PDX-Atlas muralportal.pdxatlas.org

Portal integrating clinical, genomic, transcriptomic, and drug-response data from patient-derived xenograft models.

MoNA MassBank of North America mona.fiehnlab.ucdavis.edu

Meta-database of metabolite mass spectra, metadata, and associated compounds.

MoleculeNet moleculenet.ai

Benchmark datasets for molecular machine learning.

miRBase mirbase.org

Reference repository for microRNA gene annotations, sequences, and experimentally validated targets.

MIMIC-IV mimic.mit.edu

Freely accessible critical care database.

MDAnalysis mdanalysis.org

Python library for analyzing and altering molecular dynamics simulation trajectories.

MassBank massbank.jp

Open source databases and tools for mass spectrometry reference spectra.

LIPID MAPS lipidmaps.org

Database of lipids.

LINCS L1000 lincsproject.org

Gene expression profiles (978 landmark genes) for >20,000 chemical and genetic perturbations across cell lines.

KEGG REST API kegg.jp

API for accessing KEGG pathways, compounds, genes, and reactions.

BACE kaggle.com

Binary classification and regression dataset for β-secretase 1 (BACE-1) inhibitor binding affinity.

JASPAR jaspar.genereg.net

Database of transcription factor binding profiles.

Kinase Inhibitor Bioactivity Data (KIBA) janeliascicomp.github.io

Integrated bioactivity scores for kinase inhibitors combining Ki, Kd, and IC50 measurements.

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.

SpatialGlue github.com

Graph attention network for spatial multi-omics integration jointly embedding spatial transcriptomics with chromatin accessibility or proteomics.

SaProt github.com

Structure-aware protein language model using structure-aware tokens that encode both sequence and backbone geometry for improved function prediction.

MOFGCN github.com

GCN + heterogeneous network.

Drug Mechanism Database (DrugMechDB) github.com

Mechanisms of action from drug to disease.

TOSICA github.com

Transformer-based framework for one-stop interpretable cell-type annotation supporting cross-dataset and cross-species transfer.

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.

HiDRA github.com

Hierarchical network model incorporating gene and pathway-level information for cancer drug response prediction.

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.