From 8bdb2a9183eb700c10b80df7ef586ec6a6b1b1ff Mon Sep 17 00:00:00 2001 From: Adam Graefe Date: Tue, 24 Mar 2026 15:38:02 +0100 Subject: [PATCH 1/8] updated gitignor for ds_store removal --- .gitignore | 5 +++++ res/.DS_Store | Bin 6148 -> 6148 bytes 2 files changed, 5 insertions(+) diff --git a/.gitignore b/.gitignore index 3d86fa9..2519580 100644 --- a/.gitignore +++ b/.gitignore @@ -61,6 +61,11 @@ local_settings.py db.sqlite3 db.sqlite3-journal +# macOS metadata +.DS_Store +**/.DS_Store +res/.DS_Store + # Flask stuff: instance/ .webassets-cache diff --git a/res/.DS_Store b/res/.DS_Store index c9df89b3e265ecb7191ea5427d79a3251cd5d280..c46f9119c4f36c6886ff49b7af3a002164d90cd7 100644 GIT binary patch delta 365 zcmZoMXfc=|#>B!ku~2NHo}wrh0|Nsi1A_nqLlHwNLvc>JVQ_N(W=5vv%=I8Cc7`;D zOonuZQe^4e0-y{7gJwTFri$Er7nh`*{3M_ZN9ASn^X*;79kHoOA*f1-p|~IeL5yI?l61B`mu~2NHo}wrd0|Nsi1A_nqLp*~)Qh9MfQcix-#KPs14MbQb&u4kG wnUn1w<7Nd8c9w|^f}7bn_&I=jHw$unXP(S2VhPj+)($cSWDLvZ2$40+0LP>j2mk;8 From 23a720d7f9a8f5d5ee8fca5dc28a459772eba784 Mon Sep 17 00:00:00 2001 From: Adam Graefe Date: Tue, 24 Mar 2026 15:38:26 +0100 Subject: [PATCH 2/8] updated the code systems versions to align with bioportal --- src/rd_cdm/instances/v2_0_2/code_systems.yaml | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/src/rd_cdm/instances/v2_0_2/code_systems.yaml b/src/rd_cdm/instances/v2_0_2/code_systems.yaml index c168536..50f500f 100644 --- a/src/rd_cdm/instances/v2_0_2/code_systems.yaml +++ b/src/rd_cdm/instances/v2_0_2/code_systems.yaml @@ -2,22 +2,22 @@ code_systems: # Codesystems that encode elements and value set items - id: SNOMEDCT namespace_iri: http://purl.bioontology.org/ontology/SNOMEDCT/ - version: "SNOMEDCT_US_2024_09_01" + version: "2025AB" title: "Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT)" - id: LOINC namespace_iri: http://loinc.org - version: "LNC278" + version: "281" title: "Logical Observation Identifiers Names and Codes (LOINC)" - id: HP namespace_iri: http://purl.obolibrary.org/obo/HP - version: "2025-05-06" + version: "2026-02-16" title: "Human Phenotype Ontology (HPO)" - id: NCIT namespace_iri: http://purl.obolibrary.org/obo/NCIT/ - version: "24.01e" + version: "26.02d" title: "NCI Thesaurus (NCIT) OBO Edition" - id: HL7FHIR @@ -32,18 +32,18 @@ code_systems: - id: CustomCode namespace_iri: https://github.com/BIH-CEI/rd-cdm - version: "v2.0.0" - title: "Custom Code System RD CDM v2.0.0" + version: "v2.0" + title: "Custom Code System RD CDM v2.0" # Codesystems that can encode values of data elements - id: NCBITAXON namespace_iri: http://purl.obolibrary.org/obo/NCBITAXON/ - version: "NCBI2024_04_02" + version: "2025_04_10" title: "NCBI organismal classification" - id: GENO namespace_iri: http://purl.obolibrary.org/obo/GENO/ - version: "2023-10-08" + version: "2026-02-02" title: "GENO – The Genotype Ontology" - id: SO @@ -53,27 +53,27 @@ code_systems: - id: UO namespace_iri: http://purl.obolibrary.org/obo/UO/ - version: "2023-05-25" + version: "2026-01-16" title: "Units Ontology (UO)" - id: ECO namespace_iri: http://purl.obolibrary.org/obo/ECO/ - version: "2025-06-23" + version: "releases/2025-06-23" title: "Evidence & Conclusion Ontology (ECO)" - id: ICD10CM namespace_iri: http://purl.bioontology.org/ontology/ICD10CM/ - version: "CD10CM_2025" + version: "2026" title: "International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)" - id: MONDO namespace_iri: http://purl.obolibrary.org/obo/MONDO/ - version: "2025-06-03" + version: "2026-03-03" title: "Mondo Disease Ontology" - id: ORDO namespace_iri: http://purl.obolibrary.org/obo/ORDO/ - version: "4.7" + version: "4.8" title: "Orphanet Rare Disease Ontology (ORDO)" - id: HGNC @@ -83,7 +83,7 @@ code_systems: - id: OMIM namespace_iri: http://purl.bioontology.org/ontology/OMIM/ - version: "OMIM2024_08_09" + version: "2025_08_04" title: "Online Mendelian Inheritance in Man (OMIM)" - id: HGVS From ace1be33306ed93ed65884058c0a28f52b4984a3 Mon Sep 17 00:00:00 2001 From: Adam Graefe Date: Tue, 24 Mar 2026 15:38:59 +0100 Subject: [PATCH 3/8] updated labels of two value set items to match the ones fetched from BioPortal (i.e. the preferreld labels) --- src/rd_cdm/instances/v2_0_2/value_sets.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/rd_cdm/instances/v2_0_2/value_sets.yaml b/src/rd_cdm/instances/v2_0_2/value_sets.yaml index 8498285..787d15e 100644 --- a/src/rd_cdm/instances/v2_0_2/value_sets.yaml +++ b/src/rd_cdm/instances/v2_0_2/value_sets.yaml @@ -465,7 +465,7 @@ value_sets: codes: - system: LOINC code: 'LA9658-1' - label: Wild Type + label: Wild type - system: LOINC code: 'LA6692-3' label: Deletion @@ -523,7 +523,7 @@ value_sets: codes: - system: LOINC code: 'LA30200-2' - label: Very Strong evidence pathogenic + label: Very strong evidence pathogenic - system: LOINC code: 'LA30201-0' label: Strong evidence pathogenic From 3844e4f242f75785bca7074264bd3568eddb7718 Mon Sep 17 00:00:00 2001 From: Adam Graefe Date: Tue, 24 Mar 2026 17:18:03 +0100 Subject: [PATCH 4/8] updated dependencies in project toml --- pyproject.toml | 30 +++++++++++------------------- 1 file changed, 11 insertions(+), 19 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4abd877..0941d43 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "rd-cdm" -version = "2.0.2" +version = "2.0.3" description = "An ontology-based rare disease common data model (RD-CDM) harmonising international registries, HL7 FHIR, and GA4GH Phenopackets." readme = "README.md" license = "MIT" @@ -46,43 +46,35 @@ packages = [ include = [ "src/rd_cdm/schema/rd_cdm.yaml", - "src/rd_cdm/instances/*/*.yaml", - "src/rd_cdm/instances/*/jsons/*.json", - "src/rd_cdm/instances/*/csvs/*.csv", + "src/rd_cdm/instances/*.yaml", + "src/rd_cdm/instances/jsons/*.json", + "src/rd_cdm/instances/csvs/*.csv", "src/rd_cdm/python_classes/*.py", ] [tool.poetry.dependencies] python = ">=3.10,<3.13" -numpy = "*" -jsonschema = "*" "ruamel.yaml" = ">=0.17.21" requests = ">=2.31.0,<3.0.0" -requests-cache = ">=1.2.1,<2.0.0" +tqdm = ">=4.0.0" linkml-runtime = ">=1.9.4" -linkml = ">=1.7.0" -oaklib = ">=0.6.23" pydantic = ">=2.4,<3.0" pydantic-settings = ">=2.3,<3.0" -# make test/docs deps optional here (with versions!) pytest = { version = ">=7.0.0,<9.0.0", optional = true } requests-mock = { version = ">=1.11.0", optional = true } - sphinx = { version = ">=7.0.0", optional = true } sphinx-rtd-theme = { version = ">=1.3.0", optional = true } sphinx-copybutton = { version = ">=0.5.0", optional = true } +linkml = { version = ">=1.9.0", optional = true } [tool.poetry.extras] -# extras list ONLY the package names (no versions) test = ["pytest", "requests-mock"] docs = ["sphinx", "sphinx-rtd-theme", "sphinx-copybutton"] +dev = ["linkml"] [tool.poetry.scripts] -rdcdm-merge = "rd_cdm.utils.merge_instances:main" -rdcdm-json = "rd_cdm.utils.json_parsing:main" -rdcdm-csv = "rd_cdm.utils.csv_parsing:write_csvs_from_instances" -rdcdm-validate = "rd_cdm.utils.validation:main" - -[tool.poetry.plugins."oaklib.plugins"] -rdcdm = "oakx_rdcdm.rdcdm_implementation:RdCdmValidator" \ No newline at end of file +rd-cdm-merge = "rd_cdm.utils.merge_instances:main" +rd-cdm-json = "rd_cdm.utils.json_parsing:main" +rd-cdm-csv = "rd_cdm.utils.csv_parsing:main" +rd-cdm-validate = "rd_cdm.utils.validation:main" \ No newline at end of file From ef6799bababfa38846709f63994cfa26cd6a3558 Mon Sep 17 00:00:00 2001 From: Adam Graefe Date: Tue, 24 Mar 2026 17:18:10 +0100 Subject: [PATCH 5/8] updated readme to v2.0.3 --- README.md | 201 +++++++++++++++++++++++++++--------------------------- 1 file changed, 101 insertions(+), 100 deletions(-) diff --git a/README.md b/README.md index 928956f..f0431af 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,15 @@ # ontology-based rare disease common data model -Welcome to the repo of the ontology-based rare disease common data model (RD-CDM) harmonising international registry use, HL7® FHIR®, and the GA4GH Phenopacket Schema. +Welcome to the repo of the ontology-based rare disease common data model (RD-CDM) +harmonising international registry use, HL7® FHIR®, and the GA4GH Phenopacket Schema. - [![CI](https://github.com/BIH-CEI/rd-cdm/actions/workflows/ci.yml/badge.svg)](https://github.com/BIH-CEI/rd-cdm/actions/workflows/ci.yml) [![Documentation Status](https://readthedocs.org/projects/rd-cdm/badge/?version=latest)](https://rd-cdm.readthedocs.io/en/latest/?badge=latest) [![DOI](https://zenodo.org/badge/863993011.svg)](https://doi.org/10.5281/zenodo.13891625) ![Python Versions](https://img.shields.io/badge/python-3.10%20|%203.11%20|%203.12-blue) [![PyPI](https://img.shields.io/pypi/v/rd-cdm.svg)](https://pypi.org/project/rd-cdm/) [![Downloads](https://img.shields.io/pypi/dm/rd-cdm.svg?label=downloads)](https://pypi.org/project/rd-cdm/) -[![LinkML](https://img.shields.io/badge/LinkML-1.8.0+-green.svg)](https://linkml.io/) +[![LinkML](https://img.shields.io/badge/LinkML-1.9.0+-green.svg)](https://linkml.io/) **Latest docs:** https://rd-cdm.readthedocs.io/en/latest/ @@ -29,7 +29,6 @@ https://www.nature.com/articles/s41597-025-04558-z - [Quick start (pip)](#quick-start-pip) - [Development install](#development-install) - [CLI tools](#cli-tools) -- [Versioning & File Layout](#versioning--file-layout) - [Validating with BioPortal](#validating-with-bioportal) - [Contributing & Contact](#contributing--contact) - [Resources](#resources) @@ -41,7 +40,11 @@ https://www.nature.com/articles/s41597-025-04558-z ## Project Description -The ontology-based RD-CDM harmonizes rare disease data capture across registries. It integrates ERDRI-CDS, HL7 FHIR, and GA4GH Phenopacket Schema to support interoperable data for research and care. RD-CDM v2.0.x comprises 78 data elements covering formal criteria, personal information, patient status, disease, genetic findings, phenotypic findings, and family history. +The ontology-based RD-CDM harmonizes rare disease data capture across registries. +It integrates ERDRI-CDS, HL7 FHIR, and GA4GH Phenopacket Schema to support +interoperable data for