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 ...
This page lists changes for the Beacon+ implementation of the “Beacon” genomics API.
2020-10-01: 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 ...
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 ...
Wherever possible, data annotation in Progenetix uses {S}[B] OntologyClass
objects for categorical values, with CURIEs as id values. So far, the
Progenetix databases had used pubmed: for PubMed identifiers and ncit:
for NCI Metathesaurus (Neoplasm) ids.
@mbaudis 2020-03-30: 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 ...
The current implementation of the Progenetix APIs uses 2 URL endpoints:
2020-06-20: more ...
The Progenetix website has been completely rebuilt using a JavaScript / React based framework and API based content delivery. At its core, the site is built around the Beacon standard, with some extensions for data colections and advanced query options.
@mbaudis 2020-09-21: more ...
.pgxsegProgenetix 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.
@mbaudis 2021-02-22: 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
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 ...
After many years of using a CreativeCommons CC-BY-SA (“attribution + share alike”), the Progenetix resource has dropped the “SA - share alike” attribute and is now “attribution” only. This may facilitate the use of the data in more complex and/or commercial scenarios - enjoy!
@mbaudis 2020-08-05: 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 ...
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 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 ...
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 ...