Fix documentatioj (#21)

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_build/html/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 45ad4954641211c682a428c6267bf25a
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_build/html/_sources/background/background_file.rst.txt

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+.. _background_file:
+
+RD CDM Background
+=================
+
+.. attention::
+    The RD CDM paper is currently under review. As soon as it is published, we
+    will provide a link to the paper here and all tables and figures will be
+    available in the paper.
+
+Introduction
+------------
+
+Rare diseases (RDs), though individually rare, collectively impact over 260 
+million people worldwide, with over 17 million affected in Europe. These
+conditions, defined by their low prevalence of fewer than 5 in 10,000 
+individuals, are often genetically driven, with over 70% of cases suspected to 
+have a genetic cause. Despite significant advances in medical research, 
+RD patients still face lengthy diagnostic delays, often due to a lack of 
+awareness in general healthcare settings and the rarity of RD-specific knowledge
+among clinicians. Misdiagnosis and underrepresentation in routine care further 
+compound the challenges, leaving many patients without timely and accurate 
+diagnoses.
+
+Interoperability plays a critical role in addressing these challenges, 
+ensuring the seamless exchange and interpretation of medical data through the 
+use of internationally agreed standards. In the field of rare diseases, where 
+data is often scarce and scattered, the importance of structured, standardized, 
+and reusable medical records cannot be overstated. Interoperable data formats 
+allow for more efficient research, better care coordination, and a clearer 
+understanding of complex clinical cases. However, existing medical systems often
+fail to support the depth of phenotypic and genotypic data required for rare 
+disease research and treatment, making interoperability a crucial enabler for 
+improving outcomes in RD care.
+
+To address these needs, we introduce our RD CDM v2.0.0— a common data model 
+specifically designed for rare diseases. This RD CDM simplifies the capture, 
+storage, and exchange of complex clinical data, enabling researchers and 
+healthcare providers to work with harmonized datasets across different 
+institutions and countries. The RD CDM is based on the ERDRI-CDS,
+a common data set developed by the European Rare Disease Research
+Infrastructure (ERDRI) to support the collection of harmonized data for rare
+disease research. By extending the ERDRI-CDS with additional concepts and
+relationships, based on HL7 FHIR v4.0.1 and the GA4GH Phenopacket Schema v2.0,
+the RD CDM provides a comprehensive model for capturing detailed clinical
+information alongisde precise genetic data on rare diseases.
+
+RD CDM Overview
+---------------
+
+.. image:: ../_static/v2_0_0_dev0/figure1_rd_cdm.png
+   :alt: RD CDM Diagram
+   :width: 1400px
+
+Overview of the RD CDM v2.0.0 showing the data elements and sections. The RD CDM
+does not define cardinalities or relationships to allow for nation-specific 
+balloting and implementation.
+
+.. note::
+    The RD CDM is a community-driven project, and we welcome contributions from
+    researchers, clinicians, and other stakeholders in the rare disease community.
+    If you would like to contribute to the RD CDM, please read our `contributing
+    guidelines <https://rd-cdm.readthedocs.io/en/latest/contributing.html>`_.
+
+
+RD CDM Table Columns
+--------------------
+
+.. image:: ../_static/v2_0_0_dev0/figure2_rd_cdm.jpeg
+   :alt: RD CDM Table Columns
+   :width: 600px
+
+This Figure Provides an overview of the table columns used to depict our Rare 
+Disease Common Data Model (RD CDM). Each column's abbreviation, further 
+definitions, and explanations are given. We recommend referring to this figure 
+when reading the tables for each section of our RD CDM. 
+
+.. note:: 
+    The table can be found in Figshare at the following link:
+    `RD CDM v2.0.0 Excel Table <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>`_.
+
+
+RD CDM Layers of harmonisation
+------------------------------
+
+.. image:: ../_static/v2_0_0_dev0/figure3_rd_cdm.jpeg
+   :alt: RD CDM Layers of Harmonisation
+   :width: 600px
+
+We analysed to what extent interoperability requirements were met 
+while harmonising data elements from the ERDRI-CDS, HL7 FHIR resources and 
+the GA4GH Phenopacket Schema to a single RD CDM. We identified six layers of 
+harmonisation on the level of each data element: (1) the Alignment Layer, 
+(2) the Labelling Layer, (3) the Terminology Binding Layer, (4) the Data 
+Type Layer, (5) the Value Set Layer, and (6) the Value Set Choice Layer. All 
+layers and their selection criteria are depicted in the figure below. 
+
+While over 95% of all data elements are directly aligned with HL7 FHIR or GA4GH 
+Phenopackets, only one-third of terminology bindings and 80% of value types 
+match the specifications outlined by these standards. Our ontology-based 
+approach results in less than 41% of value sets being directly derived from HL7 
+FHIR and GA4GH Phenopacket Schema, with slightly more than 45% of value set 
+choices were encoded accordingly. 
+
+.. note::
+    The RD CDM paper is currently under review. As soon as it is published, we
+    will provide a link to the paper here and all tables and figures will be
+    available in the paper.
+