research and care. RD-CDM v2.0.x comprises 78 data elements +covering formal criteria, personal information, patient status, disease, genetic +findings, phenotypic findings, and family history. --- @@ -50,24 +53,28 @@ The ontology-based RD-CDM harmonizes rare disease data capture across registries Installing `rd-cdm` from PyPI provides: - **Schema** - - `src/rd_cdm/schema/rd_cdm.yaml` - -- **Versioned instances (data packs)** - - `src/rd_cdm/instances/v2_0_1/*.yaml` (e.g., `code_systems.yaml`, `data_elements.yaml`, `value_sets.yaml`) - - merged file: `src/rd_cdm/instances/v2_0_1/rd_cdm_v2_0_1.yaml` - - exports (if present or generated locally): - - `src/rd_cdm/instances/v2_0_1/jsons/*.json` - - `src/rd_cdm/instances/v2_0_1/csvs/*.csv` - -- **Generated Python & Pydantic classes (LinkML)** - - `src/rd_cdm/python_classes/rd_cdm.py` (LinkML runtime dataclasses) - - `src/rd_cdm/python_classes/rd_cdm_pydantic.py` (generated from the schema via LinkML’s Pydantic generator) - -- **Utilities / CLI entry points** - - `rdcdm-merge` – merge instance parts into `rd_cdm_vX_Y_Z.yaml` - - `rdcdm-json` – per-file JSON export + combined `rd_cdm_vX_Y_Z.json` - - `rdcdm-csv` – per-file CSV export + combined `rd_cdm_vX_Y_Z.csv` - - `rdcdm-validate` – validate ontology codes via BioPortal + - `src/rd_cdm/schema/rd_cdm.yaml` — LinkML schema defining the data model + structure. The `version` and `date` fields here are the single source of + truth for the data model version. + +- **Instances** + - `src/rd_cdm/instances/code_systems.yaml` + - `src/rd_cdm/instances/data_elements.yaml` + - `src/rd_cdm/instances/value_sets.yaml` + - `src/rd_cdm/instances/rd_cdm.yaml` — merged instance, version-stamped + with `rd_cdm_version` and `rd_cdm_date` at the top + - `src/rd_cdm/instances/jsons/rd_cdm.json` + - `src/rd_cdm/instances/csvs/rd_cdm.csv` + +- **Generated Python classes (LinkML)** + - `src/rd_cdm/python_classes/rd_cdm.py` — LinkML runtime dataclasses + - `src/rd_cdm/python_classes/rd_cdm_pydantic.py` — Pydantic v2 models + +- **CLI entry points** + - `rd-cdm-merge` — merge instance parts into `rd_cdm.yaml` + - `rd-cdm-json` — export to `jsons/rd_cdm.json` + - `rd-cdm-csv` — export to `csvs/rd_cdm.csv` + - `rd-cdm-validate` — validate ontology codes via BioPortal --- @@ -76,81 +83,86 @@ Installing `rd-cdm` from PyPI provides: - **Interoperability**: Aligns with HL7 FHIR v4.0.1 and GA4GH Phenopacket v2.0 - **Ontology-driven**: Uses SNOMED CT, LOINC, NCIT, MONDO, OMIM, HPO, and more - **Modular**: Clear separation of schema, instances, and exports -- **Versioned data**: Instances shipped and resolved per version (e.g., `v2_0_1`) -- **Tooling**: Merge, export, and validation utilities with simple CLIs -- **(Optional) Pydantic models**: Strict runtime validation generated from LinkML +- **Self-describing exports**: Every YAML, JSON, and CSV file carries + `rd_cdm_version` and `rd_cdm_date` so outputs are unambiguous without + needing to know which package version was installed +- **Tooling**: Merge, export, and validation utilities via simple CLI commands +- **Pydantic models**: Runtime validation generated from the LinkML schema --- -### Installation +## Installation From PyPI: - ```bash pip install rd-cdm ``` -Optional extras for testing/docs: - +Optional extras: ```bash -pip install rd-cdm[test] # pytest, etc. -# or -pip install rd-cdm[docs] +pip install rd-cdm[test] # pytest, requests-mock +pip install rd-cdm[docs] # sphinx, sphinx-rtd-theme, sphinx-copybutton +pip install rd-cdm[dev] # linkml (for regenerating Python classes) ``` ### Development install - ```bash git clone https://github.com/BIH-CEI/rd-cdm.git cd rd-cdm -# (Recommended) create a venv python -m venv .venv && source .venv/bin/activate pip install -U pip -pip install -e .[test] +pip install -e ".[test,dev]" pytest -q ``` -> We use a **src/** layout. If you run tools directly, ensure `PYTHONPATH=src` or use the installed CLI entry points shown below. +> We use a **src/** layout. Use the installed CLI entry points shown below +> rather than running scripts directly. --- ## CLI tools -After installation you should have these commands: - +After installation the following commands are available: ```bash -# Merge the versioned parts into rd_cdm_vX_Y_Z.yaml (auto-resolves latest if not given) -rdcdm-merge # or: rdcdm-merge --version 2.0.1 +# Merge instance parts → src/rd_cdm/instances/rd_cdm.yaml +rd-cdm-merge -# Export JSON (per-file .json + combined rd_cdm_vX_Y_Z.json) -rdcdm-json # or: rdcdm-json -v 2.0.1 +# Export merged YAML → src/rd_cdm/instances/jsons/rd_cdm.json +rd-cdm-json -# Export CSV (per-file .csv + combined rd_cdm_vX_Y_Z.csv) -rdcdm-csv # or: rdcdm-csv -v 2.0.1 +# Export merged YAML → src/rd_cdm/instances/csvs/rd_cdm.csv +rd-cdm-csv -# Validate merged instance file against ontologies via BioPortal -rdcdm-validate # or: rdcdm-validate -v 2.0.1 (Note: set up BioPortal API key for this) +# Validate all ontology codes against BioPortal +rd-cdm-validate ``` -### BioPoratal API Key Setup for Validation -The ``rdcdm-validate`` command uses the BioPortal API -to check ontology term validity. This requires an API key to be set as an environment variable. +The recommended order when updating the model is: +```bash +rd-cdm-merge && rd-cdm-json && rd-cdm-csv && rd-cdm-validate +``` + +--- + +## Validating with BioPortal -#### Get an API key: +`rd-cdm-validate` checks all ontology codes in the merged instance against +BioPortal and reports version drift and missing or deprecated terms. -Sign up (or log in) at https://bioportal.bioontology.org/accounts/new +### Get an API key -- Go to your account settings and copy your API Key. -- Set the API key in your environment +Sign up at https://bioportal.bioontology.org/accounts/new, go to your account +settings, and copy your API key. -#### macOS / Linux (bash/zsh): +### Set the environment variable +macOS / Linux: ```bash export BIOPORTAL_API_KEY="your-key-here" ``` -#### Windoes (PowerShell): -```bash +Windows (PowerShell): +```powershell setx BIOPORTAL_API_KEY "your-key-here" ``` @@ -158,72 +170,61 @@ setx BIOPORTAL_API_KEY "your-key-here" ## Contributing and Contact -The RD-CDM is a community-driven effort and we invite open and international -collaboration. Please feel free to create issues, discuss features, -or submit pull requests to help enhance this project. For larger contributions, -consider reaching out to discuss collaboration opportunities. -Please find more information on how to contact us and contribute -in the [`Contribution` section of our documentation](https://rd-cdm.readthedocs.io/en/latest/contributing.html). +The RD-CDM is a community-driven effort. Please feel free to open issues, +discuss features, or submit pull requests. For larger contributions consider +reaching out directly. -## RareLink +See the [`Contributing` section of our documentation](https://rd-cdm.readthedocs.io/en/latest/contributing.html) +for full guidelines. -RareLink is a novel rare disease framework in REDCap linking international -registries, FHIR, and Phenopackets based on the RD-CDM. It is designed to -support the collection of harmonized data for rare disease research -across any REDCap project worldwide and allows for the preconfigured export of -the RD-CDM data in FHIR and Phenopackets formats. +## RareLink -For more information on RareLink, please see the: +RareLink is a REDCap-based framework for rare disease research linking +international registries to FHIR and Phenopackets, built on the RD-CDM. - [RareLink Documentation](https://rarelink.readthedocs.io/en/latest/index.html) - [RareLink GitHub](https://github.com/BIH-CEI/rarelink) -## Resources +--- + +## Resources ### Ontologies + - 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/) +- ICD-11 [🔗](https://icd.who.int/en) +- ICD-10-CM [🔗](https://www.cdc.gov/nchs/icd/icd10cm.htm) +- NCBI Taxonomy [🔗](https://www.ncbi.nlm.nih.gov/taxonomy) +- LOINC [🔗](https://loinc.org/) +- HGNC [🔗](https://www.genenames.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). +For the ontology versions used in each RD-CDM release, see the +[resources page in our documentation](https://rd-cdm.readthedocs.io/en/latest/resources/resources_file.html). -### Submodules -- [RareLink](https://github.com/BIH-CEI/RareLink) +--- ## License -This project is licensed under the terms of the [MIT License](https://github.com/BIH-CEI/rd-cdm/blob/develop/LICENSE) +[MIT License](https://github.com/BIH-CEI/rd-cdm/blob/develop/LICENSE) ## Citing -If you use the model for your research, do not hesitate to reach out and -please cite our article: - -> Graefe, A.S.L., Hübner, M.R., Rehburg, F. et al. An ontology-based rare disease common data model harmonising international registries, FHIR, and Phenopackets. Sci Data 12, 234 (2025). https://doi.org/10.1038/s41597-025-04558-z +> Graefe, A.S.L., Hübner, M.R., Rehburg, F. et al. An ontology-based rare +> disease common data model harmonising international registries, FHIR, and +> Phenopackets. *Sci Data* 12, 234 (2025). +> https://doi.org/10.1038/s41597-025-04558-z ## Acknowledgements -We would like to extend our thanks to all the authors involved in the -development of this RD-CDM model. - ---- - -- Authors: - - [Adam SL Graefe](https://github.com/aslgraefe) - - [Filip Rehburg](https://github.com/frehburg) - - [Samer Alkarkoukly](https://github.com/alkarkoukly) - - [Daniel Danis](https://github.com/ielis) - - [Peter N. Robinson](https://github.com/pnrobinson) - - Oya Beyan - - Sylvia Thun - +- [Adam SL Graefe](https://github.com/aslgraefe) +- [Filip Rehburg](https://github.com/frehburg) +- [Samer Alkarkoukly](https://github.com/alkarkoukly) +- [Daniel Danis](https://github.com/ielis) +- [Peter N. Robinson](https://github.com/pnrobinson) +- Oya Beyan +- Sylvia Thun \ No newline at end of file From a942cf9354f5e67ff3ad55efa927c3e30223730e Mon Sep 17 00:00:00 2001 From: Adam Graefe Date: Tue, 24 Mar 2026 17:18:23 +0100 Subject: [PATCH 6/8] updated changelog for v2.0.3 --- docs/changelog.rst | 193 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 193 insertions(+) diff --git a/docs/changelog.rst b/docs/changelog.rst index 9e9d868..6b7b5b0 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -14,6 +14,199 @@ This changelog provides a history of the changes to the RD-CDM. not publicly available. +v2.0.3 (2026-03-24) +-------------------- + +Code System Version Updates +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +All ontology and code system versions have been updated to their latest +releases as reported by BioPortal. The following version drifts were +resolved: + +.. list-table:: + :header-rows: 1 + :widths: 20 30 30 + + * - Code System + - Previous Version + - Updated Version + * - SNOMEDCT + - SNOMEDCT_US_2024_09_01 + - 2025AB + * - LOINC + - LNC278 + - 281 + * - HP + - 2025-05-06 + - 2026-02-16 + * - NCIT + - 24.01e + - 26.02d + * - NCBITAXON + - NCBI2024_04_02 + - 2025_04_10 + * - GENO + - 2023-10-08 + - 2026-02-02 + * - UO + - 2023-05-25 + - 2026-01-16 + * - ECO + - 2025-06-23 + - releases/2025-06-23 + * - ICD10CM + - ICD10CM_2025 + - 2026 + * - MONDO + - 2025-06-03 + - 2026-03-03 + * - ORDO + - 4.7 + - 4.8 + +Data Element Update: Sex at Birth (2.2) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The code for data element **2.2 Sex at Birth** has been updated. The +previous SNOMED CT concept ``281053000 | Sex of baby at delivery +(observable entity)`` was identified as inactive (deprecated) in the +SNOMED CT browser. + +The element is now coded using the LOINC concept: + +- **LOINC 76689-9** — *Sex assigned at birth* + +This aligns with HL7 FHIR's ``Patient`` resource and is semantically +precise as a question/observable code. The value set choices (Female, +Male, Unknown, etc.) remain SNOMED CT encoded as before. + +Repository and Package Structure Refactor +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The versioned folder structure inside ``src/rd_cdm/instances/`` has been +removed. Previously, each data model version occupied a dedicated +subdirectory (e.g., ``instances/v2_0_2/``) with the version repeated in +filenames (e.g., ``rd_cdm_v2_0_2.yaml``). This created redundancy since +Git tags and PyPI versioning already serve as the version archive. + +**New structure:** + +.. code-block:: text + + src/rd_cdm/ + ├── schema/ + │ └── rd_cdm.yaml # LinkML schema — version defined here + ├── instances/ + │ ├── code_systems.yaml + │ ├── data_elements.yaml + │ ├── value_sets.yaml + │ └── rd_cdm.yaml # merged, version-stamped output + │ ├── jsons/ + │ │ └── rd_cdm.json + │ └── csvs/ + │ ├── code_systems.csv + │ ├── data_elements.csv + │ ├── value_sets.csv + │ └── rd_cdm.csv + +**Version is now embedded in every exported file.** The fields +``rd_cdm_version`` and ``rd_cdm_date`` are defined in the LinkML schema +(``schema/rd_cdm.yaml``) and written into every merged and exported file +by ``rd-cdm-merge``. Every standalone YAML, JSON, or CSV file is +therefore self-describing. + +To use an older version of the model, use the corresponding Git tag or +pin the PyPI package: + +.. code-block:: bash + + pip install rd-cdm==2.0.2 + +CLI Naming Update +~~~~~~~~~~~~~~~~~ + +All CLI commands have been renamed from ``rdcdm-*`` to ``rd-cdm-*`` for +consistency with the PyPI package name ``rd-cdm``: + +.. list-table:: + :header-rows: 1 + :widths: 40 40 + + * - Old command + - New command + * - ``rdcdm-merge`` + - ``rd-cdm-merge`` + * - ``rdcdm-json`` + - ``rd-cdm-json`` + * - ``rdcdm-csv`` + - ``rd-cdm-csv`` + * - ``rdcdm-validate`` + - ``rd-cdm-validate`` + +The ``--version`` / ``-v`` argument has been removed from all CLI tools +since version resolution via subdirectories is no longer needed. + +The recommended workflow after updating instance files is: + +.. code-block:: bash + + rd-cdm-merge && rd-cdm-json && rd-cdm-csv && rd-cdm-validate + +Validation Improvements +~~~~~~~~~~~~~~~~~~~~~~~~ + +The ``rd-cdm-validate`` command now shows progress bars (via ``tqdm``) +for each of the three validation phases: code system version checking, +data element validation, and value set code validation. The current +element being checked is shown in the progress bar postfix. + +The validation summary now reports the data model version at the top: + +.. code-block:: text + + === RD-CDM VALIDATION SUMMARY (model version: 2.0.3) === + +Dependency Changes +~~~~~~~~~~~~~~~~~~ + +The following dependencies were removed as they were not used by the +package: + +- ``numpy`` +- ``requests-cache`` +- ``jsonschema`` +- ``oaklib`` + +``linkml`` has been moved from a core runtime dependency to an optional +``dev`` extra, since it is only needed to regenerate the Python classes +from the schema. Users installing ``rd-cdm`` for data access do not +require it: + +.. code-block:: bash + + pip install rd-cdm # no linkml + pip install rd-cdm[dev] # includes linkml for schema development + +``tqdm`` has been added as a core dependency for validation progress +reporting. + +Python Class Generation +~~~~~~~~~~~~~~~~~~~~~~~~ + +The ``gen_pydantic.py`` utility now generates both output files from the +schema in a single run: + +- ``src/rd_cdm/python_classes/rd_cdm.py`` — LinkML runtime dataclasses + (via ``PythonGenerator``) +- ``src/rd_cdm/python_classes/rd_cdm_pydantic.py`` — Pydantic v2 models + (via ``PydanticGenerator``) + +Custom top-level schema fields (``date``) that are not valid +``SchemaDefinition`` fields are stripped into a temporary file before +generation to avoid ``SchemaDefinition.__init__()`` errors. + + Version 2.0.1 (2025-08-07) -------------------------- From 6cf01102897792fa008a0892b347f0284ef3a19a Mon Sep 17 00:00:00 2001 From: Adam Graefe Date: Tue, 24 Mar 2026 17:18:55 +0100 Subject: [PATCH 7/8] updated conf py of docs with new version --- docs/conf.py | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index c2a38dd..ee29600 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -15,7 +15,7 @@ project = 'Ontology-based rare disease common data model (RD-CDM)' copyright = 'Berlin Institute of Health, Charité Universitätsmedizin Berlin' author = 'Adam S.L. Graefe' -release = '2.0.0' +release = '2.0.3' extensions = [ 'sphinx.ext.autodoc', @@ -42,11 +42,6 @@ doctest_path = [src_path] doctest_test_doctest_blocks = "" -# code to be executed before each doctest block -doctest_global_setup = """ -import numpy as np -""" - doctest_default_flags = (doctest.REPORT_ONLY_FIRST_FAILURE | doctest.ELLIPSIS | doctest.IGNORE_EXCEPTION_DETAIL @@ -60,7 +55,6 @@ "requests": ("https://docs.python-requests.org/en/stable/", None), "scipy": ("https://docs.scipy.org/doc/scipy-1.11.0/", None), "statsmodels": ("https://www.statsmodels.org/stable/", None), - "numpy": ("https://numpy.org/doc/stable/", None), } # -- Options for HTML output ------------------------------------------------- From def957d0eaeae329f8a2677a470e1abef62cb40a Mon Sep 17 00:00:00 2001 From: Adam Graefe Date: Tue, 24 Mar 2026 17:19:11 +0100 Subject: [PATCH 8/8] updated version to v2.0.3 --- .../instances/{v2_0_2 => }/code_systems.yaml | 0 .../{v2_0_2 => }/csvs/code_systems.csv | 26 +- .../{v2_0_2 => }/csvs/data_elements.csv | 2 +- .../rd_cdm_v2_0_1.csv => csvs/rd_cdm.csv} | 283 +- .../{v2_0_2 => }/csvs/value_sets.csv | 4 +- .../instances/{v2_0_2 => }/data_elements.yaml | 6 +- .../{v2_0_2 => }/jsons/code_systems.json | 28 +- .../{v2_0_2 => }/jsons/data_elements.json | 6 +- src/rd_cdm/instances/jsons/rd_cdm.json | 3166 +++++++++++++++++ .../{v2_0_2 => }/jsons/value_sets.json | 0 .../rd_cdm_v2_0_1.yaml => rd_cdm.yaml} | 40 +- .../instances/v2_0_2/csvs/rd_cdm_v2_0_2.csv | 141 - .../instances/v2_0_2/jsons/rd_cdm_v2_0_1.json | 2184 ------------ .../instances/v2_0_2/jsons/rd_cdm_v2_0_2.json | 2184 ------------ .../instances/v2_0_2/rd_cdm_v2_0_2.yaml | 2292 ------------ .../instances/{v2_0_2 => }/value_sets.yaml | 0 src/rd_cdm/python_classes/rd_cdm.py | 71 +- src/rd_cdm/python_classes/rd_cdm_pydantic.py | 86 +- src/rd_cdm/schema/rd_cdm.yaml | 13 + src/rd_cdm/utils/config.py | 30 +- src/rd_cdm/utils/csv_parsing.py | 130 +- src/rd_cdm/utils/gen_pydantic.py | 113 +- src/rd_cdm/utils/json_parsing.py | 89 +- src/rd_cdm/utils/merge_instances.py | 79 +- src/rd_cdm/utils/settings.py | 8 +- src/rd_cdm/utils/validation.py | 225 +- src/rd_cdm/utils/versioning.py | 90 +- tests/test_csv_parsing.py | 61 +- tests/test_json_parsing.py | 72 +- tests/test_merge_instances.py | 55 +- tests/test_versioning.py | 44 +- 31 files changed, 3977 insertions(+), 7551 deletions(-) rename src/rd_cdm/instances/{v2_0_2 => }/code_systems.yaml (100%) rename src/rd_cdm/instances/{v2_0_2 => }/csvs/code_systems.csv (80%) rename src/rd_cdm/instances/{v2_0_2 => }/csvs/data_elements.csv (98%) rename src/rd_cdm/instances/{v2_0_2/csvs/rd_cdm_v2_0_1.csv => csvs/rd_cdm.csv} (76%) rename src/rd_cdm/instances/{v2_0_2 => }/csvs/value_sets.csv (99%) rename src/rd_cdm/instances/{v2_0_2 => }/data_elements.yaml (99%) rename src/rd_cdm/instances/{v2_0_2 => }/jsons/code_systems.json (88%) rename src/rd_cdm/instances/{v2_0_2 => }/jsons/data_elements.json (99%) create mode 100644 src/rd_cdm/instances/jsons/rd_cdm.json rename src/rd_cdm/instances/{v2_0_2 => }/jsons/value_sets.json (100%) rename src/rd_cdm/instances/{v2_0_2/rd_cdm_v2_0_1.yaml => rd_cdm.yaml} (99%) delete mode 100644 src/rd_cdm/instances/v2_0_2/csvs/rd_cdm_v2_0_2.csv delete mode 100644 src/rd_cdm/instances/v2_0_2/jsons/rd_cdm_v2_0_1.json delete mode 100644 src/rd_cdm/instances/v2_0_2/jsons/rd_cdm_v2_0_2.json delete mode 100644 src/rd_cdm/instances/v2_0_2/rd_cdm_v2_0_2.yaml rename src/rd_cdm/instances/{v2_0_2 => }/value_sets.yaml (100%) diff --git a/src/rd_cdm/instances/v2_0_2/code_systems.yaml b/src/rd_cdm/instances/code_systems.yaml similarity index 100% rename from src/rd_cdm/instances/v2_0_2/code_systems.yaml rename to src/rd_cdm/instances/code_systems.yaml diff --git a/src/rd_cdm/instances/v2_0_2/csvs/code_systems.csv b/src/rd_cdm/instances/csvs/code_systems.csv similarity index 80% rename from src/rd_cdm/instances/v2_0_2/csvs/code_systems.csv rename