Clinvar-build documentation

Clinvar-build is a Python packages which allows the user to create a custom SQLite database using the publicly available XML files updated weekly by ClinVar.

The latest version of the XML files can be obtained from their public FTP: server. These files contain both VCV (Variation ClinVar) and RCV (Reference ClinVar) records. The VCV represents the aggregate record for a single genetic variant across all submissions. The RCV captures condition-specific interpretations for that variant and aggregates the corresponding SCV records, which represent individual submissions to ClinVar.

The package is designed to allow the user full control about which information they want to extract, encoding both the schema structure and parsing instructions (based on XPaths) in JSON configuration files.

Installation

The package can be installed from GitLab.

ClinVar documentation

Please refer to ClinVar’s detailed documentation. for an overview of the XML content. Additionally refer to the XSD files which can be use to validate the XML files. The XSD files used to build the current version of the module are included here.