PharmGKB ClinVar Submission Library

This is a collection of Java classes and enums that were created when converting the ClinVar XML submission schema into a JAXB-compatible package using the command:

xjc -p org.pharmgkb.io.exporter.clinvar clinvar_submission.xsd

This resulting classes are compatible with JAXB Marshaller. For example, you can generate XML files with something similar to this:

private void writeSubmissionFile(Path filePath) throws JAXBException {

    JAXBContext context = JAXBContext.newInstance(SubmissionSetType.class);
    Marshaller marshaller = context.createMarshaller();
    marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);

    ObjectFactory objectFactory = new ObjectFactory();
    marshaller.marshal(objectFactory.createClinvarSubmissionSet(makeSubmission()), filePath.toFile());
}

The XML Schema document can be found on the NCBI FTP server in the ClinVar folder.

This library should be updated when ClinVar updates their submission schema. The major/minor version numbers of this library will match ClinVar's submission schema's version.

This code is maintained by PharmGKB and is neither supported nor endorsed by NCBI or ClinVar.

A Note on Versioning

This project will share the release version numbers of the XSD documents that it's meant to be used with. "Bugfix" releases will append a third-level version number.

For example, a "1.5.2" version of this library will reflect the "1.5" version of the ClinVar XSD and would be a second "bugfix" release.