed for biomedical question answering and text generation.

Virchow2 huggingface.co

632M-parameter pathology vision transformer pretrained on 3.1M whole-slide images with mixed-magnification self-supervision.

Virchow huggingface.co

Million-slide digital pathology foundation model using a vision transformer and self-supervised distillation for tile-level pathology image representation.

Phikon-v2 huggingface.co

Updated pathology foundation model for general-purpose histology feature extraction and transfer learning.

Phikon huggingface.co

ViT-based pathology foundation model pretrained with iBOT self-supervision on TCGA whole-slide images.

BiomedCLIP huggingface.co

CLIP-based vision-language foundation model for biomedical images and text trained on PubMed figure–caption pairs.

Tahoe-100M huggingface.co

Giga-scale single-cell perturbation atlas with >100 million profiles from 50 cancer cell lines exposed to ~1,100 small molecules.

TCGA virtual spatial transcriptomics atlas huggingface.co

DeepSpot-M predicted transcriptome-wide ST for TCGA H&E (FF + FFPE; 28,664 slides / 32 cancer types; gated). Paper: DeepSpot-M.

HEST Xenium virtual spatial transcriptomics huggingface.co

DeepSpot-M predicted transcriptome-wide ST for 59 HEST-1k 10x Xenium samples (~13.3M cells) (gated). Paper: DeepSpot-M.

Geneformer huggingface.co

Context-aware, attention-based deep learning model pretrained on a large corpus of single-cell transcriptomes.

H-Optimus-1 huggingface.co

1.1B-parameter pathology foundation model trained on billions of histology images from more than one million slides and 800K+ patients.

H-Optimus-0 huggingface.co

1.1B-parameter histopathology foundation model trained with self-supervised learning on a large multi-center slide corpus.

UNI2-h huggingface.co

Billion-parameter histopathology vision foundation model for tile-level feature extraction and downstream computational pathology tasks.

AI4Chem/ChemLLM-7B-Chat huggingface.co

LLM for chemical & molecular science.

Human Phenotype Ontology (HPO) hpo.jax.org

Standardized vocabulary of phenotypic abnormalities in human disease, linking genes, variants, and clinical features.

HMDB (Human Metabolome Database) hmdb.ca

Comprehensive database of small molecule metabolites found in the human body.

The Genotype-Tissue Expression (GTEx) gtexportal.org

Human gene expression and regulation resource.

MSigDB (Molecular Signatures Database) gsea-msigdb.org

Curated gene sets derived from pathways and biological processes.

TRRUST v2 grnpedia.org

Manually curated database of human and mouse transcriptional regulatory interactions between transcription factors and their target genes, expanded with literature-derived evidence.

DrugBank go.drugbank.com

Database of drugs and targets (University of Alberta).

gnomAD gnomad.broadinstitute.org

Genome Aggregation Database; genetic variation from large-scale sequencing projects.

MOFGCN github.com

GCN + heterogeneous network.

Drug Mechanism Database (DrugMechDB) github.com

Mechanisms of action from drug to disease.

Uni-Mol2 github.com

Scaled molecular pretraining model using atomic, graph, and 3D geometry features, with models up to 1.1B parameters pretrained on 800M conformations.

Enformer github.com

Transformer model predicting gene expression from DNA sequence.

KEGG PATHWAY genome.jp

Collection of pathway maps.

KEGG DRUG genome.jp

Comprehensive, approved drug information.

KEGG COMPOUND genome.jp

Collection of small molecules and biopolymers.

QM9 figshare.com

Quantum chemistry properties for 134K stable small organic molecules computed at DFT level.

Norman et al. 2019 CRISPRa Perturb-seq figshare.com

Large-scale CRISPR activation Perturb-seq in K562 cells spanning single-gene and combinatorial perturbations.

FANTOM5 fantom.gsc.riken.jp

Functional annotation of mammalian genome; comprehensive atlas of active enhancers, promoters, and transcription start sites across human and mouse cell types.

EU Drug Regulating Authorities Clinical Trials DB (EudraCT) eudract.ema.europa.eu

European clinical trial database.

ENCODE encodeproject.org

Encyclopedia of DNA Elements; regulatory and functional genomic elements across the genome.

MGnify ebi.ac.uk

Resource for metagenomic and metatranscriptomic data.

Pfam ebi.ac.uk

Database of protein families described by multiple sequence alignments and hidden Markov models.

InterPro ebi.ac.uk

Protein families, domains, and functional sites database integrating 14 member databases including Pfam and PROSITE.

IntAct ebi.ac.uk

Open-source molecular interaction database and analysis system from EMBL-EBI.

ChEMBL Web Services ebi.ac.uk

REST API for bioactive molecules, targets, and bioassays.

ChEMBL ebi.ac.uk

Bioactive molecules with drug-like properties.

ChEBI ebi.ac.uk

Database focused on small chemical compounds.

DUD-E (Directory of Useful Decoys, Enhanced) dude.docking.org

Structure-based virtual screening benchmark with active ligands and challenging decoy sets across diverse protein targets.

NCI60 dtp.cancer.gov

Focuses on 60 cancer cell lines and many drugs.

DrugTargetCommons drugtargetcommons.fimm.fi

Community platform for curating and integrating experimental bioactivity data across drugs and targets.

DrugCentral drugcentral.org

Online drug compendium with drug mode of action and indication information.

CLM-X doi.org

Multi-way Transformer foundation model jointly handling RNA-only, ATAC-only, and paired RNA–ATAC single-cell inputs for integration, translation, annotation, and perturbation prediction.