Data sources
Every outside dataset behind Enigma Clinical, what it is used for and the terms it comes under.
Summary
- 98
- Sources listed
- 67
- In use
- 11
- Link-out only
- 10
- Off pending licence
- 10
- Planned
- 13+ 22 to confirm
- Need a licence before resale
How Enigma Clinical uses outside data
Enigma Clinical sets its own cohort beside public reference data. The server fetches every outside source through cached routes, so the browser never calls a third party directly and no sample identifiers leave the server. Small reference tables, such as curation lists and ontology indices, are bundled with the application and refreshed from their providers; everything else is read live and cached.
Only sources whose terms allow use in a product that is sold are shown by default. Restricted sources (OMIM, OncoKB, COSMIC and the predictors that dbNSFP leaves out of its commercial build) appear only as links, and each has a switch in the deployment configuration so that a deployment holding the licence can turn it on.
Chromosomal, cytogenetic and tandem-repeat resources—including high-resolution GRCh38 cytoband ideograms (UCSC), curated human imprinted chromosomal regions for uniparental disomy (UPD), DECIPHER syndrome cross-references, STRchive pathogenic repeat loci, and standardized ISCN nomenclature—are bundled or linked under open public domain or attribution-only terms.
Terms were read on each provider’s own page on 25 Oct 2026. Where a page could not be read automatically, the table says so. This record is not legal advice: confirm the terms with each provider before the platform is resold. How to cite each source is described on the citation page.
All sources
Filter by status, category, licence type or what is needed before resale. Export downloads the filtered rows.
| Source | Status | Category | Used for | Licence | Licence type | Before resale | What the terms say | Version | Access |
|---|---|---|---|---|---|---|---|---|---|
Saudi cohortSaudi Genomics Platform | In use | Cohort | Cohort allele counts and frequencies, homozygotes and carriers; the cohort track in the genome browser. Home · Gene · Variant · Region | Owned by the operator; aggregate counts only Terms · not read automatically | Operator-owned | Operator's own data | Only aggregate counts leave the server; sample identifiers are never sent to the browser. A deployment for another institute loads that institute’s own cohort, so this data is not part of a resale. | Saudi cohort v1 | Signed-in API (server proxy) |
Enigma Clinical SV, CNV, repeat and MEI callsetsEnigma Genomics | Planned | Cohort | Cohort counts on structural-variant, CNV, repeat-expansion and mobile-element pages once the cohort is called for these classes. SV / CNV · Repeat · MEI | Owned by the operator; aggregate counts only Terms · not read automatically | Operator-owned | Operator's own data | Until callsets exist, these pages show reference data and say that cohort data are not yet available. | Not yet available | Not connected |
gnomAD v4 short variants(opens in a new tab)Broad Institute | In use | Population frequencies | Allele frequencies by genetic-ancestry group, homozygotes, filtering allele frequency, site coverage, gene and transcript models, constraint (LOEUF, missense Z) and gnomAD’s ClinVar import. Search · Gene · Variant · Transcript · Region | ODbL 1.0 Terms(opens in a new tab) · read 25 Oct 2026 | Share-alike | Attribution + share-alike | Free to share and adapt as long as public use is attributed. A database adapted from gnomAD must stay open and be offered under ODbL, which matters for any bundled or cached copy (for example the missense-constraint table in src/data/oncogenicity). gnomAD asks users to cite its papers and acknowledge the consortium. | v4.1 (live API) | Live API, no key |
gnomAD-SV v4 and exome CNV v4(opens in a new tab)Broad Institute | In use | Population frequencies | Population structural variants and exome CNVs that overlap an SV, a CNV, an insertion site or a gene. SV / CNV · MEI · Gene · Variant | ODbL 1.0 Terms(opens in a new tab) · read 25 Oct 2026 | Share-alike | Attribution + share-alike | Same terms as gnomAD: attribution of public use, and adapted databases stay open under ODbL. | gnomAD SV v4, CNV v4 (live API) | Live API, no key |
gnomAD v4 short tandem repeats(opens in a new tab)Broad Institute | In use | Population frequencies | Repeat-length distributions by genetic-ancestry group at disease loci. Repeat | ODbL 1.0 Terms(opens in a new tab) · read 25 Oct 2026 | Share-alike | Attribution + share-alike | Same terms as gnomAD: attribution of public use, and adapted databases stay open under ODbL. | v4 (live API) | Live API, no key |
Before resale
What has to be settled before the platform is sold to another institute, as the sources are used today.
