.. _resources_file:

Resources
=================

.. tip::
    The RD-CDM paper has now been published at Nature Scientific Data. You can 
    read it `here <https://www.nature.com/articles/s41597-025-04558-z>`_!

In here you find all resources that are available in the RD-CDM to download.

.. hint:: 
    Here you can find the general RD-CDM LinkML schema file:
    :download:`RD-CDM LinkML general schema <../../src/rd_cdm/schema/rd_cdm.yaml>`.

.. hint:: 
    Here you can find more information on LinkML and how to use it:
    `LinkML <https://linkml.io/linkml/>`_.

RD-CDM v2.0.2
-------------------

The RD-CDM v2.0.2 is the latest version of the Rare Disease Common Data Model.
It is based on the RD-CDM v2.0.0 and includes some minor changes to the
data elements and value sets. The changes are documented in the
:ref:`_changelog`.


The entire LinkML-based RD-CDM v2.0.2 can be downloaded as a JSON or CSV file:

- :download:`Entire RD-CDM v2.0.2 JSON <../../src/rd_cdm/instances/v2_0_2/jsons/rd_cdm_v2_0_2.json>`
- :download:`Entire RD-CDM v2.0.2 CSV <../../src/rd_cdm/instances/v2_0_2/csvs/rd_cdm_v2_0_2.csv>`

The RD-CDM v2.0.2 consists of the following components:

- :download:`Code Systems v2.0.2 JSON <../../src/rd_cdm/instances/v2_0_2/jsons/code_systems.json>`
- :download:`Code Systems v2.0.2 CSV <../../src/rd_cdm/instances/v2_0_2/csvs/code_systems.csv>`
- :download:`Data Elements v2.0.2 JSON <../../src/rd_cdm/instances/v2_0_2/jsons/data_elements.json>`
- :download:`Data Elements v2.0.2 CSV <../../src/rd_cdm/instances/v2_0_2/csvs/data_elements.csv>`
- :download:`Value Sets v2.0.2 JSON <../../src/rd_cdm/instances/v2_0_2/jsons/value_sets.json>`
- :download:`Value Sets v2.0.2 CSV <../../src/rd_cdm/instances/v2_0_2/csvs/value_sets.csv>`

The corresponding LinkML .yaml schema files can be found in the

:download:`RD-CDM v2.0.2 schema <../../src/rd_cdm/instances/v2_0_2/rd_cdm_v2_0_2.yaml>`

and the

:download:`RD-CDM v2.0.2 code systems schema <../../src/rd_cdm/instances/v2_0_2/codes_ystems.yaml>`.
:download:`RD-CDM v2.0.2 code systems schema <../../src/rd_cdm/instances/v2_0_2/value_sets.yaml>`.
:download:`RD-CDM v2.0.2 code systems schema <../../src/rd_cdm/instances/v2_0_2/data_elements.yaml>`.




RD-CDM v2.0.0 (outdated)
-------------------------

Excel Table
~~~~~~~~~~~~
The table provides an overview of the table columns used to depict our Rare 
Disease Common Data Model (RD-CDM). You can download the RD-CDM v2.0.0
in an Excel here:

- :download:`RD-CDM v2.0.0 Excel Table <../_static/v2_0_0/RD-CDM v2.0.0.xlsx>`

or access it on: `Figshare <https://figshare.com/articles/dataset/_b_Common_Data_Model_for_Rare_Diseases_b_based_on_the_ERDRI-CDS_HL7_FHIR_and_the_GA4GH_Phenopackets_Schema_v2_0_/26509150>`_.

.. note::
    Each column's abbreviation, further 
    definitions, and explanations see :ref:`background_file`.

JSON Files
~~~~~~~~~~~~~~~~~~~~~~~~
- :download:`Entire RD-CDM v2.0.0 JSON <../../res/v2_0_0/rd_cdm_v2_0_0.json>`
- :download:`Code Systems v2.0.0 JSON <../../res/v2_0_0/rd_cdm_codesystems_v2_0_0.json>`
- :download:`Data Elements v2.0.0 JSON <../../res/v2_0_0/rd_cdm_data_elements_v2_0_0.json>`
- :download:`Value Sets v2.0.0 JSON <../../res/v2_0_0/rd_cdm_value_sets_v2_0_0.json>`

CSV Files
~~~~~~~~~~~~~~~~~~~~~~~~
- :download:`Combined RD-CDM v2.0.0 CSV <../../res/v2_0_0/rd_cdm_v2_0_0.csv>`
- :download:`Code Systems v2.0.0 CSV <../../res/v2_0_0/rd_cdm_codesystems_v2_0_0.csv>`
- :download:`Data Elements v2.0.0 CSV <../../res/v2_0_0/rd_cdm_data_elements_v2_0_0.csv>`
- :download:`Value Sets v2.0.0 CSV <../../res/v2_0_0/rd_cdm_value_sets_v2_0_0.csv>`


For additional details, see :ref:`background_file`.