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.
/filtering_terms
/biosamples/{id}
biosamples.{datasetid(s)} where containing list(s) of
the biosamples data objects (the multi-dataset approach seems strange here but
in the case of progenetix & arraymap could in some cases make sense …){
"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
},
...
/biosamples/{id}/g_variants
/g_variants?{query}
/g_variants/{id}
id parameter should be unique, variants are grouped as “equivalent”
using the “digest” parameter. Remapping of the positional “id” argument to digest
is handled internally./g_variants/{id}/biosamples
biosamples data./get-datasetids/
{
"datasets": [
{ "id": "arraymap", "name": "arraymap" },
{ "id": "progenetix", "name": "progenetix" ...
scopeidresponse
Only providing scope or response without id will only work if other valid
query parameters are provided.