Data sources & attribution¶
Yeliztli's own source code is released under the MIT license. To annotate your genome it
draws on several public scientific datasets, each retained under its own license. This
page summarises them; the repository
NOTICE file holds the full,
authoritative attribution text, and LICENSE
covers Yeliztli's code.
For sizes and how each is obtained, see reference data.
Bundled / redistributed data¶
These are packaged with Yeliztli (or its release bundles), so their licenses permit redistribution.
| Source | Used for | License | Key citation |
|---|---|---|---|
| gnomAD v2.1.1 (GRCh37) | Population allele frequencies, observed allele counts, and homozygous counts only | CC0 1.0 | Karczewski et al., Nature 581:434 (2020), doi:10.1038/s41586-020-2308-7 |
| ClinGen gene–disease validity | Context-only gene-validity guardrail | CC0 1.0 (attribution requested) | Strande et al., AJHG 100:895 (2017), doi:10.1016/j.ajhg.2017.04.015 |
| AlphaMissense (hg19) | Missense-pathogenicity context (complements REVEL) | CC-BY-4.0 (per Zenodo record 10813168) | Cheng et al., Science 381:eadg7492 (2023), doi:10.1126/science.adg7492 |
| PharmGKB (LoE + DPWG) | Cross-source pharmacogenomic evidence, context-only | CC-BY-SA-4.0 (share-alike honored) | Whirl-Carrillo et al., CPT 110:563 (2021), doi:10.1002/cpt.2350 |
| FDA PGx labeling (via PharmGKB) | Drug-label testing-level classification, context-only | CC-BY-SA-4.0 (PharmGKB derivative; FDA text is public-domain) | — |
| GTEx v8 | Tissue eQTL regulatory context (summary stats only) | Open-access summary statistics | GTEx Consortium, Science 369:1318 (2020), doi:10.1126/science.aaz1776 |
| PGS Catalog (3 bundled scores) | Polygenic-score weights — research-use only | CC-BY-4.0 (per score) | Lambert et al., Nat. Genet. 56:1989 (2024), doi:10.1038/s41588-024-01937-x |
Only redistributable scores are bundled
Of the PGS Catalog, only the clearly redistributable CC-BY-4.0 scores are bundled — PGS000713 (type-2 diabetes), PGS005198 (BMI), and PGS000688 (LDL cholesterol). Non-commercial or author-restricted scores (such as the eBMD score, PGS000657) are not bundled and must be fetched by the user. Yeliztli deliberately excludes academic-license-restricted predictor columns (SpliceAI, CADD, REVEL, SIFT, PolyPhen) from the gnomAD bundle.
Downloaded from the provider¶
The complete runtime exports are fetched from their original providers during setup/updates
and used locally; Yeliztli does not redistribute those full runtime files. Compact public
provenance excerpts may be retained under data/science-evidence/ with their documented,
artifact-specific terms.
| Source | Used for | License |
|---|---|---|
| ClinVar (NCBI) | Clinical variant classifications | Public domain |
| dbNSFP | In-silico predictions (REVEL, CADD, …) | Academic / non-commercial |
| CPIC | Pharmacogenomic allele & guideline data | CC0-1.0 |
| PharmVar | Star-allele definitions | Open |
| GWAS Catalog (EBI) | Trait/disease associations | Open |
| dbSNP (NCBI) | rsID identity resolution | Public domain |
| MONDO / Human Phenotype Ontology | Disease-scoped phenotype associations | MONDO download formats: CC BY 4.0; HPO: project terms requiring acknowledgement/citation, displayed version/date, and unaltered HPO files |
UCSC Genome Browser hg19 + RefSeq (refGene) |
Optional local Genome Browser reference sequence and gene track | UCSC Genome Browser data terms |
| Ensembl VEP | Variant consequence predictions (the VEP bundle) | Open (Ensembl) |
Mind the licenses for your use
Some sources — notably dbNSFP (academic/non-commercial) and the share-alike PharmGKB/FDA-derived data — carry conditions. If you build on Yeliztli or its data, make sure your use complies with each source's terms.
MONDO and HPO acknowledgement
This service uses the Human Phenotype Ontology (HPO). HPO source versions and dates are recorded with installed reference data and with any publicly displayed HPO excerpt; see the HPO license and requested citation. MONDO's published download formats are listed as CC BY 4.0 on its download page. Individual mapping artifacts can carry more specific or different metadata, so Yeliztli records source-level terms rather than treating the broad MONDO notice as an automatic license for every file.
Independence¶
"gnomAD", "Broad Institute", "ClinGen", "AlphaMissense", "Google DeepMind", "PharmGKB", "DPWG", "FDA", "GTEx", "PGS Catalog", "UCSC Genome Browser", "RefSeq", and other names appear here solely for source attribution. Yeliztli is an independent project and is not affiliated with, sponsored by, or endorsed by any of these organisations.