17 rd cdm paper revision (#23)

* updates * updates * updates * updates * update
BIH-CEI · Oct 7, 2024 · 55deddf · 55deddf
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diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # Ontology-Based Rare Disease Common Data Model
 
-An ontology-based Rare Disease Common Data Model (RD CDM) to enable 
-international registry use, HL7 FHIR, and GA4GH Phenopackets.
+An ontology-based Rare Disease Common Data Model harmonising international 
+registry use, FHIR, and the Phenopacket Schema
 
 <!-- Python CI and Documentation Status Badges -->
 [![Python CI](https://github.com/BIH-CEI/rd-cdm/actions/workflows/python_ci.yml/badge.svg)](https://github.com/BIH-CEI/rd-cdm/actions/workflows/python_ci.yml)
@@ -14,6 +14,8 @@ international registry use, HL7 FHIR, and GA4GH Phenopackets.
 ![CSV Created](https://img.shields.io/badge/CSV%20Created%20Successfully-6A5ACD)
 ![Validation Successful](https://img.shields.io/badge/Validation%20Successful-brightgreen)
 
+![Latest Documentation](https://rd-cdm.readthedocs.io/en/latest/)
+
 > **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.
@@ -37,7 +39,7 @@ The Rare Disease Common Data Model (RD CDM) is designed to harmonize rare
 disease data capture across international registries. It integrates standards 
 such as the ERDRI-CDS, HL7 FHIR, and GA4GH Phenopacket Schema, creating a 
 scalable, ontology-driven framework that supports advanced interoperability for 
-research and care. The RD CDM Version 2.0 consists of 66 data elements, 
+research and care. The RD CDM Version 2.0.0 consists of 78 data elements, 
 extending the ERDRI-CDS and allowing deeper insights into genetic findings, 
 phenotypic features, and family history of individuals.
 
@@ -53,10 +55,10 @@ phenotypic features, and family history of individuals.
 - Cross-registry Compatibility: Enables data reuse across multiple registries 
     with consistent encoding and semantic alignment.
 
-
 ## Getting Started
 
-This section provides instructions for getting started with the RD CDM.
+This section provides instructions for getting started with the RD CDM. For more
+detail please read our  ![Documentation](https://rd-cdm.readthedocs.io/en/latest/)
 
 ### Prerequisites
 
@@ -90,15 +92,21 @@ consider reaching out to discuss collaboration opportunities.
 ## Resources 
 
 ### Ontologies
-- Human Phenotype Ontology (HP, Version 2024-08-13) [🔗](http://www.human-phenotype-ontology.org)
-- Monarch Initiative Disease Ontology (MONDO, Version Version 2024-09-03) [🔗](https://mondo.monarchinitiative.org/)
-- Online Mendelian Inheritance in Man (OMIM, Version 2024-09-12) [🔗](https://www.omim.org/)
-- Orphanet Rare Disease Ontology (OPRHA, Version 2024-09-12) [🔗](https://www.orpha.net/)
-- National Center for Biotechnology Information Taxonomy (NCBITaxon, Version 2024-07-03) [🔗](https://www.ncbi.nlm.nih.gov/taxonomy)
-- Logical Observation Identifiers Names and Codes (LOINC, Version 2.78) [🔗](https://loinc.org/)
-- HUGO Gene Nomenclature Committee (HGNC, Version 2024-08-23) [🔗](https://www.genenames.org/)
-- Gene Ontology (GENO, Version 2023-10-08) [🔗](https://geneontology.org/)
-- NCI Thesaurus OBO Edition (NCIT, Version Version 24.04e ) [🔗](https://obofoundry.org/ontology/ncit.html)
+- Human Phenotype Ontology [🔗](http://www.human-phenotype-ontology.org)
+- Monarch Initiative Disease Ontology [🔗](https://mondo.monarchinitiative.org/)
+- Online Mendelian Inheritance in Man [🔗](https://www.omim.org/)
+- Orphanet Rare Disease Ontology [🔗](https://www.orpha.net/)
+- SNOMED CT [🔗](https://www.snomed.org/snomed-ct)
+- ICD 11 [🔗](https://icd.who.int/en)
+- ICD10CM [🔗](https://www.cdc.gov/nchs/icd/icd10cm.htm)
+- National Center for Biotechnology Information Taxonomy [🔗](https://www.ncbi.nlm.nih.gov/taxonomy)
+- Logical Observation Identifiers Names and Codes [🔗](https://loinc.org/)
+- HUGO Gene Nomenclature Committee [🔗](https://www.genenames.org/)
+- Gene Ontology[🔗](https://geneontology.org/)
+- NCI Thesaurus OBO Edition [🔗](https://obofoundry.org/ontology/ncit.html)
+
+For the versions used in a specific RD-CDM version, please see the [resources 
+in our documentation]('https://rd-cdm.readthedocs.io/en/latest/resources/resources_file.html').
 
