Data Use and Citation¶

ClinVar-GKM re-represents ClinVar data. ClinVar is produced by the National Center for Biotechnology Information (NCBI), part of the U.S. National Library of Medicine (NLM). ClinVar-GKM is produced by ClinGen. ClinGen's CC0 dedication covers what ClinGen adds. The ClinVar content inside the files remains subject to NCBI's and ClinVar's own policies, which apply to everyone who uses or redistributes these files.

Data source¶

The ClinVar content comes from the public XML releases of ClinVar, at NCBI, NLM, National Institutes of Health (NIH). The pipeline adds the GKM structure and the VRS identifiers it computes. Weekly and delta file names carry the ClinVar release date, and each version line's index.json and the Parquet manifest.json name the release each file was built from; see How Releases Work.

ClinVar is an archive of classifications made by its submitters. When submitters disagree, ClinVar's FAQ says that "ClinVar does not arbitrate and resolve these conflicts", and its disclaimer says that "NIH does not independently verify the submitted information." ClinVar-GKM changes the representation, not the classifications. It keeps each submission's submitter and dates: every SCV statement's contributions reference a record in the submitter section. ClinVar remains the authoritative source. Check a record on ClinVar before you rely on it, and see Known Issues for what the transformation does not yet carry.

Clinical use¶

ClinVar's disclaimer and data use policy applies to ClinVar-GKM data as it does to ClinVar:

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website.

NLM's Medical Information and Advice Disclaimer urges users "to consult with a qualified physician for diagnosis and for answers to your personal questions." The same advice applies to this data.

How to cite¶

ClinVar¶

ClinVar asks for attribution in its data use policy: "If you distribute or copy data from ClinVar, we ask that you provide attribution to ClinVar as a data source in publications and websites." It asks you to cite one of the ClinVar publications. The newest is:

Landrum MJ, Chitipiralla S, Kaur K, et al. ClinVar: updates to support classifications of both germline and somatic variants. Nucleic Acids Res. 2025;53(D1):D1313–D1321. doi:10.1093/nar/gkae1090. PMID: 39578691.

The data use policy gives PMID 29165669 as an example (Landrum MJ et al., Nucleic Acids Res. 2018;46(D1):D1062–D1067).

To refer to a specific ClinVar record, follow ClinVar's FAQ: cite the SCV accession and version for a submission, and the VCV or RCV accession and version for an aggregate record. ClinVar-GKM keeps these accessions and versions in its statement ids and extensions.

ClinVar-GKM¶

If you used these files, also cite ClinVar-GKM and name the release you used, for example the bundle file name or the Parquet manifest.json source_release:

Babb L, Ferriter K, O'Neill T. ClinVar-GKM. ClinGen. doi:10.5281/zenodo.18343663.

The repository's CITATION.cff has the machine-readable citation, and GitHub's Cite this repository button formats it.

License¶

ClinGen dedicates the ClinVar-GKM code and the published files, the transformed bundles and Parquet sets, to the public domain under CC0 1.0 Universal. CC0 covers what ClinGen contributes: the transformation, the structure and the identifiers it computes. It adds no restriction of its own.

CC0 does not change the terms that apply to the ClinVar content inside the files:

• NCBI's Molecular Data Usage policy says that "NCBI itself places no restrictions on the use or distribution of the data". It also says that some submitters "may claim patent, copyright, or other intellectual property rights in all or a portion of the data", and that NCBI "cannot provide comment or unrestricted permission concerning the use, copying, or distribution" of it. CC0 waives only rights that ClinGen holds, so it grants nothing in rights that a submitter may claim.
• ClinVar's submission policy says that "Once the data are in ClinVar, they are available for unrestricted distribution."
• CC0 itself (section 4) offers the work as-is, with no warranty, and disclaims responsibility for clearing other people's rights in it.

You are responsible for following NCBI's and ClinVar's policies, including their attribution request, when you use or redistribute this data.

Redistributing the data¶

You may redistribute ClinVar-GKM files, or data derived from them, under CC0. When you do:

• Keep the attribution. Name ClinVar as the data source, as ClinVar asks, and name ClinVar-GKM and the release.
• Keep the disclaimer visible. Carry the clinical use disclaimer, or link to it, wherever people see the data. NCBI asks the same of services built on its servers: its Guidelines for Scripting Calls to NCBI Servers state that "NCBI's Disclaimer and Copyright notice must be evident to users of your service."
• Keep the submitter attribution. ClinVar's introduction says that "Each submitter is explicitly acknowledged". Do not strip the submitter records or SCV contributions from data you pass on as ClinVar's classifications.
• Don't imply endorsement. See No endorsement.

In the published files¶

The same source, attribution and disclaimer are carried with the data: in each version line's README.txt (for example v1/1.1/README.txt) and in the Parquet manifest.json (fields source, attribution, disclaimer, license). The frozen v1/1.0/ line is unchanged and predates them.

No endorsement¶

ClinVar-GKM is not an NCBI, NLM or NIH product and is not endorsed by them. NCBI's Website Disclaimer says that "NCBI does not endorse or recommend any commercial products, processes, or services", and NLM's logo policy restricts use of its logo. ClinVar-GKM uses no NCBI or NLM logo. Products built on this data should likewise name ClinVar as a source without suggesting that NCBI, NLM, NIH or ClinGen endorses them.