to src/rd_cdm/instances/csvs/code_systems.csv index f58aeaf..1e9af4c 100644 --- a/src/rd_cdm/instances/v2_0_2/csvs/code_systems.csv +++ b/src/rd_cdm/instances/csvs/code_systems.csv @@ -1,21 +1,21 @@ id,namespace_iri,title,version -SNOMEDCT,http://purl.bioontology.org/ontology/SNOMEDCT/,Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT),SNOMEDCT_US_2024_09_01 -LOINC,http://loinc.org,Logical Observation Identifiers Names and Codes (LOINC),LNC278 -HP,http://purl.obolibrary.org/obo/HP,Human Phenotype Ontology (HPO),2025-05-06 -NCIT,http://purl.obolibrary.org/obo/NCIT/,NCI Thesaurus (NCIT) OBO Edition,24.01e +SNOMEDCT,http://purl.bioontology.org/ontology/SNOMEDCT/,Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT),2025AB +LOINC,http://loinc.org,Logical Observation Identifiers Names and Codes (LOINC),281 +HP,http://purl.obolibrary.org/obo/HP,Human Phenotype Ontology (HPO),2026-02-16 +NCIT,http://purl.obolibrary.org/obo/NCIT/,NCI Thesaurus (NCIT) OBO Edition,26.02d HL7FHIR,http://hl7.org/fhir/,"Health Level Seven Fast Healthcare Interoperability Resources, Release 4",v4.0.1 GA4GH,https://ga4gh.github.io/phenopacket-v2/,Global Alliance for Genomics and Health Phenopackets Schema,v2.0 -CustomCode,https://github.com/BIH-CEI/rd-cdm,Custom Code System RD CDM v2.0.0,v2.0.0 -NCBITAXON,http://purl.obolibrary.org/obo/NCBITAXON/,NCBI organismal classification,NCBI2024_04_02 -GENO,http://purl.obolibrary.org/obo/GENO/,GENO – The Genotype Ontology,2023-10-08 +CustomCode,https://github.com/BIH-CEI/rd-cdm,Custom Code System RD CDM v2.0,v2.0 +NCBITAXON,http://purl.obolibrary.org/obo/NCBITAXON/,NCBI organismal classification,2025_04_10 +GENO,http://purl.obolibrary.org/obo/GENO/,GENO – The Genotype Ontology,2026-02-02 SO,http://purl.obolibrary.org/obo/SO/,Sequence Ontology,2.6 -UO,http://purl.obolibrary.org/obo/UO/,Units Ontology (UO),2023-05-25 -ECO,http://purl.obolibrary.org/obo/ECO/,Evidence & Conclusion Ontology (ECO),2025-06-23 -ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/,"International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)",CD10CM_2025 -MONDO,http://purl.obolibrary.org/obo/MONDO/,Mondo Disease Ontology,2025-06-03 -ORDO,http://purl.obolibrary.org/obo/ORDO/,Orphanet Rare Disease Ontology (ORDO),4.7 +UO,http://purl.obolibrary.org/obo/UO/,Units Ontology (UO),2026-01-16 +ECO,http://purl.obolibrary.org/obo/ECO/,Evidence & Conclusion Ontology (ECO),releases/2025-06-23 +ICD10CM,http://purl.bioontology.org/ontology/ICD10CM/,"International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)",2026 +MONDO,http://purl.obolibrary.org/obo/MONDO/,Mondo Disease Ontology,2026-03-03 +ORDO,http://purl.obolibrary.org/obo/ORDO/,Orphanet Rare Disease Ontology (ORDO),4.8 HGNC,http://identifiers.org/hgnc/,HUGO Gene Nomenclature Committee (HGNC),2024-08-23 -OMIM,http://purl.bioontology.org/ontology/OMIM/,Online Mendelian Inheritance in Man (OMIM),OMIM2024_08_09 +OMIM,http://purl.bioontology.org/ontology/OMIM/,Online Mendelian Inheritance in Man (OMIM),2025_08_04 HGVS,https://varnomen.hgvs.org/,Human Genome Variation Society Nomenclature,21.0.0 ICD11,http://id.who.int/icd/release/11/mms/,"International Classification of Diseases, Eleventh Revision (ICD-11)",2024-09-01 ISO3166,https://www.iso.org/iso-3166-country-codes.html,International Organization for Standardization – ISO 3166 Country Codes,2020(en) diff --git a/src/rd_cdm/instances/v2_0_2/csvs/data_elements.csv b/src/rd_cdm/instances/csvs/data_elements.csv similarity index 98% rename from src/rd_cdm/instances/v2_0_2/csvs/data_elements.csv rename to src/rd_cdm/instances/csvs/data_elements.csv index 020e15e..dbbafef 100644 --- a/src/rd_cdm/instances/v2_0_2/csvs/data_elements.csv +++ b/src/rd_cdm/instances/csvs/data_elements.csv @@ -2,7 +2,7 @@ dataSpecification,dataType,description,elementCode,elementCodeSystem,elementName ['n/a'],Identifier,The (local) patient-related identification code.,"{'system': 'SNOMEDCT', 'code': '422549004'}",SNOMEDCT,Pseudonym,Patient.identifier.value,1.1,Individual.id,n/a,string,1. Formal Criteria, ['YYYY-MM-DD'],Date,The date of admission or data capture of the individual.,"{'system': 'SNOMEDCT', 'code': '399423000'}",SNOMEDCT,Date of Admission,Encounter.period.start,1.2,Individual.time_at_last_encounter,n/a,TimeElement,1. Formal Criteria, "['YYYY', 'YYYY-MM', 'YYYY-MM-DD']",Date,The individual's date of birth.,"{'system': 'SNOMEDCT', 'code': '184099003'}",SNOMEDCT,Date of Birth,Patient.birthDate,2.1,Individual.date_of_birth,n/a,TimeElement,2. Personal Information, -"['VSe', 'VSc']",Code,The individual's sex that was assigned at birth.,"{'system': 'SNOMEDCT', 'code': '281053000'}",SNOMEDCT,Sex at Birth,Patient.extension:individual-recordedSexOrGender,2.2,Individual.sex,Recorded Sex Or Gender Type,Sex,2. Personal Information,Sex at Birth Value Set v2.0.0 +"['VSe', 'VSc']",Code,The individual's sex that was assigned at birth.,"{'system': 'LOINC', 'code': '76689-9'}",LOINC,Sex at Birth,Patient.extension:individual-recordedSexOrGender,2.2,Individual.sex,Recorded Sex Or Gender Type,Sex,2. Personal Information,Sex at Birth Value Set v2.0.0 ['VSc'],Code,The chromosomal sex of an individual.,"{'system': 'SNOMEDCT', 'code': '1296886006'}",SNOMEDCT,Karyotypic Sex,Observation.value,2.3,Individual.karyotypic_sex,n/a,Karyotypic Sex,2. Personal Information,Karyotypic Sex Value Set v2.0.0 "['VSe', 'VSc']",Code,The self-assigned gender of the individual.,"{'system': 'SNOMEDCT', 'code': '263495000'}",SNOMEDCT,Gender Identity,Patient.extension:individual-genderIdentity,2.4,Individual.gender,Gender Identity,OntologyClass,2. Personal Information,Gender Identity Value Set v2.0.0 ['VS'],Code,The individual's country of birth.,"{'system': 'SNOMEDCT', 'code': '370159000'}",SNOMEDCT,Country of Birth,Patient.extension:patient-birthPlace,2.5,n/a,DataType: Address,n/a,2. Personal Information, diff --git a/src/rd_cdm/instances/v2_0_2/csvs/rd_cdm_v2_0_1.csv b/src/rd_cdm/instances/csvs/rd_cdm.csv similarity index 76% rename from src/rd_cdm/instances/v2_0_2/csvs/rd_cdm_v2_0_1.csv rename to src/rd_cdm/instances/csvs/rd_cdm.csv index 7dc6b43..c636956 100644 --- a/src/rd_cdm/instances/v2_0_2/csvs/rd_cdm_v2_0_1.csv +++ b/src/rd_cdm/instances/csvs/rd_cdm.csv @@ -1,141 +1,142 @@ -_section,codes,dataSpecification,dataType,description,elementCode,elementCodeSystem,elementName,fhirExpression_v4_0_1,id,label,namespace_iri,ordinal,phenopacketSchemaElement_v2_0,recommendedDataSpec_fhir,recommendedDataSpec_phenopackets,section,title,valueSet,version -code_systems,,,,,,,,,SNOMEDCT,,http://purl.bioontology.org/ontology/SNOMEDCT/,,,,,,Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT),,SNOMEDCT_US_2024_09_01 -code_systems,,,,,,,,,LOINC,,http://loinc.org,,,,,,Logical Observation Identifiers Names and Codes (LOINC),,LNC278 -code_systems,,,,,,,,,HP,,http://purl.obolibrary.org/obo/HP,,,,,,Human Phenotype Ontology (HPO),,2025-05-06 -code_systems,,,,,,,,,NCIT,,http://purl.obolibrary.org/obo/NCIT/,,,,,,NCI Thesaurus (NCIT) OBO Edition,,24.01e -code_systems,,,,,,,,,HL7FHIR,,http://hl7.org/fhir/,,,,,,"Health Level Seven Fast Healthcare Interoperability Resources, Release 4",,v4.0.1 -code_systems,,,,,,,,,GA4GH,,https://ga4gh.github.io/phenopacket-v2/,,,,,,Global Alliance for Genomics and Health Phenopackets Schema,,v2.0 -code_systems,,,,,,,,,CustomCode,,https://github.com/BIH-CEI/rd-cdm,,,,,,Custom Code System RD CDM v2.0.0,,v2.0.0 -code_systems,,,,,,,,,NCBITAXON,,http://purl.obolibrary.org/obo/NCBITAXON/,,,,,,NCBI organismal classification,,NCBI2024_04_02 -code_systems,,,,,,,,,GENO,,http://purl.obolibrary.org/obo/GENO/,,,,,,GENO – The Genotype Ontology,,2023-10-08 -code_systems,,,,,,,,,SO,,http://purl.obolibrary.org/obo/SO/,,,,,,Sequence Ontology,,2.6 -code_systems,,,,,,,,,UO,,http://purl.obolibrary.org/obo/UO/,,,,,,Units Ontology (UO),,2023-05-25 -code_systems,,,,,,,,,ECO,,http://purl.obolibrary.org/obo/ECO/,,,,,,Evidence & Conclusion Ontology (ECO),,2025-06-23 -code_systems,,,,,,,,,ICD10CM,,http://purl.bioontology.org/ontology/ICD10CM/,,,,,,"International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)",,CD10CM_2025 -code_systems,,,,,,,,,MONDO,,http://purl.obolibrary.org/obo/MONDO/,,,,,,Mondo Disease Ontology,,2025-06-03 -code_systems,,,,,,,,,ORDO,,http://purl.obolibrary.org/obo/ORDO/,,,,,,Orphanet Rare Disease Ontology (ORDO),,4.7 -code_systems,,,,,,,,,HGNC,,http://identifiers.org/hgnc/,,,,,,HUGO Gene Nomenclature Committee (HGNC),,2024-08-23 -code_systems,,,,,,,,,OMIM,,http://purl.bioontology.org/ontology/OMIM/,,,,,,Online Mendelian Inheritance in Man (OMIM),,OMIM2024_08_09 -code_systems,,,,,,,,,HGVS,,https://varnomen.hgvs.org/,,,,,,Human Genome Variation Society Nomenclature,,21.0.0 -code_systems,,,,,,,,,ICD11,,http://id.who.int/icd/release/11/mms/,,,,,,"International Classification of Diseases, Eleventh Revision (ICD-11)",,2024-09-01 -code_systems,,,,,,,,,ISO3166,,https://www.iso.org/iso-3166-country-codes.html,,,,,,International Organization for Standardization – ISO 3166 Country Codes,,2020(en) -code_systems,,,,,,,,,ICF,,https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health,,,,,,"International Classification of Functioning, Disability and Health (ICF)",,1.0.2 -data_elements,,['n/a'],Identifier,The (local) patient-related identification code.,"{'system': 'SNOMEDCT', 'code': '422549004'}",SNOMEDCT,Pseudonym,Patient.identifier.value,,,,1.1,Individual.id,n/a,string,1. Formal Criteria,,, -data_elements,,['YYYY-MM-DD'],Date,The date of admission or data capture of the individual.,"{'system': 'SNOMEDCT', 'code': '399423000'}",SNOMEDCT,Date of Admission,Encounter.period.start,,,,1.2,Individual.time_at_last_encounter,n/a,TimeElement,1. Formal Criteria,,, -data_elements,,"['YYYY', 'YYYY-MM', 'YYYY-MM-DD']",Date,The individual's date of birth.,"{'system': 'SNOMEDCT', 'code': '184099003'}",SNOMEDCT,Date of Birth,Patient.birthDate,,,,2.1,Individual.date_of_birth,n/a,TimeElement,2. Personal Information,,, -data_elements,,"['VSe', 'VSc']",Code,The individual's sex that was assigned at