_build/html/_sources/changelog.rst.txt

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+.. _changelog: 
+
+RD CDM Changelog
+================
+
+.. attention::
+    The RD CDM paper is currently under review. As soon as it is published, we
+    will update the version to 2.0.0 and provide a link to the paper here.
+    The version 2.0.0.dev0 is the initial release of the RD CDM under review.
+
+This changelog provides a history of the changes to the RD CDM.
+
+.. note::
+    The RD CDM is currently under active development. We are working on a new 
+    version of the RD CDM which will be available on `Read the Docs <https://rd-cdm.readthedocs.io/en/latest/>`_.
+
+.. note:: 
+    Previous versions (v1.0 - v1.7) were developed in a German context and are
+    not publicly available.
+
+Version 2.0.0.dev0 (2024-09-30)
+-------------------------------
+
+- Initial release of the RD CDM.
+

_build/html/_sources/contributing.rst.txt

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+.. _contributing:
+
+RD CDM Contributing
+===================
+
+As we are actively developing the RD CDM, we welcome contributions in the form 
+of new resources, new concepts, or new relationships. This RD CDM is a
+non-balloted extension of the ERDRI-CDS which aims to provide as an 
+internationally viable template for the development of country-specific 
+common data models. Furhtermore, the RD CDM is designed to be compatible with
+the GA4GH Phenopacket Schema, HL7 FHIR, and the International Patient Summary.
+
+We encourage contributions to the RD CDM. These contributions can be in the
+form of new resources, new concepts, relationships, or implementations.
+
+If you would like to contribute, please consider the following:
+
+1. GitHub Issues
+-----------------
+Feel free to create a new issue on our `GitHub repository <https://github.com/BIH-CEI/rd-cdm/issues>`_.
+We welcome feedback, suggestions, and bug reports.
+
+2. Reach out directly
+---------------------
+
+If you have any questions or suggestions, please feel free to reach out to us. 
+You can contact us via email at [email protected].
+
+3. Implementation
+-----------------
+
+We actively encourage users to impleemnt and test our RD CDM in various 
+healthcare information systems. If you have implemented the RD CDM in your
+system, please let us know. We would be happy to hear about your experience
+and any feedback you may have.
+
+.. note::
+    We are currently working on an implementation of the RD CDM in
+    REDCap to enable the generation of FHIR Resources and Phenopackets from 
+    REDCap. If you would like to contribute to the implementation or have any 
+    questions, feel free to reach out or find us on `GitHub <https://github.com/BIH-CEI/RareLink>`_.
+
+4. Documentation
+----------------
+
+If you would like to contribute to the documentation, please feel free create 
+an issue in our `GitHub repository <https://github.com/BIH-CEI/rd-cdm/issues>_` 
+or reach out to us directly. We are always looking for ways to improve our 
+documentation and welcome any suggestions.
+
+.. note::
+    We are currently working on a new version of the RD CDM documentation
+    which will be available on `Read the Docs <https://rd-cdm.readthedocs.io/en/latest/>`_.
+
+
+
+

_build/html/_sources/index.rst.txt

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+.. _index:
+
+
+Welcome to the RD CDM Documentation!
+====================================
+
+.. image:: https://readthedocs.org/projects/rd-cdm/badge/?version=latest
+    :target: https://rd-cdm.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+The Rare Disease Common Data Model (RD CDM) is a non-balloted extension of the 
+ERDRI-CDS which aims to provide as an internationally viable template for the 
+development and implementation of country-specific Rare disease common data 
+models. The RD CDM is designed to be compatible with the GA4GH Phenopacket 
+Schema, HL7 FHIR, and the International Patient Summary. The ontology-based 
+approach of the RD CDM allows for the integration of various data sources and 
+the harmonization of data across different systems.
+
+.. attention::
+    The RD CDM paper is currently under review. As soon as it is published, we
+    will provide a link to the paper here and all tables and figures will be
+    available in the paper.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   background/background_file
+   resources/resources_file
+   usage/usage_file
+   contributing
+   license
+   changelog
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

