Data sources
Data source inventory.
- Sources
- 53 +20 sub
- Categories
- 7
By category
- Genome 15
- Ont & Lit 13
- Transcriptome 11
- Proteome 10
- Therapeutics 7
- Visualization 3
- Phenome 2
Key highlights
- Genome
- Clinical variants (ClinVar, Orphanet), structural variation (dbVar), 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 from population cohort studies (Open Targets Platform), tumor proteomics
- Phenome
- UK Biobank case/control cohorts, phenotype labels, and ICD-10/EFO mappings; cross-species knockout phenotypes (IMPC)
- Therapeutics
- Drug-target-indication evidence (ChEMBL, IDG), pharmacogenomics (ClinPGx), 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), patents (Google Patents, EPO)
- 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 |
| dbVar | Genome | 6M+ variants |
| 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 | 11 sub-sources |
| Open Targets Platform Includes plasma proteomics data from large-scale population cohort studies. | Genome Proteome | 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 |
| 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 |
| European Patent Office (EPO) | Ont & Lit | ~150M records |
| Gene Ontology (GO) | Ont & Lit | 40,440 terms |
| Google Patents | Ont & Lit | ~150M records |
| 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 |
| International Mouse Phenotyping Consortium (IMPC) | Phenome | ~9,000 targets · 1,000+ 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 |
| STRING Soon | Proteome | 12,174 proteins · 8,387,240 interactions |
| 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 |
| ClinPGx | Therapeutics | 700+ compounds |
| 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 |
| No sources match your search. | ||
Data attributions
Kasvu Discovery integrates data from a wide range of publicly available scientific databases and resources. We are grateful to the teams and communities behind each of these efforts. Where required by licence terms, we provide the following attributions.
- UK Biobank
- Genomic and phenotypic summary statistics are sourced via the Pan-UK Biobank project and used in accordance with the UK Biobank terms of access. Karczewski, Gupta, Kanai et al., "Pan-UK Biobank GWAS improves discovery, analysis of genetic architecture, and resolution into ancestry-enriched effects." medRxiv. 2024. doi: 10.1101/2024.03.13.24303864.
- gnomAD
- Data from the Genome Aggregation Database (gnomAD). Karczewski et al., "The mutational constraint spectrum quantified from variation in 141,456 humans." Nature. 2020. doi: 10.1038/s41586-020-2308-7.
- Gene Ontology
- Gene Ontology data and data products are licensed under the Creative Commons Attribution 4.0 International licence. Ashburner et al., "Gene Ontology: tool for the unification of biology." Nature Genetics. 2000. doi: 10.1038/75556. The Gene Ontology Consortium, "The Gene Ontology knowledgebase in 2023." Genetics. 2023. doi: 10.1093/genetics/iyad031.
- GTEx
- Data were obtained from the GTEx Portal. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health.
- TCGA
- Data were generated by The Cancer Genome Atlas Research Network. We acknowledge the TCGA Research Network and the study participants who contributed to this resource.
- Human Protein Atlas
- Data from the Human Protein Atlas, available at proteinatlas.org. Uhlén et al., "Proteomics: Tissue-based map of the human proteome." Science. 2015. doi: 10.1126/science.1260419.
- ChEMBL
- Data sourced from ChEMBL (EMBL-EBI), made available under the Creative Commons Attribution-ShareAlike 3.0 Unported licence (CC BY-SA 3.0).
- FinnGen
- We acknowledge the FinnGen study. Kurki et al., "FinnGen provides genetic insights from a well-phenotyped isolated population." Nature. 2023. doi: 10.1038/s41586-022-05473-8.
- ICD-10
- ICD-10 codes are copyright of the World Health Organization. Source: World Health Organization. Used under the Creative Commons Attribution-NoDerivs 3.0 IGO licence (CC BY-ND 3.0 IGO).
- Reactome
- Pathway data sourced from Reactome, a free, open-source, curated and peer-reviewed pathway database. Gillespie et al., "The reactome pathway knowledgebase 2022." Nucleic Acids Research. 2022. doi: 10.1093/nar/gkab1028.
- UMLS
- UMLS terminology data sourced from the Unified Medical Language System (UMLS), National Library of Medicine, National Institutes of Health.
All third-party database names and trademarks are the property of their respective owners. Listing a data source on this page does not imply endorsement by, or affiliation with, the providing organisation.