birth.,"{'system': 'SNOMEDCT', 'code': '281053000'}",SNOMEDCT,Sex at Birth,Patient.extension:individual-recordedSexOrGender,,,,2.2,Individual.sex,Recorded Sex Or Gender Type,Sex,2. Personal Information,,Sex at Birth Value Set v2.0.0, -data_elements,,['VSc'],Code,The chromosomal sex of an individual.,"{'system': 'SNOMEDCT', 'code': '1296886006'}",SNOMEDCT,Karyotypic Sex,Observation.value,,,,2.3,Individual.karyotypic_sex,n/a,Karyotypic Sex,2. Personal Information,,Karyotypic Sex Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The self-assigned gender of the individual.,"{'system': 'SNOMEDCT', 'code': '263495000'}",SNOMEDCT,Gender Identity,Patient.extension:individual-genderIdentity,,,,2.4,Individual.gender,Gender Identity,OntologyClass,2. Personal Information,,Gender Identity Value Set v2.0.0, -data_elements,,['VS'],Code,The individual's country of birth.,"{'system': 'SNOMEDCT', 'code': '370159000'}",SNOMEDCT,Country of Birth,Patient.extension:patient-birthPlace,,,,2.5,n/a,DataType: Address,n/a,2. Personal Information,,, -data_elements,,"['VSe', 'VSc']",Code,The individual’s general clinical status orvital status.,"{'system': 'SNOMEDCT', 'code': '278844005'}",SNOMEDCT,Vital Status,Patient.deceased.deceasedBoolean|Observation.value,,,,3.1,Individual.VitalStatus.status,Boolean|Code,Value Set: VitalStatus.Status,3. Patient Status,,Vital Status Value Set v2.0.0, -data_elements,,"['YYYY', 'YYYY-MM', 'YYYY-MM-DD']",Date,"If deceased, the individual’s date of death.","{'system': 'SNOMEDCT', 'code': '398299004'}",SNOMEDCT,Time of Death,Patient.deceasedDateTime,,,,3.2,Individual.VitalStatus.time_of_death,DateTime,TimeElement,3. Patient Status,,, -data_elements,,['ICD-10CM'],Code,"If deceased, the individual’s primary cause of death.","{'system': 'SNOMEDCT', 'code': '184305005'}",SNOMEDCT,Cause of Death,Observation.value.coding.code,,,,3.3,Individual.VitalStatus.cause_of_death,Code|CodeableConcept,OntologyClass,3. Patient Status,,, -data_elements,,['VSe'],Code,The individual's age category at thetime of data capture.,"{'system': 'SNOMEDCT', 'code': '105727008'}",SNOMEDCT,Age Category,Observation.value.coding.code,,,,3.4,Individual.time_at_last_encounter,CodableConcept,TimeElement,3. Patient Status,,Age Category Value Set v2.0.0, -data_elements,,['XX+X'],String,"The duration of the pregnancy in weeks and days,formatted as XX+X (weeks+days).","{'system': 'SNOMEDCT', 'code': '412726003'}",SNOMEDCT,Length of Gestation at Birth [weeks+days],Observation.component:weeks.valueQuantity|Observation.component:days.valueQuantity,,,,3.5,n/a,Quantity,n/a,3. Patient Status,,, -data_elements,,['VSe'],Code,Identifies cases where an RD diagnosis has notbeen established.,"{'system': 'SNOMEDCT', 'code': '723663001'}",SNOMEDCT,Undiagnosed RD Case,(Condition.code),,,,3.6,(Disease.term),Code(e.g. ORDO:616874 - Rare disorderwithout a determined diagnosis afterfull investigation),(OntologyClass (e.g. ORDO:616874 - Rare disorder without a determineddiagnosis after full investigation)),3. Patient Status,,Undiagnosed RD Case Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,The beginning of an encounter of the individual.,"{'system': 'HL7FHIR', 'code': 'encounter.period.start'}",HL7FHIR,Encounter Start,Encounter.period.start,,,,4.1,n/a,DateTime,n/a,4. Care Pathway,,, -data_elements,,['YYYY-MM-DD'],Date,The end of an encounter of the individual.,"{'system': 'HL7FHIR', 'code': 'encounter.period.end'}",HL7FHIR,Encounter End,Encounter.period.end,,,,4.2,n/a,DateTime,n/a,4. Care Pathway,,, -data_elements,,"['VSe', 'VSc']",Code,The status of an encounter of the individual at thetime of data capture.,"{'system': 'SNOMEDCT', 'code': '305058001'}",SNOMEDCT,Encounter Status,Encounter.status,,,,4.3,n/a,ValueSet: EncounterStatus,n/a,4. Care Pathway,,Encounter Status Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The class of an encounter of the individualat the time of data capture.,"{'system': 'HL7FHIR', 'code': 'encounter.class'}",HL7FHIR,Encounter Class,Encounter.class,,,,4.4,n/a,ValueSet: EncounterClass,n/a,4. Care Pathway,,Encounter Class Value Set v2.0.0, -data_elements,,"['Ontology Class (MONDO, ORDO, ICD-10, ICD-11, OMIM_g, OMIM_p)']",Code,"A disease that the individual was affected by. If agenetic diagnosis or subtypes were diagnosed, please also provide the respective OMIM_g and OMIM_p codes.","{'system': 'SNOMEDCT', 'code': '64572001'}",SNOMEDCT,Disease,Condition.code,,,,5.1,Disease.term,Code,OntologyClass,5. Disease,,n/a, -data_elements,,['VS'],Code,The verification status of the disease.,"{'system': 'LOINC', 'code': '99498-8'}",LOINC,Verification Status,Condition.verificationStatus,,,,5.2,(Disease.excluded),ValueSet: Condition Verficication Status,boolean,5. Disease,,Verification Status Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The age at the onset of the first symptomsor signs of the disease.,"{'system': 'SNOMEDCT', 'code': '424850005'}",SNOMEDCT,Age at Onset,Condition.onsetString orObservation.valueCodeableConcept,,,,5.3,Disease.onset,Disease.onset,Disease.onset,5. Disease,,Age at Onset Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,The date at onset of first symptoms orsigns of the disease.,"{'system': 'SNOMEDCT', 'code': '298059007'}",SNOMEDCT,Date of Onset,Condition.onset,,,,5.4,Disease.onset,DateTime,TimeElement,5. Disease,,n/a, -data_elements,,"['VSe', 'VSc']",Code,The individual’s age when the diagnosis was made.,"{'system': 'SNOMEDCT', 'code': '423493009'}",SNOMEDCT,Age at Diagnosis,Observation.value,,,,5.5,(Disease.onset),CodeableConcept,(TimeElement),5. Disease,,Age at Diagnosis Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,The date on which the disease was determined.,"{'system': 'SNOMEDCT', 'code': '432213005'}",SNOMEDCT,Date of Diagnosis,Condition.recordedDate,,,,5.6,(Disease.onset),DateTime,(TimeElement),5. Disease,,n/a, -data_elements,,['VS'],Code,The specific body site affected by disease is encodedusing all descendants of SCT Body Structure (123037004).,"{'system': 'SNOMEDCT', 'code': '363698007'}",SNOMEDCT,Body Site,Condition.bodySite.coding:SNOMEDCT-ct,,,,5.7,Disease.primary_site,CodeableConcept,OntologyClass,5. Disease,,Body Site Value Set v2.0.0, -data_elements,,['VS'],Code,"The clinical status of the disease indicates whetherit is active, inactive, or resolved.","{'system': 'SNOMEDCT', 'code': '263493007'}",SNOMEDCT,Clinical Status,Condition.clinicalStatus,,,,5.8,n/a,ValueSet: ClinicalStatus,n/a,5. Disease,,Clinical Status Value Set v2.0.0, -data_elements,,['VS'],Code,The severity of the disease is categorised byclinical evaluation.,"{'system': 'SNOMEDCT', 'code': '246112005'}",SNOMEDCT,Severity,Condition.severity,,,,5.9,n/a,ValueSet: ConditionSeverity,n/a,5. Disease,,Severity Value Set v2.0.0, -data_elements,,"['OMIM_p', 'MONDO']",Code,The genomic diagnoses can correspond to the diagnoseddisease in (5.1) if the same OMIM codes are used.,"{'system': 'SNOMEDCT', 'code': '106221001'}",SNOMEDCT,Genomic Diagnosis,Condition.code,,,,6.1.1,Interpretation.Diagnosis.disease,Code,OntologyClass,6. Genetic Findings,,n/a, -data_elements,,['VS'],Code,The interpretation has a ProgressStatus that refers tothe status of the attempted diagnosis.,"{'system': 'GA4GH', 'code': 'progress_status'}",GA4GH,Progress Status of Interpretation,Condition.extension,,,,6.1.2,Interpretation.progress_status,VS: GA4GH ProgressStatus,ValueSet: ProgressStatus,6. Genetic Findings,,Progress Status Value Set v2.0.0, -data_elements,,['VS'],Code,An enumeration that describes the conclusion made about the genomic interpretation.,"{'system': 'GA4GH', 'code': 'interpretation_status'}",GA4GH,Interpretation Status,Condition.extension,,,,6.1.3,GenomicInterpretation.interpretation_status,VS: GA4GH InterpretationStatus,ValueSet: InterpretationStatus,6. Genetic Findings,,Interpretation Status Value Set v2.0.0, -data_elements,,"['VS', 'LOINC']",Code,The method used to analyse structural variants in the genome.,"{'system': 'LOINC', 'code': '81304-8'}",LOINC,Structural Variant Analysis Method,Observation.method,,,,6.1.4,n/a,CodeableConcept,n/a,6. Genetic Findings,,Structural Variant Analysis Method Value Set v2.0.0, -data_elements,,['VS'],Code,The reference genome used for analysing the genetic variant.,"{'system': 'LOINC', 'code': '62374-4'}",LOINC,Reference Genome,Observation.component:reference-sequence-assembly,,,,6.1.5,n/a,CodeableConcept,n/a,6. Genetic Findings,,Reference Genome Value Set v2.0.0, -data_elements,,['n/a'],String,An unvalidated (HGVS) string that describes the variant change,"{'system': 'LOINC', 'code': 'LP7824-8'}",LOINC,Genetic Mutation String,Observation.component:Variant.valueString,,,,6.1.6,VariationDescriptor.Extension.value,string,string,6. Genetic Findings,,n/a, -data_elements,,['g.HGVS'],Code,The specific change in the genomic DNA sequence encoded with a validated g.HGVS expression.,"{'system': 'LOINC', 'code': '81290-9'}",LOINC,Genomic DNA Change,Observation.component:Variant.valueCode,,,,6.1.7,VariationDescriptor.Expression.value,Code,string,6. Genetic Findings,,n/a, -data_elements,,['c.HGVS'],Code,The specific change in the DNA sequence at the nucleotide level with a validated c.HGVS expression.,"{'system': 'LOINC', 'code': '48004-6'}",LOINC,Sequence DNA Change,Observation.component:Variant.valueCode,,,,6.1.8,VariationDescriptor.Expression.value,Code,string,6. Genetic Findings,,n/a, -data_elements,,['p.HGVS'],Code,The specific change in the amino acid sequence resulting from agenetic variant as a validated p.HGVS expression.,"{'system': 'LOINC', 'code': '48005-3'}",LOINC,Amino Acid Change,Observation.component:Variant.valueCode,,,,6.1.9,VariationDescriptor.Expression.value,Code,string,6. Genetic Findings,,n/a, -data_elements,,['HGNC'],Code,The specific gene or genes that were analysed or identified in the study.,"{'system': 'LOINC', 'code': '48018-6'}",LOINC,Gene,Observation.component:Gene,,,,6.1.10,GeneDescriptor.value_id,Code,string,6. Genetic Findings,,n/a, -data_elements,,"['VSe', 'VSc', 'LOINC']",Code,The zygosity of the