Data sources
Data source inventory.
- Sources
- 48 +21 sub
- Categories
- 7
By category
- Genome 13
- Transcriptome 11
- Ont & Lit 11
- Proteome 10
- Therapeutics 6
- Visualization 2
- Phenome 1
Key highlights
- Genome
- Clinical variants (ClinVar, Orphanet), common & rare-variant GWAS/PheWAS, fine-mapped credible sets, somatic cancer mutations, gnomAD constraint, polygenic risk scores, eQTL/cCRE overlays
- Transcriptome
- Bulk and single-cell expression across normal tissues, tumors, and cell lines (GTEx, TCGA, HPA, CPTAC, CELLxGENE); CRISPR/DepMap genetic dependencies; cross-species orthology (Bgee)
- Proteome
- Protein-protein interactions (BioGRID, InnateDB, MatrixDB, STRING), UniProt features & domains, plasma pQTLs (UKB-PPP, SomaScan), tumor proteomics
- Phenome
- UK Biobank case/control cohorts, phenotype labels, and ICD-10/EFO mappings
- Therapeutics
- Drug-target-indication evidence (ChEMBL, IDG), drug sensitivity (PharmacoDB), antibody-drug conjugates (ADCdb), antibody sequences (PLAbDab), clinical trials
- Ont & Lit
- Disease ontologies (MONDO, EFO, HPO, Orphanet, ICD-10, UMLS, OncoTree), pathway/function (GO, Reactome, MSigDB, OmniPath), tissue/anatomy (UBERON), literature (EuropePMC, OpenAlex, NCBI)
- Visualization
- 3D protein structures (AlphaFold, PDBe, SWISS-MODEL), homology & isoform models, subcellular localization pictograms
Complete list
| Data source ↕ | Category ↑ | Summary statistics |
|---|---|---|
| Cancer Hotspots | Genome | 2,675 variants · 224 transcripts |
| cBioPortal | Genome | 8,815,313 mutations · 495 sources |
| CIViC | Genome | clinical interpretations of variants |
| ClinVar | Genome | 553,894 variants · 29,025 phenotypes |
| EBI eQTL Catalogue | Genome | 32 studies |
| ENCODE SCREEN cCREs | Genome | ~2.3M cCREs |
| Ensembl | Genome | 87,893 genes |
| FinnGen | Genome | 11,814 targets · 2,591 phenotypes |
| GENIE | Genome | 290,583 variants · 1,738 transcripts |
| gnomAD | Genome | ~17,500 transcripts |
| GWAS Catalog | Genome | 255,022 variants · 12,583 phenotypes |
| Open Targets Scores | Genome Transcriptome Proteome Ont & Lit | 12 sub-sources |
| Open Targets Platform | Genome | 78,691 targets · 47,030 diseases · 22,230 drugs · 34M+ evidence strings |
| Open Targets Genetics Portal | Genome | 17,982 targets · 4,202 phenotypes |
| CRISPRbrain | Transcriptome | 7,329 targets · 45 phenotypes |
| DepMap CRISPR Genetic Dependency | Transcriptome | 302 targets · 99 phenotypes |
| Expression Atlas | Transcriptome | 24,786 transcripts · 856 phenotypes |
| Project Score | Transcriptome | 302 targets · 99 phenotypes |
| EuropePMC | Ont & Lit | 23,744 targets · 14,017 phenotypes |
| Experimental Factor Ontology (EFO) | Ont & Lit | 12,690 phenotypes · 48,436 cross-references |
| Human Phenotype Ontology (HPO) | Ont & Lit | 2,293 phenotypes |
| MONDO | Ont & Lit | 12,996 terms |
| Ontology of Biological Attributes (OBA) | Ont & Lit | 17,394 terms |
| UBERON | Ont & Lit | 819 terms · 208 tissue groups |
| Orphanet | Genome Ont & Lit | 2,300 phenotypes · 7,875 cross-references |
| PGS Catalog | Genome | 5,332 models · 669 traits · 781 publications |
| Gene Ontology (GO) | Ont & Lit | 40,440 terms |