Shown today, licence needed
- M-CAP(opens in a new tab) · CC BY-NC 4.0
- PrimateAI(opens in a new tab) · Free for academic and not-for-profit use; commercial licence from Illumina
Kept off until licensed
- VarSome(opens in a new tab) · Paid licence
- GeneBe(opens in a new tab) · Research and educational, non-commercial use only
- OMIM(opens in a new tab) · Licence from Johns Hopkins for any redisplay
- REVEL(opens in a new tab) · Left out of dbNSFP’s commercial build
- CADD(opens in a new tab) · Free for non-commercial applications; commercial licence through UW CoMotion
- PolyPhen-2(opens in a new tab) · Left out of dbNSFP’s commercial build
- VEST4(opens in a new tab) · Left out of dbNSFP’s commercial build
- ClinPred(opens in a new tab) · Left out of dbNSFP’s commercial build
- SpliceAI(opens in a new tab) · Precomputed scores free for academic and not-for-profit use; commercial licence from Illumina
- COSMIC(opens in a new tab) · Downloads free for academic and non-profit users; paid for for-profit organisations
- OncoKB(opens in a new tab) · Licensed non-exclusively to commercial entities by MSK
Terms silent or unclear: confirm in writing
- Monarch Initiative(opens in a new tab) · No single data licence stated; code BSD-3-Clause
- dbNSFP(opens in a new tab) · Academic build “a”; commercial build “c” leaves out PolyPhen-2, VEST, REVEL, ClinPred, CADD, LINSIGHT, GenoCanyon and MutScore
- BayesDel(opens in a new tab) · Not stated by the provider; in dbNSFP’s commercial build
- MutationTaster(opens in a new tab) · Free and open to all users; no licence stated
- FATHMM and FATHMM-XF(opens in a new tab) · Not stated by the provider
- ESM1b(opens in a new tab) · Code MIT; precomputed scores not separately licensed
- SIFT and SIFT4G(opens in a new tab) · Not stated by the provider
- MetaRNN(opens in a new tab) · Not stated by the provider
- MutationAssessor(opens in a new tab) · Not stated by the provider
- LIST-S2(opens in a new tab) · Not stated by the provider
- DEOGEN2(opens in a new tab) · Not stated by the provider
- LRT(opens in a new tab) · Not stated by the provider
- GERP++ and GERP (91 mammals)(opens in a new tab) · Not stated by the provider
- cBioPortal public studies(opens in a new tab) · ODbL; some studies restrict commercial use
- PubMed(opens in a new tab) · Citations public domain; abstracts supplied by publishers
- VariantValidator(opens in a new tab) · Code AGPL-3.0; web-service terms say nothing about commercial use
- DECIPHER(opens in a new tab) · DECIPHER Terms of Use (academic / clinical open access; bulk data display agreement required for patient records)
- EVE(opens in a new tab) · Code MIT; terms for the scores not stated
- ChimerDB 4.0(opens in a new tab) · Not stated; citation requested
- Common Metabolic Diseases Knowledge Portal(opens in a new tab) · Not yet checked
- DepMap(opens in a new tab) · Not yet checked
- Drug Repurposing Hub(opens in a new tab) · Not yet checked
Recommended attribution
Text to carry in the footer, the about page or the documentation of a deployment, one line per source or group of sources in use.
gnomAD v4 short variants, gnomAD-SV v4 and exome CNV v4, gnomAD v4 short tandem repeats
Population data from the Genome Aggregation Database (gnomAD), Broad Institute, used under the Open Database License (ODbL 1.0). Cite the gnomAD papers listed on its terms page.
STRchive
Repeat loci from STRchive by Harriet Dashnow and colleagues, licensed under CC BY 4.0 (Hiatt et al., Genome Medicine 2025).
ClinVar, MedGen, PubMed, LitVar2, PubTator3, NCBI Variation Services, dbSNP, RefSeq and NCBI Gene
Data from the National Center for Biotechnology Information (NCBI), U.S. National Library of Medicine. NCBI does not endorse this product.
