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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.
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
.
2020-10-20: more ...
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.
2021-04-16: more ...
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For non-genomic parameters, the Progenetix resource uses a query syntax based around the Beacon v2 “filters” concept.
@qingyao 2021-04-14: more ...
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The current implementation of the Progenetix APIs uses 2 URL endpoints:
2020-06-20: more ...
The group is an active contributor to several public ontologies, both through mapping efforts (ICDOntologies, icdot2uberon) and by requesting terms relevant for genomic and metadata e.g. for EFO.
@mbaudis 2021-01-14: more ...
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.pgxseg
Progenetix uses a variation of a standard tab-separated columnar text file such as produced by array or sequencing CNV software, with an optional metadata header for e.g. plot or grouping instructions.
Wile the first edition only was geared towards sample-linked segment annotations, a variation is now being provided for CNV frequencies.
@mbaudis 2021-04-16: more ...
The standard format for (plot-)images generated on Progenetix is Scalable Vector Graphics (SVG). As the name implies, SVG is scalable, i.e. images can be scaled up without loosing quality or expanding in storage size. However, some of teh generated images use also embedded rastered components which will deteriorate during scaling - this is e.g. the case for array probe plots.
According to Wikipedia
All major modern web browsers—including Mozilla Firefox, Internet Explorer, Google Chrome, Opera, Safari, and Microsoft Edge—have SVG rendering support
On most pages where plots are being displayed there is a download option for the images - (please alert us where those are missing). Browsers also have the option to export SVGs themselves e.g. as PDF.
@mbaudis 2021-02-12: 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
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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.
2021-04-16: 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 ...
Note: This page has been uppdated to reflect the new GeoJSON complete schema version from January 2021.
We have now a new standard structure for geo_location objects, which has been implemented
for biosamples
and publications
.
@mbaudis 2021-01-25: more ...
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2020-10-20: more ...