Since July 2017, the Progenetix project has a registered namespace prefix at EBI’s identifiers.org.
This prefix will gradually be used to implement a REST syntax with stable endpoints for all Progenetix resources (e.g. arraymap.org, cnvar.org …), as well as to guide to our code mapping resources.
Michael Baudis 2018-05-10: more ...
The current implementation of the Progenetix APIs uses 2 URL endpoints:
2020-06-20: more ...
The Progenetix and arrayMap resources use the coding schemas of the _International Classification of Diseases in Oncology__ (3rd edition; “ICD-O 3”), to classify all biosamples for which experimental data is available. Users can get a list of ICD-O 3 codes in the Progenetix format through the Progenetix Services.
Michael Baudis 2020-09-29: more ...
While the pgx prefix had been registered in 2017 with identifiers.org
we recently changed the resolver and target mappings on the Progenetix server.
This went hand-in-hand with the generation of unique & persistant identifiers
for the main data items.
2020-10-09: 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 ...
2020-10-20: more ...
This script parses either:
assemblyId, cytoBands)
chroBases parameter
7:23028447-45000000X:992026602020-10-20: more ...
accessid parameterdeliveryKeys list
(can be comma-concatenated or multiple times parameter)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:
geolongitudegeolatitudegeodistance
2500000 around Heidelberg…)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 ...
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 ...
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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 ...
Following the launch of the updated Progenetix website (new interface, now much
more data with >130’000 samples…) and the recent introduction of the new
Python based bycon API for BeaconPlus and Progenetix Services
we now also have some structured information for the different API options.
2020-10-21: 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
byconicdot2uberon
ICDOntologies
2021-02-06: more ...
schemas
byconicdot2uberon
ICDOntologies
2021-02-06: more ...