ClinGen Evidence Repository, ClinGen Criteria Specification Registry (CSpec), ClinGen Allele Registry, ClinGen Dosage Sensitivity, ClinGen Gene–Disease Validity
Includes curated content from the Clinical Genome Resource (ClinGen), clinicalgenome.org (CC0 1.0).
Human Imprinted Chromosomal Regions (UPD)
Curated imprinted chromosomal regions and uniparental disomy (UPD) profiles compiled from international clinical consensus guidelines and Orphanet.
Curated Chromosomal Aneuploidy Syndromes & ISCN
Chromosomal aneuploidy syndromes and cytogenetic ISCN features curated from Orphanet and clinical consensus.
GenCC
Gene–disease validity from the Gene Curation Coalition (GenCC) and its submitters, thegencc.org (CC0 1.0).
Orphanet (Orphadata Science)
Orphadata Science: free access data from Orphanet. © INSERM 1999. Available on www.orphadata.com, data version of 23 June 2026, CC BY 4.0. Orphanet is not responsible for how this product presents the data.
Monarch Initiative
Gene, disease and phenotype associations from the Monarch Initiative knowledge graph (monarchinitiative.org) and its sources.
Mondo Disease Ontology
Disease terms from the Mondo Disease Ontology (CC BY 4.0), mondo.monarchinitiative.org.
Human Phenotype Ontology
This service/product uses the Human Phenotype Ontology (version information). Find out more at http://www.human-phenotype-ontology.org
Ontology Lookup Service (OLS4)
Ontology graphs from the EMBL-EBI Ontology Lookup Service (OLS4).
MyVariant.info
Variant annotations retrieved through MyVariant.info (BioThings).
dbNSFP
Predictor scores compiled by dbNSFP (Liu et al.), retrieved through MyVariant.info.
AlphaMissense
AlphaMissense predictions © Google DeepMind, CC BY 4.0 (Cheng et al., Science 2023).
phyloP and phastCons
Conservation scores from the UCSC Genome Browser (phyloP, phastCons).
CIViC
Clinical evidence from CIViC (civicdb.org), CC0 1.0.
Cancer Genome Interpreter biomarkers
Biomarkers from the Cancer Genome Interpreter (Tamborero et al., Genome Medicine 2018), CC0 1.0.
cBioPortal public studies
Tumour mutation data from cBioPortal for Cancer Genomics (cbioportal.org) and the original studies, under the Open Database License.
NCI Genomic Data Commons
Somatic mutation data from the NCI Genomic Data Commons (portal.gdc.cancer.gov), including TCGA.
IntOGen Compendium of Cancer Genes
Cancer driver genes from the IntOGen Compendium of Cancer Genes (release 2024.09.20, CC0 1.0).
OncoTree
Tumour types from OncoTree, Memorial Sloan Kettering Cancer Center (CC BY 4.0).
CPIC
Pharmacogenomic guideline data from CPIC® (cpicpgx.org), CC0 1.0. Guidelines are updated over time; check ClinPGx for the current version.
RxNorm (RxNav APIs)
This product uses publicly available data from the U.S. National Library of Medicine (NLM), National Institutes of Health, Department of Health and Human Services; NLM is not responsible for the product and does not endorse or recommend this or any other product.
UniProtKB
Protein data from UniProtKB, The UniProt Consortium (CC BY 4.0).
InterPro and Pfam
Protein domains from InterPro and Pfam, EMBL-EBI (CC0 1.0).
AlphaFold Protein Structure Database
Structure predictions from the AlphaFold Protein Structure Database (DeepMind and EMBL-EBI), CC BY 4.0.
GTEx Portal
Expression and QTL data from the GTEx Portal (gtexportal.org), Adult GTEx V11, retrieved on the date shown.
Europe PMC
Citation data from Europe PMC (EMBL-EBI).
ClinicalTrials.gov
Clinical trial records from ClinicalTrials.gov (U.S. National Library of Medicine), processed on the date shown. Enigma Clinical filters and summarises these records.
Ensembl REST and VEP
Variant consequences from Ensembl VEP (EMBL-EBI).
HGNC
Gene nomenclature from Genenames.org, the HGNC resources (CC0).
UCSC Genome Browser
Reference data from the UCSC Genome Browser (genome.ucsc.edu).
UCSC GRCh38 Cytobands & ISCN Ideograms
Chromosomal cytobands and coordinates derived from the UCSC Genome Browser GRCh38 cytoBand table (genome.ucsc.edu).