genetic variant.,"{'system': 'LOINC', 'code': '53034-5'}",LOINC,Zygosity,Observation.component:geneticsAllele.State,,,,6.1.11,VariationDescriptor.allelic_state,VS: Allelic State,OntologyClass,6. Genetic Findings,,Zygosity Value Set v2.0.0, -data_elements,,['VS'],Code,"The classification of the genomic source, such as germline, somatic, or other origins.","{'system': 'LOINC', 'code': '48002-0'}",LOINC,Genomic Source Class,Observation.component:GenomicSourceClass,,,,6.1.12,n/a,CodeableConcept,n/a,6. Genetic Findings,,Genomic Source Class Value Set v2.0.0, -data_elements,,['VS'],Code,"The variant’s type of DNA change, such as point mutation, deletion, insertion, or other types.","{'system': 'LOINC', 'code': '48019-4'}",LOINC,DNA Change Type,Observation.component:Variant.Type,,,,6.1.13,n/a,Code,n/a,6. Genetic Findings,,DNA Change Type Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,"The clinical significance of the genetic variant, indicating its impact on health and disease.","{'system': 'LOINC', 'code': '53037-8'}",LOINC,Clinical Significance [ACMG],Observation.component:Variant.Interpretation,,,,6.1.14,VariantInterpretation.acmg_pathogenicity_classification,,ValueSet: AcmgPathogenicityClassification,6. Genetic Findings,,Clinical Significance ACMG Value Set v2.0.0, -data_elements,,['VS'],Code,"An enumeration flagging the variant as being a candidate for treatment or clinical intervention, which could improve the clinical outcome.","{'system': 'GA4GH', 'code': 'therapeutic_actionability'}",GA4GH,Therapeutic Actionability,n/a,,,,6.1.15,VariantInterpretation.therapeutic_actionability,n/a,ValueSet: TherapeuticActionability,6. Genetic Findings,,Therapeutic Actionability Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The level of evidence supporting the clinical annotation of the genetic variant.,"{'system': 'LOINC', 'code': '93044-6'}",LOINC,Clinical Annotation Level Of Evidence,Observation.extension:Variant.Interpretation,,,,6.1.16,n/a,CodeableConcept,n/a,6. Genetic Findings,,Clinical Annotation Level Of Evidence Value Set v2.0.0, -data_elements,,['HPO'],Code,An observed physical and clinical characteristicencoded with HPO.,"{'system': 'SNOMEDCT', 'code': '8116006'}",SNOMEDCT,Phenotypic Feature,Observation.code,,,,6.2.1,PhenotypicFeature.type,Code,OntologyClass,6. Phenotypic Feature,,n/a, -data_elements,,"['VSe', 'VSc']",Code,"The current status of the phenotypic feature, indicating whether it is confirmed or refuted.","{'system': 'SNOMEDCT', 'code': '363778006'}",SNOMEDCT,Status,Observation.status,,,,6.2.2,PhenotypicFeature.excluded,ValueSet: ObservationStatus,boolean,6.2 Phenotypic Feature,,Phenotype Status Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,The date on which the phenotypic feature was observed or recorded. We recommend capturing the time acharacteristic was observed.,"{'system': 'SNOMEDCT', 'code': '439272007:704321009=363778006'}",SNOMEDCT,Determination Date,Observation.effectiveDateTime,,,,6.2.3,PhenotypicFeature.onset,DateTime,TimeElement,6. Phenotypic Feature,,n/a, -data_elements,,['YYYY-MM-DD'],Date,Time at which the feature resolved or abated.,"{'system': 'HP', 'code': '0034382'}",HP,Resolution Date,Observation.effectiveDateTime,,,,6.2.4,PhenotypicFeature.resolution,DateTime,TimeElement,6.2 Phenotypic Feature,,n/a, -data_elements,,"['VSe', 'VSc']",Code,Time at which the feature was first observed within HPO onset categories.,"{'system': 'HP', 'code': '0003674'}",HP,Onset Category,Observation.category,,,,6.2.5,PhenotypicFeature.onset,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,Onset Category Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The speed at which disease manifestations appear and develop.,"{'system': 'HP', 'code': '0011008'}",HP,Temporal Pattern,Observation.interpretation,,,,6.2.6,PhenotypicFeature.modifiers,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,Temporal Pattern Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,A description of the severity of the feature.,"{'system': 'HP', 'code': '0012824'}",HP,Severity,Observation.interpretation,,,,6.2.7,PhenotypicFeature.severity,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,Severity Value Set v2.0.0, -data_elements,,"['OntologyClass (HPO, NCBITAXON, SCT)']",Code,"Any number of additional modifiers describing a specific phenotypic feature further, such as severity (HP:0012824), clinical modifiers (HP:0012823), or linking causative infectious agents using the NCBITAXON Ontology.","{'system': 'GA4GH', 'code': 'phenotypicfeature.modifier'}",GA4GH,Modifiers,Suggested: Observation.extension,,,,6.2.8,PhenotypicFeature.modifiers,CodeableConcept,list of OntologyClass,6. Phenotypic Feature,,n/a, -data_elements,,['ECO'],Code,The evidence for an assertion of the observation of a type defined within the Evidence & Conclusion Ontology (ECO).,"{'system': 'GA4GH', 'code': 'phenotypicfeature.evidence'}",GA4GH,Evidence,Observation.method,,,,6.2.9,PhenotypicFeature.evidence,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,n/a, -data_elements,,['OntologyClass (e.g. LOINC)'],Code,A class that describes the assay used to producethe measurement.,"{'system': 'NCIT', 'code': 'C60819'}",NCIT,Assay,Observation.code,,,,6.3.1,Measurement.assay,Code,OntologyClass,6.3 Measurement,,n/a, -data_elements,,['float'],Value,The result of the measurement.,"{'system': 'NCIT', 'code': 'C25712'}",NCIT,Value,Observation.value[x],,,,6.3.2,Measurement.measurement_value,Quantity|integer,Quantity[double/float],6.3 Measurement,,n/a, -data_elements,,['UO'],Code,The unit of the result's measurement.,"{'system': 'NCIT', 'code': 'C92571'}",NCIT,Value Unit,Observation.value[x].unit,,,,6.3.3,Measurement.measurement_value,CodeableConcept,OntologyClass,6.3 Measurement,,n/a, -data_elements,,['NCIT'],Code,"The interpretation of the measurement (e.g.: Below/Within/Above age-related reference range, Absent/Low/Normal, or Positive/Negative).","{'system': 'NCIT', 'code': 'C41255'}",NCIT,Interpretation,Observation.interpretation,,,,6.3.4,n/a,n/a,n/a,6.3 Measurement,,n/a, -data_elements,,['YYYY-MM-DD'],Date,Time at which the measurement was performed.,"{'system': 'NCIT', 'code': 'C82577'}",NCIT,Time Observed,Observation.effectiveDateTime,,,,6.3.5,Measurement.time_observed,DateTime,TimeElement,6.3 Measurement,,n/a, -data_elements,,"['OntologyClass (e.g. NCIT, SNOMEDCT)']",Code,Clinical procedure performed to acquire the sample used for the measurement.,"{'system': 'SNOMEDCT', 'code': '122869004'}",SNOMEDCT,Procedure,Procedure.code,,,,6.3.6,Measurement.procedure,Measurement.procedure,Measurement.procedure,6.3 Measurement,,n/a, -data_elements,,['n/a'],Identifier,A unique identifier or local pseudonym for the familymember.,"{'system': 'CustomCode', 'code': 'family_member_id'}",CustomCode,Family Member Pseudonym,FamilyMemberHistory.identifier,,,,6.4.1,Family.Pedigree.Person.individual_id,Identifier,string,6.4 Family History,,n/a, -data_elements,,"['VSe', 'VSc']",Code,"Is the individual the first affected family member who seeks medical attention for a genetic disorder, leading to the diagnosis of other family members. Disclaimer: The SCT code for propositus (64245008) refers to any gender.","{'system': 'SNOMEDCT', 'code': '64245008'}",SNOMEDCT,Propositus/-a,n/a,,,,6.4.2,(Family.relatives → 1 Phenopacket per family member),n/a,(Family.relatives → 1 Phenopacket per family member),6.4 Family History,,Propositus Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,Specifies the familial relationship of the individual being evaluated to the propositus. Disclaimer: The SNOMEDCT code for propositus (64245008) refers to any gender.,"{'system': 'SNOMEDCT', 'code': '408732007'}",SNOMEDCT,Relationship of the Individual to the Propositus,n/a,,,,6.4.3,(Family.relatives → 1 Phenopacket per family member),n/a,(Family.relatives → 1 Phenopacket per family member),6.4 Family History,,Family Relationship To Index Case Value Set v2.0.0, -data_elements,,['VSe'],Code,"The presence of a biological relationship between parents who are related by blood, typically as first or second cousins.","{'system': 'SNOMEDCT', 'code': '842009'}",SNOMEDCT,Consanguinity,n/a,,,,6.4.4,Family.consanguinous_parents,n/a,boolean,6.4 Family History,,Consanguinity Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,Specifies the relationship of the selected family member to the patient.,"{'system': 'SNOMEDCT', 'code': '444018008'}",SNOMEDCT,Family Member Relationship,FamilyMemberHistory.relationship.coding,,,,6.4.5,Family.Pedigree.Person.individual_id,ValueSet: FamilyMember,string,6.4 Family History,,FamilyMember Value Set v2.0.0, -data_elements,,['VS'],Code,Specifies the record’s status of the family history of a specific family member.,"{'system': 'HL7FHIR', 'code': 'familymemberhistory.status'}",HL7FHIR,Family Member Record Status,FamilyMemberHistory.status,,,,6.4.6,n/a,,n/a,6.4 Family,,FamilyHistoryStatus Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,"Specifies the sex (or gender) of the specific family member. If possible, the sex assigned at birth should be selected.","{'system': 'LOINC', 'code': '54123-5'}",LOINC,Family Member Sex,FamilyMemberHistory.sex,,,,6.4.7,Family.Pedigree.Person.sex,ValueSet: AdministrativeGender,ValueSet: Sex,6.4 Family,,AdministrativeGender Value Set v2.0.0, -data_elements,,['Integer'],Integer,Records the current age of the selected family member.,"{'system': 'LOINC', 'code': '54141-7'}",LOINC,Family Member Age,FamilyMemberHistory.ageAge,,,,6.4.8,(Family.relatives → 1 Phenopacket per family member),Age,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,n/a, -data_elements,,['YYYY-MM-DD'],Date,Records the date of birth of the selected family member.,"{'system': 'LOINC', 'code': '54124-3'}",LOINC,Family Member Date of Birth,FamilyMemberHistory.bornDate,,,,6.4.9,(Family.relatives → 1 Phenopacket per family member),DateTime,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,n/a, -data_elements,,['VSe'],Code,Indicates whether the selected family member is deceased.,"{'system': 