API for the Progenetix and arrayMap Cancer Genome Repositories

The base address for all API calls is

This has to be appended by
  • a database db (options: db=progenetix; db=arraymap); this defaults to db=progenetix
  • at least one query parameter for sample selection
  • a scope selection api_scope (api_scope=publications, api_scope=samples); defaults to api_scope=samples and is therefore rarely needed
  • an output option api_out; defaults to api_out=histogram (more in the API Examples
  • a format option api_doctype (e.g. api_doctype=tab, api_doctype=json, api_doctype=svg, api_doctype=png); this varies for the different output options

Additional parameters can be defined, e.g. labels and status information for genes or genome regions:
  • genes_m: comma concatenated genes for labeling and adding to status tables. Use a "$" sign at the end for exact matches - e.g. genes_m=MYCN,TP53$,CDKN2B

Api Examples

This page lists various examples of API usage, which can serve as templates for user specified cancer genome data mining and visualisation.

Api Examples: R Integration

The Progenetix API can easily be used to import data into R. This page provides some examples.

Api Parameters

The listing of Progenetix/arrayMap API parameters helps to devise your own queries against the databases.

arrayMap Keys

The list of arrayMap data keys (attributes) can be used both for API call modifications, as well as in evaluating return values.
Topic revision: r8 - 06 Jan 2016, MichaelBaudis
This site is powered by FoswikiCopyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Progenetixwiki? Send feedback