Legacy API Documentation

The current implementation of the Progenetix APIs uses 2 URL endpoints:

The documentation below concerns the legacy Perl API. Most of this will still be functional as of 2020, but services should be preferred if providing the needed functionality.

API syntax

The query elements are ordered in the URL

  1. api
    • fixed, required; i.e. the request has to start with /api/
  2. database (parameter apidb)
    • mostly “progenetix”
  3. collection (apiscope)
  4. method (apimethod)
    • see examples/documentation below
  5. filters (filters)
    • essentially query parameters in a simplified format
    • comma-concatenated
    • can also be omitted for query string
  6. output parameter (apioutput)
    • optional
  7. query string
    • optional
    • can be used for any parameter; e.g. a query can be formatted completely as standard query string:
      • progenetix.org/api/?apidb=progenetix&apiscope=publications ...

API Shortcuts

Some API functions (i.e. such targeting a canonical database and/or collection) can be accessed through shortcuts which omit the respective elements. These api_shortcuts work through a simple expansion of the short URL element by the full API URL elements, before the query deparsing stages.

API Examples

Biosamples

Scopes
Methods

ICD mappings

Scopes

The icdmaps collection reflects data from the “ICDontologies” project which provides mappings between ICD-O 3 Morphology & Topography codes and the NCIt cancer core codes.

Methods

Publication data

Scopes
Methods

Data subsets

Scopes
Methods

Code notes

2020-06-20