2021

BeaconPlus and Site Changes

This page lists changes for the Beacon+ implementation of the “Beacon” genomics API, as well as related updates for the Progenetix front-end.

2021-11-25: Publication page fix

  • The publication details pages did not display content due to the changed Beacon response structure. Fixed.

2021-04-30: Closing in on Beacon v2

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:

2021-11-25: more ...

Publications - Progenetix Citations and Better Map

progenetixuse Page

We 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.

Improved Map

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 ...

API: Biosample Schema Update

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)
  1. 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 ...

API: Beacon Paths Updates

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 ...

API: JSON Exports now camelCased

In “forward-looking” conformity with the Beacon v2 API, the JSON attributes of the API responses has been changed from snake_cased to camelCased. Please adjust your code, where necessary.

@mbaudis 2021-07-01: more ...

Beacon+ and Progenetix Queries by Gene Symbol

Gene Symbol Selector ExampleWe 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 ...

arrayMap is Back

arrayMapAfter some months of dormancy, the arrayMap resource has been relaunched through integration with the new Progenetix site. All of the oiginal arrayMap data has now been integrated into Progenetix, and of today the arraymap.org domain maps to a standard Progenetix search page, where only data samples with existing source data (e.g. probe specific array files) will be presented.

@mbaudis 2021-02-06: more ...

TCGA CNV Data

TCGA CNV DataWhile the Progenetix resource has provided access to the CNV data from The Cancer Genome Annotation Project (TCGA*; www.cancer.gov/tcga) for quite some time, we have now launched a dedicated search page to facilitate data access and visualization using the standard Progenetix tools.

@mbaudis 2021-02-06: more ...

2020

pgx namespace and persistant identifiers

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 ...

Progenetix at GA4GH 2020 Plenary

GA4GH 8th Plenary

Michael Baudis

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 ...

GA4GH Beacon v2 - Evolving Reference Standard for Genomic Data Exchange

GA4GH 8th Plenary

Gary Saunders, Jordi Rambla de Argila, Anthony Brookes, Juha Törnroos and Michael Baudis

For the ELIXIR Beacon project, GA4GH Discovery work stream and the international network of Beacon API developers

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 ...

New Progenetix Website

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 ...

CURIE Prefix Remapping - NCIT & PMID

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 ...

BeaconPlus in ELIXIR Beacon Network

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 ...

2019

2018

2013

2012