VarioML Dialects
Overview | JSON | RDF | SKOS

    VarioML Data Portability

    VarioML clarifies the relationships among variation and phenotypic data from separate sources, paving the way for conversion of variation data to RDF and JSON, formats critical for data intergation and application building at web-scale.

    VarioML has been designed to enable the portability of variation data from existing databases, spreadsheets, and flat files, to:

    Tools and guides for using VarioML to convert variation and associated phenotypic data to these formats is forthcoming (2011-2012).

    VarioML to JSON

    VarioML can be used to transport variation data both to and from XML and JSON using the VarioML Java library, incorporating VarioML JSON via JAXB and Jackson annotations


    JSON is the common data serialization format emerging as the lingua franca for data exchange over the web. This reflects both its native Javascript/web browser format, and also its alternative to much more complex previous attempts at a general web data transport format, such as XML. Serializing to JSON facilitates applying programming techniques to data, to create interactive content, user interface components, formats native to the web, simplifying the provision of data access. VarioML provides a JSON implementation, currently defined using JAXB and Jackson annotations, which are implemented in a VarioML Java library, which can be used to read and write XML and JSON versions of the format. The API is auto-generated from XML instances, providing Java object representations for all VarioML objects. The API will be kept synchronized with the format, and can be used as a helper tool in Java applications.


    VarioML to RDF

    VarioML can be converted to RDF using:

    • D2RQ Platform

    The popular RDB to RDF mapping platform - D2RQ provides only a read-only RDF view on relational databases. It enables executing SPARQL queries on data in relational databases, mapped to RDF.

    Related: D2RQ Pheno-OM Mappings

    Pedro Lopes @ GEN2PHEN has made a guide to building D2RQ mappings to Pheno-OM, the Object Model behind VarioML. The process for mapping VarioML implementations to RDF is similar:

    VarioML and SKOS