This information is over 2 years old. Information was current at time of publication.

Share Human Variant Data with New NCBI ClinVar API

Do you work with human genetic variants? Have you sought out relevant publications, clinically significant evidence, and/or publicly available data? Are you ready to contribute to the scientific and patient-care community by sharing your own research output?

You likely already know about and use ClinVar, the go-to resource for the clinical genetics community that aggregates information about genomic variation and its relationship to human health. ClinVar recently reached the significant milestone of including 1 million unique variants in its database. Over 1,800 organizations from 82 countries have submitted almost 1.5 million records in ClinVar, including more than 11,000 curated variants from 14 expert panels.

Now it is easier than ever to reciprocate and be a supportive community member by submitting your human genetic variant data using the new ClinVar Submission API. The workflow for submissions is fast and automated, thanks to a RESTful API—a particular architectural style for an application program interface (API) allowing two software programs to communicate with each other to access and use data.

There are three one-time activities for the ClinVar Submission API setup:

  1. Create/update your profile and register your organization with ClinVar.
  2. Request a service account with an email to ClinVar.
  3. Create a new API key in the ClinVar Submission Portal.

Submission occurs by uploading JSON data. System errors or basic validation issues are reported immediately, with any data validation errors available via a status request. After successful processing, the ClinVar accession numbers become available and the records are published within a week.

Join your Pittsburgh research colleagues who are already active members of the ClinVar community and submit your own variant data. To see examples, check out submissions from: Magee-Womens Research Institute, Pittsburgh Clinical Genomics Laboratory, Pittsburgh Institute for Neurodegenerative Disease/Palladino Lab, and the University of Pittsburgh/Rajkovic Lab.

If you have questions about how to search ClinVar and understanding its data display, explore the ClinVar FAQ or contact HSLS Data Services.

~Carrie Iwema