Welcome to the RareLink REDCap Documentation! ============================================= .. image:: https://readthedocs.org/projects/rarelink/badge/?version=latest :target: https://rarelink.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status RareLink is a novel framework designed for managing and processing rare disease (RD) data within the REDCap. Rare diseases affect over 260 million individuals worldwide, yet data quality and scarcity pose significant challenges in research and clinical care. RareLink aims to standardize and streamline RD data management around REDCap by providing a structured project setup that ensures consistency across data collection instruments, variables, and data dictionaries. RareLink has integrated the `ontology-based rare disease common data model (RD-CDM) `_ into its core, allowing its linkage and preconifgured export to data the standards HL7 FHIR and the GA4GH Phenopacket Schema. In the following you will find detailed information on the RareLink framework, including its background, components, installation instructions, user guide, and full examples. ________________________________________________________________________________ .. figure:: _static/res/rarelink_overview.png Overview of the RareLink framework integrated with a local REDCap instance. The framework comprises the REDCap instruments based on the `RD-CDM `_, the RareLink API, the toFHIR & CDIS module for export and import to HL7 FHIR IPS and Genomic Reporting Resources, and the RareLink-Phenopackets module for direct export to GA4GH Phenopackets. Additionally, the LinkML-based import mapper facilitates data import from tabular databases into REDCap, while the Manual Data Capture Guide assists with the manual data capture of RD-CDM data in a local REDCap project. The framework is also configurable for disease-specific extensions or custom data models. ________________________________________________________________________________ .. tip:: - **Manuscript:** RareLink was recently published in npj Genomic Medicine: https://www.nature.com/articles/s41525-025-00534-z .. note:: Further links: - **GitHub Repository:** https://github.com/BIH-CEI/RareLink - **FHIR Implementation Guide:** https://bih-cei.github.io/rarelink/ ________________________________________________________________________________ .. figure:: _static/res/rarelink_docs.png ________________________________________________________________________________ Sections --------- 1) :doc:`1_background/1_0_background_file` Introduction, definitions, and explanation of all the background information, technologies, and systems used in the RareLink framework. 2) :doc:`2_rarelink_framework/2_0_rarelink_file` Overview and detailed information on the RareLink framework, its components, and architecture. 3) :doc:`3_installation/3_0_install_file` Installation guides for all components of the RareLink framework. 4) :doc:`4_user_guide/4_0_guide_file` User guides for all components of the RareLink framework. 5) :doc:`5_contributing` 6) :doc:`6_changelog` 7) :doc:`7_faq` 8) :doc:`8_glossary` 9) :doc:`9_acknowledgements` 10) :doc:`10_license` 11) :doc:`12_contact` ________________________________________________________________________________ 1) Background --------------- - :doc:`1_background/1_0_background_file` - :doc:`1_background/1_1_rd_interoperability` - :doc:`1_background/1_2_ontologies` - :doc:`1_background/1_3_ga4gh_phenopacket_schema` - :doc:`1_background/1_4_hl7_fhir` - :doc:`1_background/1_5_rd_cdm` - :doc:`1_background/1_6_redcap` ________________________________________________________________________________ 2) RareLink Framework ---------------------- - :doc:`2_rarelink_framework/2_1_rarelink_overview` - :doc:`2_rarelink_framework/2_2_rarelink_cdm` - :doc:`2_rarelink_framework/2_3_rarelink_cli` ________________________________________________________________________________ 3) Installation ----------------- - :doc:`3_installation/3_1_setup_rarelink_framework` - :doc:`3_installation/3_2_setup_redcap_project` - :doc:`3_installation/3_3_data_dictionary` - :doc:`3_installation/3_4_redcap_api` 4) User Guide -------------- - :doc:`4_user_guide/4_1_manual_data_capture` - :doc:`4_user_guide/4_2_import_mapper` - :doc:`4_user_guide/4_3_phenopackets` - :doc:`4_user_guide/4_4_fhir_module` - :doc:`4_user_guide/4_5_develop_redcap_instruments` - :doc:`4_user_guide/4_6_redcap_tools` ________________________________________________________________________________ Additional Information ----------------------- - :doc:`5_contributing` - :doc:`6_changelog` - :doc:`7_faq` - :doc:`8_glossary` - :doc:`9_acknowledgements` - :doc:`10_license` - :doc:`12_contact` ________________________________________________________________________________ .. toctree:: :caption: Background :maxdepth: 2 :hidden: 1_background/1_1_rd_interoperability 1_background/1_2_ontologies 1_background/1_3_ga4gh_phenopacket_schema 1_background/1_4_hl7_fhir 1_background/1_5_rd_cdm 1_background/1_6_redcap .. toctree:: :caption: RareLink Framework :maxdepth: 2 :hidden: 2_rarelink_framework/2_1_rarelink_overview 2_rarelink_framework/2_2_rarelink_cdm 2_rarelink_framework/2_3_rarelink_cli .. toctree:: :caption: Installation :maxdepth: 2 :hidden: 3_installation/3_1_setup_rarelink_framework 3_installation/3_2_setup_redcap_project 3_installation/3_3_data_dictionary 3_installation/3_4_redcap_api .. toctree:: :caption: User Guide :maxdepth: 2 :hidden: 4_user_guide/4_1_manual_data_capture 4_user_guide/4_2_import_mapper 4_user_guide/4_3_phenopackets 4_user_guide/4_4_fhir_module 4_user_guide/4_5_develop_redcap_instruments 4_user_guide/4_6_redcap_tools .. toctree:: :caption: Additional Information :maxdepth: 2 :hidden: 5_contributing 6_changelog 7_faq 8_glossary 9_acknowledgements 10_license 11_download_manifest 12_contact Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search`