'SNOMEDCT', 'code': '740604001'}",SNOMEDCT,Family Member Deceased,FamilyMemberHistory.deceased.deceasedBoolean,,,,6.4.10,(Family.relatives → 1 Phenopacket per family member),boolean,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,Deceased Value Set v2.0.0, -data_elements,,['ICD10CM'],Code,Records the cause of death of the selected deceasedfamily member.,"{'system': 'LOINC', 'code': '54112-8'}",LOINC,Family Member Cause of Death,FamilyMemberHistory.condition.code & FamilyMemberHistory.condition.contributedToDeath,,,,6.4.11,(Family.relatives → 1 Phenopacket per family member),Code,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,n/a, -data_elements,,['Integer'],Integer,Records the age at which the selected family member died.,"{'system': 'LOINC', 'code': '92662-6'}",LOINC,Family Member Deceased Age,FamilyMemberHistory.deceasedAge,,,,6.4.12,Family.relatives,Family.relatives,Family.relatives,6.4 Family,,n/a, -data_elements,,"['Ontology Class', 'ORDO', 'ICD-10-CM', 'ICD-11', 'MONDO', 'OMIM_p']",Code,Indicates whether the selected family member is affected by the same rare disease as the individual.,"{'system': 'LOINC', 'code': '75315-2'}",LOINC,Family Member Disease,FamilyMemberHistory.condition.code,,,,6.4.13,Family.relatives,Family.relatives,Family.relatives,6.4 Family,,n/a, -data_elements,,['VS'],Code,Indicates the current status of the consent.,"{'system': 'SNOMEDCT', 'code': '309370004'}",SNOMEDCT,Consent Status,Consent.status,,,,7.1,n/a,ValueSet: ConsentStatus,n/a,7. Consent,,Consent Status Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,Records the date when the consent was given.,"{'system': 'HL7FHIR', 'code': 'consent.datetime'}",HL7FHIR,Consent Date,Consent.dateTime,,,,7.2,n/a,DateTime,n/a,7. Consent,,n/a, -data_elements,,['n/a'],String,References to the policies that are included in thisconsent scope.,"{'system': 'SNOMEDCT', 'code': '386318002'}",SNOMEDCT,Health Policy Monitoring,Consent.policy,,,,7.3,n/a,string,n/a,7. Consent,,n/a, -data_elements,,['VSe'],Code,Indicates whether the patient agrees to be contacted for research.,"{'system': 'CustomCode', 'code': 'consent_contact_research'}",CustomCode,Agreement to be Contacted for Research,Consent.scope.coding,,,,7.4,n/a,CodeableConcept,n/a,7. Consent,,Contact for Research Value Set v2.0.0, -data_elements,,['VSe'],Code,Indicates whether the patient consents to the reuse of their data.,"{'system': 'CustomCode', 'code': 'conset_data_reuse'}",CustomCode,Consent to the Reuse of Data,Consent.scope.coding,,,,7.5,n/a,CodeableConcept,n/a,7. Consent,,Data Reuse Consent Value Set v2.0.0, -data_elements,,['VSe'],Code,Indicates whether a patient's biological sample is available for research.,"{'system': 'SNOMEDCT', 'code': '123038009'}",SNOMEDCT,Biological Sample,n/a,,,,7.6,n/a,n/a,n/a,7. Consent,,Biological Sample Consent Value Set v2.0.0, -data_elements,,['n/a'],String,"If there is a biological sample, this data element indicates the link to the biobank of the individual's biological sample.","{'system': 'CustomCode', 'code': 'biobank_link'}",CustomCode,Link to a Biobank,n/a,,,,7.7,n/a,n/a,n/a,7. Consent,,n/a, -data_elements,,['ICF'],Code,"Specifies the classification of the individualss functioning or disability according to the International Classification of Functioning, Disability and Health (ICF).","{'system': 'CustomCode', 'code': 'icf_score'}",CustomCode,Classification of Functioning / Disability,n/a,,,,8.1,n/a,n/a,n/a,8. Disability,,n/a, -value_sets,"[{'system': 'SNOMEDCT', 'code': '248152002', 'label': 'Female'}, {'system': 'SNOMEDCT', 'code': '248153007', 'label': 'Male'}, {'system': 'SNOMEDCT', 'code': '184115007', 'label': 'Patient sex unknown'}, {'system': 'SNOMEDCT', 'code': '32570691000036108', 'label': 'Intersex'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:281053000,Sex at Birth Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '734875008', 'label': 'XX'}, {'system': 'SNOMEDCT', 'code': '734876009', 'label': 'XY'}, {'system': 'SNOMEDCT', 'code': '80427008', 'label': 'X0'}, {'system': 'SNOMEDCT', 'code': '65162001', 'label': 'XXY'}, {'system': 'SNOMEDCT', 'code': '35111009', 'label': 'XXX'}, {'system': 'SNOMEDCT', 'code': '403760006', 'label': 'XXYY'}, {'system': 'SNOMEDCT', 'code': '78317008', 'label': 'XXXY'}, {'system': 'SNOMEDCT', 'code': '10567003', 'label': 'XXXX'}, {'system': 'SNOMEDCT', 'code': '48930007', 'label': 'XYY'}, {'system': 'SNOMEDCT', 'code': '74964007', 'label': 'Other'}]",,,,,,,,SNOMEDCT:1296886006,Karyotypic Sex Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '446141000124107', 'label': 'Female gender identity'}, {'system': 'SNOMEDCT', 'code': '446151000124109', 'label': 'Male gender identity'}, {'system': 'SNOMEDCT', 'code': '394743007', 'label': 'Gender unknown'}, {'system': 'SNOMEDCT', 'code': '33791000087105', 'label': 'Identifies as nonbinary gender'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:263495000,Gender Identity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '438949009', 'label': 'Alive'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '399307001', 'label': 'Unknown - Lost in follow-up'}, {'system': 'SNOMEDCT', 'code': '185924006', 'label': 'Unknown - Opted-out'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown - Other Reason'}]",,,,,,,,SNOMEDCT:278844005,Vital Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '3658006', 'label': 'Infancy'}, {'system': 'SNOMEDCT', 'code': '713153009', 'label': 'Toddler'}, {'system': 'SNOMEDCT', 'code': '255398004', 'label': 'Childhood'}, {'system': 'SNOMEDCT', 'code': '263659003', 'label': 'Adolescence'}, {'system': 'SNOMEDCT', 'code': '41847000', 'label': 'Adulthood'}, {'system': 'SNOMEDCT', 'code': '303112003', 'label': 'Fetal period'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:105727008,Age Category Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '438949009', 'label': 'Alive'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '399307001', 'label': 'Unknown - Lost in follow-up'}, {'system': 'SNOMEDCT', 'code': '185924006', 'label': 'Unknown - Opted-out'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown - Other Reason'}]",,,,,,,,SNOMEDCT:278844005,Vital Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '3658006', 'label': 'Infancy'}, {'system': 'SNOMEDCT', 'code': '713153009', 'label': 'Toddler'}, {'system': 'SNOMEDCT', 'code': '255398004', 'label': 'Childhood'}, {'system': 'SNOMEDCT', 'code': '263659003', 'label': 'Adolescence'}, {'system': 'SNOMEDCT', 'code': '41847000', 'label': 'Adulthood'}, {'system': 'SNOMEDCT', 'code': '303112003', 'label': 'Fetal period'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:105727008,Age Category Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}]",,,,,,,,SNOMEDCT:723663001,Undiagnosed RD Case Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'planned', 'label': 'Planned'}, {'system': 'HL7FHIR', 'code': 'arrived', 'label': 'Arrived'}, {'system': 'HL7FHIR', 'code': 'triaged', 'label': 'Triaged'}, {'system': 'HL7FHIR', 'code': 'in-progress', 'label': 'In Progress'}, {'system': 'HL7FHIR', 'code': 'onleave', 'label': 'On Leave'}, {'system': 'HL7FHIR', 'code': 'finished', 'label': 'Finished'}, {'system': 'HL7FHIR', 'code': 'cancelled', 'label': 'Cancelled'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}, {'system': 'HL7FHIR', 'code': 'unknown', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:305058001,Encounter Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'AMB', 'label': 'Ambulatory'}, {'system': 'HL7FHIR', 'code': 'IMP', 'label': 'Inpatient'}, {'system': 'HL7FHIR', 'code': 'OBSENC', 'label': 'Observation'}, {'system': 'HL7FHIR', 'code': 'EMER', 'label': 'Emergency'}, {'system': 'HL7FHIR', 'code': 'VR', 'label': 'Virtual'}, {'system': 'HL7FHIR', 'code': 'HH', 'label': 'Home Health'}, {'system': 'CustomCode', 'code': 'RDC', 'label': 'RD Specialist Center'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,HL7FHIR:encounter.class,Encounter Class Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'unconfirmed', 'label': 'Unconfirmed'}, {'system': 'HL7FHIR', 'code': 'provisional', 'label': 'Provisional'}, {'system': 'HL7FHIR', 'code': 'differential', 'label': 'Differential'}, {'system': 'HL7FHIR', 'code': 'confirmed', 'label': 'Confirmed'}, {'system': 'HL7FHIR', 'code': 'refuted', 'label': 'Refuted'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}]",,,,,,,,HL7FHIR:99498-8,Verification Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '118189007', 'label': 'Prenatal'}, {'system': 'SNOMEDCT', 'code': '3950001', 'label': 'Birth'}, {'system': 'SNOMEDCT', 'code': '410672004', 'label': 'Date'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:424850005,Age at Onset Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '118189007', 'label': 'Prenatal'}, {'system': 'SNOMEDCT', 'code': '3950001', 'label': 'Birth'}, {'system': 'SNOMEDCT', 'code': '410672004', 'label': 'Date'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:423493009,Age at Diagnosis Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '442083009', 'label': 'Anatomical or acquired body structure'}]",,,,,,,,SNOMEDCT:363698007,Body Site Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'active', 'label': 'Active'}, {'system': 'HL7FHIR', 'code': 'recurrence', 'label': 'Recurrence'}, {'system': 'HL7FHIR', 'code': 'relapse', 'label': 'Relapse'}, {'system': 'HL7FHIR', 'code': 'inactive', 'label': 'Inactive'}, {'system': 'HL7FHIR', 'code': 'remission', 'label': 'Remission'}, {'system': 'HL7FHIR', 'code': 'resolved', 'label': 'Resolved'}]",,,,,,,,SNOMEDCT:263493007,Clinical Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '24484000', 'label': 'Severe'}, {'system': 'SNOMEDCT', 'code': '6736007', 'label': 'Moderate severity'}, {'system': 'SNOMEDCT', 'code': '255604002', 'label': 'Mild'}]",,,,,,,,SNOMEDCT:246112005,Severity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'GA4GH', 'code': 'UNKNOWN_PROGRESS', 'label': 'No information is available aboutthe diagnosis'}, {'system': 'GA4GH', 'code': 'IN_PROGRESS', 'label': 'No diagnosis has been found to date but additional differential diagnostic work is in progress.'