The bycon environment provides a number of data services which make use of resources in the Progenetix environment. Please refer to their specific documentation.
Note: As of 2021-04-07 there are some changes - typical Beacon endpoints such as biosamples
have been moved to the /beacon/__service-name__
path:
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
.
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The bycon
project provides a combination of a Beacon-protocol based API with additional API services, used as backend and middleware for the Progenetix resource.
bycon
has been developed to support Beacon protocol development following earlier implementations of Beacon+ (“beaconPlus”) with now deprected Perl libraries. The work tightly integrates with the ELIXIR Beacon project.
The first examples are for “standard” Beacon (v1) queries and may become deprecated/remapped during the ongoing development.
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schemas
bycon
icdot2uberon
ICDOntologies
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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
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This endpoint is mostly aimed at providing biosamples handover functionality. However, the app uses the same query processing mechanism as the main byconplus application.
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This script parses either:
assemblyId
, cytoBands
)
chroBases
parameter
7:23028447-45000000
X:99202660
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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.
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The phenopackets
service is usually called as a handover endpoint, to wrap &
deliver penopackets from samples & variants … matched by a Beacon query.
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The publications
service serves as backend API for the display of genome
screening publications through the Progenetix Publications DB.
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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.
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