_build/html/_sources/license.rst.txt

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+.. _license_file:
+
+RD CDM License
+==============
+
+The RD CDM is licensed under the MIT License. The full text of the license can 
+be found in the file `LICENSE <https://github.com/BIH-CEI/rd-cdm/blob/af4eaa3589ed80cfafbec4874ed333f79831bb4d/LICENSE>`_.
+
+We encourage open-source contributions to the RD CDM. If you would like to
+contribute, please read our :ref:`contributing` guidelines.
+
+.. attention::
+
+    We cannot take responsibility for the correctness of the data in the RD CDM.
+    The RD CDM is a community-driven project and we encourage contributions from
+    the community. If you find any errors or have any suggestions, please feel
+    free to reach out to us.
+
+
+

_build/html/_sources/resources/resources_file.rst.txt

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+.. _resources_file:
+
+RD CDM Resources
+=================
+
+.. attention::
+    The RD CDM paper is currently under review. As soon as it is published, we
+    will update the version to 2.0.0 and provide a link to the paper here.
+    The version 2.0.0.dev0 is the initial release of the RD CDM under review.
+
+In here you find all resources that are available in the RD CDM to download.
+
+RD CDM v2.0.0.dev0 
+-------------------
+
+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.dev0
+in an Excel here:
+
+- :download:`RD CDM v2.0.0 Excel Table <../_static/v2_0_0_dev0/rd_cdm_v2_0_0_dev0.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
+''''''''''''''''''''
+- :download:`Entire RD CDM v2.0.0.dev0 JSON <../../res/v2_0_0_dev0/rd_cdm_v2_0_0_dev0.json>`
+- :download:`Code Systems v2.0.0.dev0 JSON <../../res/v2_0_0_dev0/rd_cdm_codesystems_v2_0_0_dev0.json>`
+- :download:`Data Elements v2.0.0.dev0 JSON <../../res/v2_0_0_dev0/rd_cdm_data_elements_v2_0_0_dev0.json>`
+- :download:`Value Sets v2.0.0.dev0 JSON <../../res/v2_0_0_dev0/rd_cdm_value_sets_v2_0_0_dev0.json>`
+
+CSV Files Download
+''''''''''''''''''''
+- :download:`Combined RD CDM v2.0.0.dev0 CSV <../../res/v2_0_0_dev0/rd_cdm_v2_0_0_dev0.csv>`
+- :download:`Code Systems v2.0.0.dev0 CSV <../../res/v2_0_0_dev0/rd_cdm_codesystems_v2_0_0_dev0.csv>`
+- :download:`Data Elements v2.0.0.dev0 CSV <../../res/v2_0_0_dev0/rd_cdm_data_elements_v2_0_0_dev0.csv>`
+- :download:`Value Sets v2.0.0.dev0 CSV <../../res/v2_0_0_dev0/rd_cdm_value_sets_v2_0_0_dev0.csv>`
+
+
+For additional details, see :ref:`background_file`.
+
+
+
+
+
+

_build/html/_sources/usage/usage_file.rst.txt

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+.. _usage_file: 
+
+RD CDM Usage
+============
+
+.. attention::
+    The RD CDM paper is currently under review. As soon as it is published, we
+    will provide a link to the paper here and all tables and figures will be
+    available in the paper. The version 2.0.0.dev0 is the initial release of 
+    the RD CDM under review.
+
+The RD CDM is developed within an open-source community and is available for use
+by researchers, clinicians, and other stakeholders in the rare disease community.
+The RD CDM is designed to support the collection of harmonized data for rare
+disease research and treatment, making interoperability a crucial enabler for
+improving outcomes in RD care.
+
+Please see the :ref:`license_file` for information on the RD CDM license.
+
+
+.. note::
+    The RD CDM is a community-driven project, and we welcome contributions from
+    researchers, clinicians, and other stakeholders in the rare disease community.
+    If you would like to contribute to the RD CDM, please read our :ref:`contributing`.
+