VarioML: Basic Implementation



    VarioML is a data integration solution that creates a layer of meaning above the many variation standards and formats, enabling them to be integrated and made sense of as a whole.

    VarioML takes the elements found in the many forms of variant data in use in research and the clinic, and makes them equivalent. These elements can now be re-used across diverse biomedical environments, between use-cases that have previously been incompatible.

    VarioML can be easily extended for specific research and clinical needs, using tools and related formats such as Cafe Variome, Alamut, Gensearch, LOVD, and DMuDB.

    To learn more about variation nomenclature, see here.

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    Cafe Variome: Variant-Centric Implementation

    To use VarioML for variant-centric data, i.e. using Cafe Variome, your elements take the following basic structure:

    N.B: This example shows multiple panels. In most variant-centric datasets, the use is even simpler: there will typically be only one panel.

    Non-transferable elements:
    When reorganizing VarioML data for transfer, some sub-elements found in one implementation may not be admissable in another. When transforming data to Cafe Variome:

    Individual - exclude all sub-elements except Gender
    Panel
    Variant

    VarioML offers an open-source toolkit for generating VarioML transformation stylesheets that can be used to automatically filter out non-transferable elements. See here.
    A basic transformation sheet for individual- and population- centric format to Cafe Variome is available here (coming soon).

    If you have created or adapted an implementation that filters elements that can be transferred from other datasets, please let us know.

    Re-mix as well as re-use
    When transferring VarioML data, new elements can be loaded from external sources, such as NCBI or OMIM.
    - See our guide on how to do this here
    - An example transformation stylesheet that loads external data into variant-centric format can be found here (coming soon).


    Variant-centric Specifications Variant Nomenclature
    To learn more about nomenclature for describing variants, see here.

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