| ICD-10 | Ont & Lit | 4,068 phenotypes |
| Molecular Signatures Database (MSigDB) | Ont & Lit | 6,269,060 gene-set memberships |
| NCBI | Ont & Lit | 95M+ gene records |
| OmniPath | Ont & Lit | 100+ resources |
| OncoTree | Ont & Lit | 834 oncotree codes · 257 cancer types |
| OpenAlex | Ont & Lit | 309M+ scholarly works |
| REACTOME | Ont & Lit | 2,863 pathway annotations |
| UMLS CUI | Ont & Lit | 726 phenotypes |
| UK Biobank | Phenome | 20,119 targets · 7,266 phenotypes |
| BioGRID | Proteome | 18,471 proteins · 5,840,810 interactions |
| InnateDB | Proteome | 3,737 proteins · 33,359 interactions |
| MatrixDB | Proteome | 10,423 proteins · 443,458 interactions |
| SomaScan Soon | Proteome | aptamer-based proteomics (Fenland / INTERVAL / deCODE) |
| STRING Soon | Proteome | 12,174 proteins · 8,387,240 interactions |
| UKB-PPP | Proteome | 2,941 proteins · 54,306 participants · 14,287 pQTLs |
| UniProt | Proteome | 20,779 protein-coding genes · 43,114 reviewed proteins · 1,425,900 features + domains |
| ADCdb | Therapeutics | 327 antigens · 6,500+ ADCs |
| ChEMBL | Therapeutics | 2,898,002 compounds · 1,001 targets · 2,811 indications |
| ClinicalTrials.gov | Therapeutics | 581,326 trials |
| Illuminating the Druggable Genome (IDG) | Therapeutics | 256 targets · 15,054 phenotypes |
| PharmacoDB | Therapeutics | 55,302 compounds · 5,712,751 measurements |
| PLAbDab | Therapeutics | 150,000+ antibody sequences |
| Bgee | Transcriptome | 60,490 genes · 3 species |
| CELLxGENE Discover | Transcriptome | 33M+ cells · 436 datasets · 2,700+ cell types |
| CPTAC (pancan) | Transcriptome Proteome | 104,235 transcripts · 1,565 samples · 10 datasets |
| Gene Expression Omnibus (GEO) Soon | Transcriptome Proteome | 273,310 series · 4,352 datasets |
| GTEx | Transcriptome | 58,988 transcripts · 68 tissues |
| Human Protein Atlas | Transcriptome Proteome | 20,141 transcripts · 59 tissues |
| PanglaoDB | Transcriptome | 178 cell types |
| Prostate Cancer Atlas | Transcriptome Proteome | 92,144 samples |
| TCGA | Transcriptome | 17,102 transcripts · 13,454 samples · 34 datasets |
| TCGA/TARGET/GTEx (UCSC XenaBrowser) | Transcriptome | 17,409 transcripts · 28,823 samples · 37 datasets |
| SWISS-MODEL | Visualization | 3,939,534 models · 234,439 structures · 12 proteomes |
| SwissBioPic Soon | Visualization | ~50 species with subcellular pictograms |
| 3D Beacons | Visualization | 9 sub-sources |
| AlphaFill Soon | Visualization | derived from 200M+ AlphaFoldDB |
| AlphaFoldDB Soon | Visualization | 200M+ structures · 48 proteomes |
| HegeLab Soon | Visualization | ~2K human isoform structures |
| isoform.io Soon | Visualization | 237,275 isoforms |
| LevyLab Soon | Visualization | ~2K quaternary-assembly models |
| ModelArchive Soon | Visualization | ~50K+ archived models |
| Protein Data Bank in Europe (PDBe) Soon | Visualization | 252,091 structures |
| Protein Ensemble Database (PED) Soon | Visualization | ~600 IDP ensembles |
| Small Angle Scattering Biological Data Bank (SASBDB) Soon | Visualization | 5,275 datasets · 6,482 models |
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