Welcome to the Progenetix documentation pages

The Progenetix Resource Documentation provides information and links related to the Progenetix cancer genome resource and the related Progenetix code repositories contains projects, such as data conversion scripts, ontology mappings and code for the Beacon+ project.

Progentix Website Code Repositories

Latest News

API: Biosample Schema Update

The Biosample schema used for exporting Progenetix data has been adjusted with respect to representation of “bio-“classifications. The previous biocharacteristics list parameter has been deprecated and its previous content is now expressed in1:

  • histologicalDiagnosis (PXF)
  • sampledTissue (PXF)
  • icdoMorphology (pgx)
  • icdoTopography (pgx)
  1. Here, “PGX” means that the attribute is part of the Phenopackets standard, while “pgx” labels it as specific to Progenetix. 

@mbaudis 2021-08-31: more ...

API: Beacon Paths Updates

For testing the rapidly evolving Beacon v2 API, we have now implemented more paths/endpoints which mostly conform to the brand new & still “flexible” v2.0.0-draft.4 version. Please check the documentation and examples.

@mbaudis 2021-07-02: more ...

API: JSON Exports now camelCased

In “forward-looking” conformity with the Beacon v2 API, the JSON attributes of the API responses has been changed from snake_cased to camelCased. Please adjust your code, where necessary.

@mbaudis 2021-07-01: more ...

BeaconPlus Changes

This page lists changes for the Beacon+ implementation of the “Beacon” genomics API.

2021-04-30: Closing in on Beacon v2

As one of the drivers of the Beacon protocol and to drive the Beacon v2 protocol process we have now started the documentation of Beacon v2 endpoints which are supported in Progenetix as part of the implementations-v2 project:

2021-04-30: more ...

Support or Contact

For requests & support, please use standard Github procedures such as pull requests or issues, or contact the developers.

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