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 Progenetix Jekyll template modifies the standard Jekyll file structure.
@mbaudis 2019-03-14: more ...
The YAML headers are necessary to process the Markdown (or HTML) files in the page collections. The Progenetix Jekyll template uses standard Jekyll headers, but also adds some additional parameters.
@mbaudis 2019-03-14: more ...
For gene coordinates, we use a mapping of the genes’ maximum CDR as derived from mapping resources.
Michael Baudis 2018-05-08: 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 ...
@mbaudis 2018-05-10: more ...
Loss of heterozygosity (LOH) is a phenomenon frequently observed in cancer genomes where the selective pressure to keep only the susceptible gene product from one allele removes the other healthy allele from the pool; In this context, copy neutral - loss of heterozygosity (CN-LOH) is commonly observed in haematological malignancies (O’keefe et al., 2010 and Mulligan et al., 2007). To Progenetix oncogenomic resource, comprising of nearly 800 cancer types (by NCIt classification) as of 2021, we expanded the new feature of LOH in our data collection, in addition to the total copy number, to open the door for the analysis of frequency and impact of this phenomenon.
Update 2021-01-28:
LOH variants can now be queried through the Search and Beacon+ interfaces, either as specific variants or together with deletions.
Please be aware that in contrast to the “complete for chromosomes 1-22” DUP and DEL calls, LOH is only determined for a subset of samples and therefore will be underreported in the statistics section.
@qingyao 2021-01-14: 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 ...
.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 ...
2012-03-23: more ...
2012-03-26: more ...
The new year brings some refinements to biosamples search and display:
@mbaudis 2021-01-04: 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 ...