 ### Submodules
 - [RareLink](https://github.com/BIH-CEI/RareLink)
@@ -117,6 +125,8 @@ development of this RD CDM model.
 - Authors:
   - [Adam SL Graefe](https://github.com/aslgraefe)
   - [Filip Rehburg](https://github.com/frehburg) 
+  - Miriam Hübner
+  - Steffen Sander
   - Prof. Peter N. Robinson
   - Prof. Sylvia Thun
   - Prof. Oya Beyan
diff --git a/docs/_static/v2_0_0_dev0/RD CDM v2.0.0.xlsx b/docs/_static/v2_0_0_dev0/RD CDM v2.0.0.xlsx
diff --git a/docs/_static/v2_0_0_dev0/RareLink Paper - ABSTRACT.pdf b/docs/_static/v2_0_0_dev0/RareLink Paper - ABSTRACT.pdf
diff --git a/docs/_static/v2_0_0_dev0/rd_cdm_v2_0_0_dev0.xlsx b/docs/_static/v2_0_0_dev0/rd_cdm_v2_0_0_dev0.xlsx
diff --git a/docs/background/background_file.rst b/docs/background/background_file.rst
@@ -1,6 +1,6 @@
 .. _background_file:
 
-RD CDM Background
+Background
 =================
 
 .. attention::
@@ -30,8 +30,8 @@ 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.
+disease research and treatment, making interoperability key 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, 
@@ -57,7 +57,7 @@ Steps in the development of the ontology-based Rare Disease Common Data Model
 steps were performed concurrently and overlapped across multiple sites, this 
 methodology should be considered a non-hierarchical approach. First, we included
 and assessed previous RD data models, followed by mapping elements to FHIR 
-basic resources v4.0.175 and Phenopacket Schema v2.0 elements17. A clinical 
+basic resources v4.0.1 and Phenopacket Schema v2.0 elements. A clinical 
 evaluation was performed to assess the relevance of these elements while 
 balancing the data model’s scope and spectrum of data granularity. We then 
 performed ontology-based encoding to establish a common denominator between the 
@@ -102,6 +102,9 @@ when reading the tables for each section of our RD CDM.
     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>`_.
 
+    or can be downloaded here: 
+    :download:`RD CDM v2.0.0 Excel Table <../_static/v2_0_0_dev0/RD CDM v2.0.0.xlsx>`. 
+
 
 RD CDM Layers of harmonisation
 ------------------------------
@@ -119,13 +122,12 @@ 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. 
+Phenopackets, only one-third of terminology bindings and 85% of value types 
+match the specifications outlined by these standards. More than 87% of value 
+sets being directly are aligned with the specifications defined by
+HL7 FHIR and GA4GH Phenopacket Schema, 
 
-.. note::
+.. 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.

diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -1,6 +1,6 @@
 .. _changelog: 
 
-RD CDM Changelog
+Changelog
 ================
 
 .. attention::
@@ -23,3 +23,9 @@ Version 2.0.0.dev0 (2024-09-30)
 
 - Initial release of the RD CDM.
 
