The Progenetix Publication DB contains articles describing whole genome screening (WGS, WES, aCGH, cCGH1) experiments in cancer. Genomic information about the analyzed cancer samples is extracted from these publications to generate cancer mutation data, with a focus on copy number abnormalities (CNV / CNA).
Whole-genome screening techniques: ↩
2021-06-17: more ...
Progenetix 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.
Wile the first edition only was geared towards sample-linked segment annotations, a variation is now being provided for CNV frequencies.
@mbaudis 2021-04-16: more ...
For non-genomic parameters, the Progenetix resource uses a query syntax based around the Beacon v2 “filters” concept.
@qingyao 2021-04-14: 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 ...
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
@mbaudis 2021-01-25: more ...