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 ...

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 ...

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 ...

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

2020-09-30: 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 ...

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 ...