Legacy API Documentation

The current implementation of the Progenetix APIs uses 2 URL endpoints:

• progenetix.org/beacon/
  • documented at Beacon paths
  • powered by the bycon project
  • target for further development
• progenetix.org/services/
  • also powered by the bycon project
  • additional, Progenetix specific functionality

Legacy API

• progenetix.org/api/ has been deprecated
  • based on the original Perl libraries
  • stepwise deprecation in favour of services
  • documentation removed

2020-06-20: more ...

Progenetix Source Code

With exception of some utility scripts and external dependencies (e.g. MongoDB) the following projects provide the vast majority of the software (from database interaction to website) behind Progenetix and Beacon+.

• bycon
  • Python based service based on the GA4GH Beacon protocol
  • software powering the Progenetix resource
  • Beacon+ implementation(s) use the same code base
• progenetix-web
  • website for Progenetix and its Beacon+ implementations
  • provides Beacon interfaces for the bycon server, as well as other Progenetix sevices (e.g. the publications repository)
  • implemented as React / Next.js project
• PGX
  • a Perl ibrary providing utility functions for Progenetix CNV data
  • used for data transformation, e.g. binning of segmental CNV data
  • main purpose now in providing the various plots (CNV histograms, clusterd CNV profiles, array plots)

Additional Projects

• schemas
  • Progenetix data schemas
  • represent an accessible/stable version of the schemas used in bycon
• icdot2uberon
  • mappings between ICD-O 3 topographies and UBERON anatomical sites
• ICDOntologies
  • mappings between ICD-O 3 morphology / topography pairs and NCIt neoplasm core cancer ontology

2021-02-06: more ...