JoGo License

Last updated: 2025-08-13 (JST)

Summary

  • Portal content (website text, documentation, figures, UI layouts, screenshots): CC BY-SA 4.0 — free for all users (including commercial), with attribution and ShareAlike. License
  • Haplotype database (ACTG haplotype IDs, corresponding sequences, population frequency tables, and related per-gene metadata): ODbL 1.0 — free to use (including commercial). If you Publicly Use or distribute a Derivative Database, it must be re-published in compliance with the ODbL 1.0 terms. License
  • JoGo name & logo (trademarks) + Selected visual assets (ACTG-haplotype / ACTG-haplotype-structure) : governed by the Brand & Visual Assets Terms (v1.0). These items are not licensed under CC BY-SA or ODbL.

Scope

Portal Content

Text, explanatory materials, documentation pages, figures/diagrams, screenshots, and UI/layout elements provided on the JoGo website.

JoGo Haplotype Database

Structured datasets covering ACTG haplotype identifiers, their corresponding sequences, population frequency tables, and related per-gene metadata curated by the JoGo project.

Exclusions and routing: Third-party materials remain under their own licenses. The JoGo name and logo and the specific ACTG visual diagrams (ACTG-haplotype, ACTG-haplotype-structure) are governed by the Brand & Visual Assets Terms.

Exclusions: Third-party data, figures, and literature displayed or linked in JoGo remain under their respective licenses (e.g., GTEx, ClinVar, GWAS Catalog, DDBJ/INSDC). JoGo does not re-license third-party materials. The JoGo name and logo, and the ACTG visual diagrams, are not covered by CC BY-SA or ODbL. See Brand & Visual Assets Terms for permitted uses.

Key Terms

CC BY-SA 4.0 (Portal Content)

  • Commercial use permitted
  • Attribution required
  • ShareAlike for modified/distributed content

Credit example:
“Portions of this documentation are © JoGo Project, licensed under CC BY-SA 4.0.”

ODbL 1.0 (Haplotype Database)

  • Commercial use permitted / Attribution required
  • If you Publicly Use or distribute a Derivative Database (e.g., a re-structured or merged database based on JoGo), it must be re-published in compliance with the ODbL 1.0 terms.
  • Produced Work (reports, figures, scores that are not a database) may be distributed under your own terms, provided proper attribution to JoGo is given.

Screenshots & mixed content: Website screenshots are Portal Content under CC BY-SA 4.0. The presence of the JoGo logo or an ACTG diagram within a screenshot does not grant standalone branding or diagram rights: do not extract and reuse the logo as a mark, and do not reuse the ACTG diagrams outside the screenshot context except as permitted by the Brand & Visual Assets Terms. Elements from third parties shown within screenshots remain under their respective licenses.

Note — ShareAlike: When an adapted/merged database based on JoGo is made available to anyone outside your organization (by distributing copies or providing its functionality via a site/API, whether free or paid, open or restricted), the adapted database must be re-published in compliance with the ODbL 1.0 terms. Produced Works are excluded.

Definition notes (ODbL-aligned)

  • Publicly Use: making the Database or a Derivative Database, or a Substantial part of it, available to parties outside your organization, either by providing copies or by providing its functionality (e.g., web app, API, SaaS, subscription portal), free or paid, open or restricted-access.
  • Internal Use: use within the same legal entity (employees/contractors). Internal Use alone does not trigger ShareAlike.
  • Substantial: a quantitatively or qualitatively substantial part of the Database.
  • Derivative Database: a database adapted from or combined with the JoGo Database Content.

Examples: (Produced Work) per-sample ACTG inference reports (PDF/images/scores), non-reconstructable visualizations; (Derivative Database) publishing a new database by adding columns to JoGo, or Publicly Using a merged database (e.g., via a web app or API offered to users outside your organization, free or paid).

Versioning & Archival

  • The portal operates a Latest version.
  • Major releases (e.g., v1.0, v2.0) will be archived with persistent DOIs; DOI details will be added after acceptance.
  • See Updates for release notes.

Disclaimer

This page is for information only and does not constitute legal advice. The JoGo Project provides the content and data "as is" without warranties of any kind. Use at your own risk.

Citation

If you use the JoGo database in your research, please cite the following publication:

Nagasaki M, Katayama T, Moriya Y, Sekiya Y, Kawashima S, Teraoka R, Machida S, Matsubara T, Hashimoto H, Asakura A, Nagano A, Yamashita R, Takada T, Mitsuhashi N, Kamada M, Ohkawa Y, Tokunaga K, Kawai Y; Variant Information Standardization Collegium.
JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes.
Nucleic Acids Res. 2025 Nov 29:gkaf1232.
DOI: 10.1093/nar/gkaf1232
PMID: 41316730

Third-Party Data Licenses

JoGo uses third-party resources to enrich haplotype annotations. The following sections summarize how we use each resource and the terms that apply. Please refer to the linked license pages for the complete and authoritative terms.

Genotype-Tissue Expression (GTEx) Project

JoGo uses GTEx Release v10 to report whether variants contained in registered haplotypes are associated with gene expression (eQTLs).

  • Use of GTEx data in JoGo complies with the GTEx Portal Data License.
  • If you use annotations in JoGo that are based on variants from the GTEx database, you must include the attribution specified by GTEx in any publications, reports, or websites.
  • We do not indicate or imply endorsement by the GTEx Portal. Where we present GTEx-derived content, we display the GTEx release used and link to the Portal for the most current data.
  • Required attribution format (per GTEx license):
    “The data used for the analyses described in this manuscript were obtained from: [insert, where appropriate] the GTEx Portal on MM/DD/YY and/or dbGaP accession number phs000424.vN.pN on MM/DD/YYYY.”

ClinVar

JoGo uses ClinVar to annotate haplotypes with clinical significance. The version currently integrated is clinvar_20250715.vcf.gz (retrieved on 2025-07-15).

  • Use follows ClinVar’s guidance: Accessing and using data in ClinVar.
  • If you use annotations in JoGo that are based on variants from the ClinVar database, you must provide attribution to ClinVar as the data source, in accordance with ClinVar’s guidance (e.g., citing a ClinVar publication).
  • Information from ClinVar is not intended for direct diagnostic use. JoGo does not imply endorsement by ClinVar, NCBI, NIH, or associated entities.
  • Where available, JoGo displays submitter names/identifiers and other provenance fields as provided in ClinVar records.

NHGRI-EBI GWAS Catalog

JoGo uses the NHGRI-EBI GWAS Catalog to annotate haplotypes with reported trait associations (dataset retrieved on 2025-07-17).

  • Use complies with the EMBL-EBI Terms of Use.
  • If you use annotations in JoGo that are based on variants from the GWAS Catalog, you must provide attribution to the GWAS Catalog in accordance with its licensing terms.
  • Summary statistics are made available under CC0 unless otherwise stated by individual datasets; JoGo respects dataset-specific license terms.
  • GWAS Catalog logos and data visualisations (e.g., the GWAS Diagram and LD plots) are available for re-use under CC BY 4.0.
  • Code for the GWAS Catalog infrastructure is available under the Apache 2.0 license.
  • JoGo provides attribution to the GWAS Catalog and does not imply endorsement.

For additional details, see the GWAS Catalog “About” page: Licensing information.