The bycon environment provides a number of data services which make use of resources in the Progenetix environment. Please refer to their specific documentation.
services.py
and URL MappingThe service URL format progenetix.org/services/__service-name__?parameter=value
is a shorthand for progenetix.org/cgi-bin/bycon/services/__service-name__.py?parameter=value
.
2020-10-20: more ...
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.
2020-10-20: more ...
schemas
bycon
icdot2uberon
ICDOntologies
2021-02-06: more ...
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
progenetix-next
bycon
server, as well as other Progenetix sevices (e.g. the publications repository)PGX
schemas
bycon
icdot2uberon
ICDOntologies
2021-02-06: more ...
This endpoint is mostly aimed at providing biosamples handover functionality. However, the app uses the same query processing mechanism as the main byconplus application.
2020-10-20: more ...
This script parses either:
assemblyId
, cytoBands
)
chroBases
parameter
7:23028447-45000000
X:99202660
2020-10-20: more ...
geneId
parameter2020-10-20: more ...
This service provides geographic location mapping for cities above 25’000 inhabitants (~22750 cities), through either:
geolongitude
geolatitude
geodistance
2500000
around Heidelberg…)2020-10-20: more ...
The ontologymaps
service provides equivalency mapping between ICD-O and other
classification systems, notably NCIt. The mappings are represented in the ICDOntologies project and accessible trough a front-end in the Progenetix Services area.
2020-10-20: more ...
The phenopackets
service is usually called as a handover endpoint, to wrap &
deliver penopackets from samples & variants … matched by a Beacon query.
2020-10-20: more ...
The publications
service serves as backend API for the display of genome
screening publications through the Progenetix Publications DB.
2020-10-20: more ...
2020-10-20: more ...
2020-10-20: more ...
accessid
parameterdeliveryKeys
list
(can be comma-concatenated or multiple times parameter)2020-10-20: more ...
The ids
service forwards compatible, prefixed ids (see config/ids.yaml
) to specific
website endpoints. There is no check if the id exists; this is left to the web
page handling itself.
Stacking with the “pgx:” prefix is allowed.
2020-10-20: more ...
2020-10-20: more ...