+
+Version 2.0.0 (tba)
+-------------------
+
+to be announced as soon as the paper is published.
+
diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -1,6 +1,6 @@
 .. _contributing:
 
-RD CDM Contributing
+Contributing
 ===================
 
 As we are actively developing the RD CDM, we welcome contributions in the form 
@@ -13,6 +13,12 @@ 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.
 
+.. 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.
+
+
 If you would like to contribute, please consider the following:
 
 1. GitHub Issues
@@ -44,7 +50,7 @@ and any feedback you may have.
 ----------------
 
 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>_` 
+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.
 

diff --git a/docs/license.rst b/docs/license.rst
@@ -1,6 +1,6 @@
 .. _license_file:
 
-RD CDM License
+License
 ==============
 
 The RD CDM is licensed under the MIT License. The full text of the license can 

diff --git a/docs/resources/resources_file.rst b/docs/resources/resources_file.rst
@@ -1,6 +1,6 @@
 .. _resources_file:
 
-RD CDM Resources
+Resources
 =================
 
 .. attention::
@@ -19,7 +19,7 @@ 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>`
+- :download:`RD CDM v2.0.0 Excel Table <../_static/v2_0_0_dev0/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>`_.
 
@@ -45,6 +45,12 @@ CSV Files Download
 For additional details, see :ref:`background_file`.
 
 
+RD CDM v2.0.0
+-------------
+
+to be updated as soon as the paper is published.
+
+
 
 
 

diff --git a/res/v2_0_0_dev0/rd_cdm_v2_0_0_dev0.json b/res/v2_0_0_dev0/rd_cdm_v2_0_0_dev0.json
@@ -5,7 +5,7 @@
   "description": "The ontology-based Rare Disease Common Data Model (RD CDM) to enable international registry use, HL7 FHIR, and GA4GH Phenopackets.",
   "metadata": {
     "author": "Author Name",
-    "creationDate": "2024-10-03"
+    "creationDate": "2024-10-07"
   },
   "codeSystems": [
     {

diff --git a/src/parsing/create_data_elements_json.py b/src/parsing/create_data_elements_json.py
@@ -7,8 +7,6 @@
 sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '../..')))
 
 from data_model.utils import json_serializer
-from src.data_model.data_elements import DataElement, DataElementModel
-from src.data_model.base_types import CodeSystem, Coding
 
 def load_data_element_definitions(version):
     """Dynamically load the data elements for a given version."""

diff --git a/src/parsing/create_value_sets_json.py b/src/parsing/create_value_sets_json.py
@@ -3,7 +3,6 @@
 import os
 import importlib
 from data_model.utils import json_serializer
-from src.data_model.value_set import ValueSet, ValueSetChoice
 from src.data_model.base_types import Coding, CodeSystem
 
 # Add the src directory to the system path

diff --git a/src/v2_0_0_dev0/rd_cdm_v2_0_0_dev0_codesystems_versions.py b/src/v2_0_0_dev0/rd_cdm_v2_0_0_dev0_codesystems_versions.py
@@ -2,10 +2,8 @@ class CODESYSTEMS_VERSIONS_V2_0_0_dev0:
     """Code system versions for v2_0_0_dev0."""
     versions = {
         "NCBITaxon": "2024-07-03",
-        "GENO": "2023-10-08",
-        "SO": "2.6",
         "ICD10CM": "2024-09-01",
-        "SNOMED": "2024-09-01",
+        "SNOMED": "2024-10-01",
         "ICD11": "2024-09-01",
         "HL7FHIR": "v4.0.1",
         "GA4GH": "v2.0",

diff --git a/tests/v2/__init__.py b/tests/v2/__init__.py
@@ -1,6 +1,5 @@
 import data_model
 import json
-import os
 
 def validate_schemas(version):
     base_path = f'../res/v{version}/'  # Adjusted for subfolder