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data schemas for the Progenetix databases
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A graph showing the basic objects and their relationships. The example attributes represent placeholders for elements defined in the general schema description.

This repository contains the data schemas for the Progenetix databases (i.e. the backends behind and the Beacon+ project.

The primary documents are in the yaml directory, with JSON versions and examples extracted from them. The "readable" documentation is also created from the YAML files and can be accessed here:

  • common object classes, which are used in the schemas themselves
  • variant The variant object includes attributes and examples for both structural (DUP, DEL, BRK) and precise genome variants.
  • callset The callset object is for technoical data and series information (e.g. used platform and analysis metods). It is not strictly needed for querying combined variant + biosample aspects, since in the current implementation the variant object contains a reference to the biosample it was derived from.
  • biosample Most relevant "bio"data (such as diagnoses, phenotypes ...) is stored in the biosample object.
  • individual The individual object contains information which pertains to the whole biological entity biosamples are derived from (e.g. sex, heritable phenotypes...).
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