progenetixuse PageWe have introduced a new publications listing page which contains links to articles that cite or use Progenetix and resources from this “ecosystem.” Please let us know if you are aware of other such cases - frequently the publications do not use a proper citation format but just refer to “according tho the Progenetix resource” or similar in the text.
For proper citation please follow these instructions.
The pop-up in th Publication maps has been updated with a proper short text listing and direct links to the article pages on EuropePMC.
@mbaudis 2021-10-12: more ...
pgxRpi is an API wrapper package to access data from Progenetix database. You can
use it to
2021-09-16: more ...
The Biosample schema used for exporting Progenetix data has been adjusted with respect to representation of “bio-“classifications. The previous biocharacteristics list parameter has been deprecated and its previous content is now expressed in1:
histologicalDiagnosis (PXF)sampledTissue (PXF)icdoMorphology (pgx)icdoTopography (pgx)Here, “PXF” means that the attribute is part of the Phenopackets standard, while “pgx” labels it as specific to Progenetix. ↩
@mbaudis 2021-08-31: more ...
For testing the rapidly evolving Beacon v2 API, we have now implemented more paths/endpoints which mostly conform to the brand new & still “flexible” v2.0.0-draft.4 version. Please check the documentation and examples.
@mbaudis 2021-07-02: more ...
This service provides access to binned CNV frequency information of data
“collations” in the Progenetix project databases. A typical use would be the
retrieval of data for a single collation, e.g. by its identifier (e.g.
NCIT:C7376, PMID:22824167, pgxcohort-TCGAcancers).
2021-05-06: more ...
The Progenetix resource’s API utilizes the bycon framework for data query and
delivery and basically represents a custom implementation of the Beacon API.
@mbaudis 2021-05-05: more ...
This page lists changes for the Beacon+ implementation of the “Beacon” genomics API.
As one of the drivers of the Beacon protocol and to drive the Beacon v2 protocol process we have now started the documentation of Beacon v2 endpoints which are supported in Progenetix as part of the implementations-v2 project:
2021-04-30: more ...
The Beacon v2 protocol uses a REST path structure for consistant data access.
The Beacon+ implementation - developed oin the bycon project
implements an expanding set of those Beacon v2 paths for the Progenetix
resource.
2021-04-23: 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.
2021-04-16: more ...
This endpoint is mostly aimed at providing variants Beacon functionality. The app uses the same query processing mechanism as the other bycon applications.
2021-04-16: 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.
2021-04-16: more ...
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 ...
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-web
bycon server, as well as other Progenetix sevices (e.g. the publications repository)PGX
icdot2uberon
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.
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 ...
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 ...
The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data from cancer studies. Especially through currently 113322 curated genomic copy number number (CNV) profiles from 1600 individual studies representing over 500 cancer types (NCIt), Progenetix empowers aggregate and comparative analyses which vastly exceed individual studies or single diagnostic concepts.
2020-09-30: more ...
The Beacon driver project was one of the earliest initiatives of the Global Alliance for Genomics and Health with the Beacon v1.0 API as first approved GA4GH standard. Version 2 of the protocol is slated to provide fundamental changes, towards a Internet of Genomics foundational standard:
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 ...
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.
2020-01-20: 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 ...
@mbaudis 2018-05-08: more ...