We have introduced a simple option to search directly by Gene Symbol, which will match to any genomic variant with partial overlap to the specified gene. This works by expanding the Gene Symbol (e.g. TP53, CDKN2A …) into a range query for its genomic coordinates (maximum CDR).
Such queries - which would e.g. return all whole-chromosome CNV events covering the gene of interest, too - should be narrowed by providing e.g. Variant Type and Maximum Size (e.g. 2000000) values.
@mbaudis 2021-02-22: more ...
schemas
byconicdot2uberon
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
byconicdot2uberon
ICDOntologies
2021-02-06: more ...
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 ...
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 ...
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 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 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 ...
This service provides geographic location mapping for cities above 25’000 inhabitants (~22750 cities), through either:
geolongitudegeolatitudegeodistance
2500000 around Heidelberg…)2020-10-20: more ...
geneId
parameter2020-10-20: more ...
accessid parameterdeliveryKeys list
(can be comma-concatenated or multiple times parameter)2020-10-20: more ...
This script parses either:
assemblyId, cytoBands)
chroBases parameter
7:23028447-45000000X:992026602020-10-20: more ...
2020-10-20: 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 ...
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 ...
This page lists changes for the Beacon+ implementation of the “Beacon” genomics API.
2020-10-01: more ...
2020-09-30: more ...
2020-09-30: more ...
The Progenetix / Beaconplus query model utilises the GA4GH core data model for genomic and (biomedical, procedural) queries and data delivery.
2020-05-26: more ...
The Beacon+ implementation of the GA4GH Beacon protocol has become a part of the ELIXIR Beacon Network, an expanding Beacon service to query multiple Beacon resources and aggregate their query results.
@mbaudis 2020-01-20: more ...
The response element of the Beacon+ interface now contains a link for displaying the matched variants e.g. of e.g. a CNV query in the UCSC genome browser.
@mbaudis 2019-10-14: more ...
Beacon - Discovery Services for Genomic DataThe Beacon protocol defines an open standard for genomics data discovery, developed by members of the Global Alliance for Genomics & Health. Since 2016, the Beacon protocols is being developed through the ELIXIR Beacon project as a GA4GH driver project.
2016-07-01: more ...