Data Downloads

Progenetix data is licenced under CC-BY 4.0 and can be freely downloaded for research and commercial purposes, with the stipulation of proper acknowledgement.

The data is provided eiher as JSON or tab-delimited text files, depending on the type of data. For several purposes both options are available.


Contents


Downloads using the GUI

Inseveral places throughout the sample and subset pages one can find links for the download of e.g. data returned from sample searches. The example above shows the standard link for the CNV frequency file corresponding to the histogram data.

Downloads using the API

The Progenetix resource utilizes the Beacon v2 API for data delivery. Some information about the standard paths & their usage can be found on the Beacon v2 path examples page. Below are the examples for the main direct data access scenarios.

Download CNV segments for a given collation (diagnosis, study…)

The different filter options are described on the Filter Documentation page.

Download tabular data through the API

Especially for biosamples it may make sense just to get the data in a tabular format using the output=datatable option.

For use cases where one e.g. just needs the identifiers of a given object, e.g. to intersect the query results with a previously accessed master table, the output=idtable format can be used.

Examples:

Custom Progenetix services

The Progenetix API implements a number of “services” which can e.g. be utilized to download aggregate data such as CNV frequency data of a disease entity.

File formats

Beacon-style JSON

With the maturation of the Beacon v2 protocol and associated data schemas, the default delivery of JSON encoded data follows the standard Beacon response format where the main data is contained in the results array.

For more information see the beaconresponse json documentation.

Columnar data files

.pgxseg segment data

.pgxseg files are tab-delimited, columnar text files where each line provides information about features or measurements associated with a genomic region. More information can be found on the file formats page.

.pgxmatrix data matrices

.pgxmatrix files are tab-delimited, columnar data matrix files where each line provides interval-mapped values, usually e.g. for 1Mb genomic intervals of a sample or classification. More information can be found on the file formats page.

@mbaudis 2021-10-01
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