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.
When reorganizing VarioML data for transfer, some sub-elements found in one implementation may not be admissable in another. When transforming data to
Individual - exclude all sub-elements except Gender
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).
To learn more about nomenclature for describing variants, see here.