Bycon - a Python-based environment for the Beacon v2 genomics API

The bycon project provides implementation of middleware & server for the Beacon API, for use with the Progenetix (i.e. GA4GH object model derived, MongoDB implemented) environment. In this project, the byconplus.py application and its libraries provide the necessary functionality to run a Beacon instance, provided the given environment.

Future versions will add methods to set-up necessary database structures from various variant and metadata files. Please contact us for further information.

Examples
Examples for v2 endpoints
{
  "biosamples": {
    "progenetix": [
      {
        "id": "PGX_AM_BS_HNSCC-GSF-an-10394",
        "individual_id": "PGX_IND_HNSCC-GSF-an-10394",
        "age_at_collection": { "age": "P50Y" },
        "biocharacteristics": [
          {
            "type" : { "id" : "icdot-C10.9", "label" : "Oropharynx" }
          },
          {
            "type" : { "id" : "icdom-80703", "label" : "Squamous cell carcinoma, NOS" }
          },
          {
            "type" : { "id" : "NCIT:C8181", "label" : "Oropharyngeal Squamous Cell Carcinoma" }
          }
        ],
        "geo_provenance" : {
          "label" : "Oberschleissheim, Germany",
          "precision" : "city",
          "city" : "Oberschleissheim",
          "country" : "Germany",
          "latitude" : 48.25,
          "longitude" : 11.56
        },
        ...
Custom (yet)

Links

2020-10-20
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