}, {'system': 'GA4GH', 'code': 'COMPLETED', 'label': 'The work on the interpretation is complete.'}, {'system': 'GA4GH', 'code': 'SOLVED', 'label': 'The interpretation is complete and also considered to be a definitive diagnosis.'}, {'system': 'GA4GH', 'code': 'UNSOLVED', 'label': 'The interpretation is complete but no definitive diagnosiswas found.'}]",,,,,,,,GA4GH:progress_status,Progress Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'GA4GH', 'code': 'UNKNOWN_STATUS', 'label': 'No information is available about the status'}, {'system': 'GA4GH', 'code': 'REJECTED', 'label': 'The variant or gene reported here is interpreted not to be related to the diagnosis.'}, {'system': 'GA4GH', 'code': 'CANDIDATE', 'label': 'The variant or gene reported here is interpreted to possibly be related to the diagnosis.'}, {'system': 'GA4GH', 'code': 'CONTRIBUTORY', 'label': 'The variant or gene reported here is interpreted to be related to the diagnosis.'}, {'system': 'GA4GH', 'code': 'CAUSATIVE', 'label': 'The variant or gene reported here is interpreted to be causative of the diagnosis.'}]",,,,,,,,GA4GH:interpretation_status,Interpretation Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA26406-1', 'label': 'Karyotyping'}, {'system': 'LOINC', 'code': 'LA26404-6', 'label': 'FISH'}, {'system': 'LOINC', 'code': 'LA26418-6', 'label': 'PCR'}, {'system': 'LOINC', 'code': 'LA26419-4', 'label': 'qPCR (real-time PCR)'}, {'system': 'LOINC', 'code': 'LA26400-4', 'label': 'SNP array'}, {'system': 'LOINC', 'code': 'LA26813-8', 'label': 'Restriction fragment length polymorphism (RFLP)'}, {'system': 'LOINC', 'code': 'LA26810-4', 'label': 'DNA hybridization'}, {'system': 'LOINC', 'code': 'LA26398-0', 'label': 'Sequencing'}, {'system': 'LOINC', 'code': 'LA26415-2', 'label': 'MLPA'}, {'system': 'LOINC', 'code': 'LA46-8', 'label': 'Other'}]",,,,,,,,LOINC:81304-8,Structural Variant Analysis Method Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA14032-9', 'label': 'NCBI Build 34 (hg16)'}, {'system': 'LOINC', 'code': 'LA14029-5', 'label': 'GRCh37 (hg19)'}, {'system': 'LOINC', 'code': 'LA14030-3', 'label': 'NCBI Build 36.1 (hg18)'}, {'system': 'LOINC', 'code': 'LA14031-1', 'label': 'NCBI Build 35 (hg17)'}, {'system': 'LOINC', 'code': 'LA26806-2', 'label': 'GRCh38 (hg38)'}]",,,,,,,,LOINC:62374-4,Reference Genome Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA6705-3', 'label': 'Homozygous'}, {'system': 'LOINC', 'code': 'LA6706-1', 'label': 'Heterozygous'}, {'system': 'LOINC', 'code': 'LA26217-2', 'label': 'Compound heterozygous'}, {'system': 'LOINC', 'code': 'LA26220-6', 'label': 'Double heterozygous'}, {'system': 'LOINC', 'code': 'LA6707-9', 'label': 'Hemizygous'}, {'system': 'LOINC', 'code': 'LA6703-8', 'label': 'Heteroplasmic'}, {'system': 'LOINC', 'code': 'LA6704-6', 'label': 'Homoplasmic'}, {'system': 'LOINC', 'code': 'LA46-8', 'label': 'Other'}]",,,,,,,,LOINC:53034-5,Zygosity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA6683-2', 'label': 'Germline'}, {'system': 'LOINC', 'code': 'LA6684-0', 'label': 'Somatic'}, {'system': 'LOINC', 'code': 'LA10429-1', 'label': 'Fetal'}, {'system': 'LOINC', 'code': 'LA18194-3', 'label': 'Likely germline'}, {'system': 'LOINC', 'code': 'LA18195-0', 'label': 'Likely somatic'}, {'system': 'LOINC', 'code': 'LA18196-8', 'label': 'Likely fetal'}, {'system': 'LOINC', 'code': 'LA18197-6', 'label': 'Unknown genomic origin'}, {'system': 'LOINC', 'code': 'LA26807-0', 'label': 'De novo'}]",,,,,,,,LOINC:48002-0,Genomic Source Class Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA9658-1', 'label': 'Wild Type'}, {'system': 'LOINC', 'code': 'LA6692-3', 'label': 'Deletion'}, {'system': 'LOINC', 'code': 'LA6686-5', 'label': 'Duplication'}, {'system': 'LOINC', 'code': 'LA6687-3', 'label': 'Insertion'}, {'system': 'LOINC', 'code': 'LA6688-1', 'label': 'Insertion/Deletion'}, {'system': 'LOINC', 'code': 'LA6689-9', 'label': 'Inversion'}, {'system': 'LOINC', 'code': 'LA6690-7', 'label': 'Substitution'}]",,,,,,,,LOINC:48019-4,DNA Change Type Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA6668-3', 'label': 'Pathogenic'}, {'system': 'LOINC', 'code': 'LA26332-9', 'label': 'Likely pathogenic'}, {'system': 'LOINC', 'code': 'LA26333-7', 'label': 'Uncertain significance'}, {'system': 'LOINC', 'code': 'LA26334-5', 'label': 'Likely benign'}, {'system': 'LOINC', 'code': 'LA6675-8', 'label': 'Benign'}, {'system': 'LOINC', 'code': 'LA4489-6', 'label': 'Unknown'}]",,,,,,,,LOINC:53037-8,Clinical Significance ACMG Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'GA4GH', 'code': 'UNKNOWN_ACTIONABILITY', 'label': 'There is not enough information at this time to support any therapeutic actionability for this variant.'}, {'system': 'GA4GH', 'code': 'NOT_ACTIONABLE', 'label': 'This variant has no therapeutic actionability.'}, {'system': 'GA4GH', 'code': 'ACTIONABLE', 'label': 'This variant is known to be therapeuticallyactionalbe.'}]",,,,,,,,GA4GH:therapeutic_actionability,Therapeutic Actionability Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA30200-2', 'label': 'Very Strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30201-0', 'label': 'Strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30202-8', 'label': 'Moderate evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30203-6', 'label': 'Supporting evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30204-4', 'label': 'Supporting evidence benign'}, {'system': 'LOINC', 'code': 'LA30205-1', 'label': 'Strong evidence benign'}, {'system': 'LOINC', 'code': 'LA30206-9', 'label': 'Stand-alone evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30207-7', 'label': 'Stand-alone evidence benign'}, {'system': 'LOINC', 'code': 'LA26333-7', 'label': 'Uncertain significance'}]",,,,,,,,LOINC:93044-6,Clinical Annotation Level Of Evidence Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '410605003', 'label': 'Confirmed present'}, {'system': 'SNOMEDCT', 'code': '723511001', 'label': 'Refuted'}]",,,,,,,,CustomCode:phenotypicfeature.excluded,Phenotype Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HP', 'code': '0011460', 'label': 'Embryonal onset'}, {'system': 'HP', 'code': '0011461', 'label': 'Fetal onset'}, {'system': 'HP', 'code': '0003577', 'label': 'Congenital onset'}, {'system': 'HP', 'code': '0003623', 'label': 'Neonatal onset'}, {'system': 'HP', 'code': '0003593', 'label': 'Infantile onset'}, {'system': 'HP', 'code': '0011463', 'label': 'Childhood onset'}, {'system': 'HP', 'code': '0003621', 'label': 'Juvenile onset'}, {'system': 'HP', 'code': '0011462', 'label': 'Young adult onset'}, {'system': 'HP', 'code': '0003596', 'label': 'Middle age onset'}, {'system': 'HP', 'code': '0003584', 'label': 'Late onset'}]",,,,,,,,HP:0003674,Onset Category Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HP', 'code': '0011009', 'label': 'Acute'}, {'system': 'HP', 'code': '0011010', 'label': 'Chronic'}, {'system': 'HP', 'code': '0031914', 'label': 'Fluctuating'}, {'system': 'HP', 'code': '0025297', 'label': 'Prolonged'}, {'system': 'HP', 'code': '0031796', 'label': 'Recurrent'}, {'system': 'HP', 'code': '0031915', 'label': 'Stable'}, {'system': 'HP', 'code': '0011011', 'label': 'Subacute'}, {'system': 'HP', 'code': '0025153', 'label': 'Transient'}]",,,,,,,,HP:0011008,Temporal Pattern Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HP', 'code': '0012827', 'label': 'Borderline'}, {'system': 'HP', 'code': '0012825', 'label': 'Mild'}, {'system': 'HP', 'code': '0012826', 'label': 'Moderate'}, {'system': 'HP', 'code': '0012829', 'label': 'Profound'}, {'system': 'HP', 'code': '0012828', 'label': 'Severe'}]",,,,,,,,HP:0012824,Severity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:64245008,Propositus Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '65656005', 'label': 'Natural mother'}, {'system': 'SNOMEDCT', 'code': '9947008', 'label': 'Natural father'}, {'system': 'SNOMEDCT', 'code': '83420006', 'label': 'Natural daughter'}, {'system': 'SNOMEDCT', 'code': '113160008', 'label': 'Natural son'}, {'system': 'SNOMEDCT', 'code': '60614009', 'label': 'Natural brother'}, {'system': 'SNOMEDCT', 'code': '73678001', 'label': 'Natural sister'}, {'system': 'SNOMEDCT', 'code': '11286003', 'label': 'Twin sibling'}, {'system': 'SNOMEDCT', 'code': '45929001', 'label': 'Half-brother'}, {'system': 'SNOMEDCT', 'code': '2272004', 'label': 'Half-sister'}, {'system': 'SNOMEDCT', 'code': '62296006', 'label': 'Natural grandfather'}, {'system': 'SNOMEDCT', 'code': '17945006', 'label': 'Natural grandmother'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:408732007,Family Relationship To Index Case Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:842009,Consanguinity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '65656005', 'label': 'Natural mother'}, {'system': 'SNOMEDCT', 'code': '9947008', 'label': 'Natural father'}, {'system': 'SNOMEDCT', 'code': '83420006', 'label': 'Natural daughter'}, {'system': 'SNOMEDCT', 'code': '113160008', 'label': 'Natural son'}, {'system': 'SNOMEDCT', 'code': '60614009', 'label': 'Natural brother'}, {'system': 'SNOMEDCT', 'code': '73678001', 'label': 'Natural sister'}, {'system': 'SNOMEDCT', 'code': '11286003', 'label': 'Twin sibling'}, {'system': 'SNOMEDCT', 'code': '45929001', 'label': 'Half-brother'}, {'system': 'SNOMEDCT', 'code': '2272004', 'label': 'Half-sister'}, {'system': 'SNOMEDCT', 'code': '62296006', 'label': 'Natural grandfather'}, {'system': 'SNOMEDCT', 'code': '17945006', 'label': 'Natural grandmother'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:444018008,FamilyMember Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'partial', 'label': 'Partial'}, {'system': 'HL7FHIR', 'code': 'completed', 'label': 'Completed'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}, {'system': 'HL7FHIR', 'code': 'health-unknown', 'label': 'Health Unknown'}]",,,,,,,,HL7FHIR:familymemberhistory.status,FamilyHistoryStatus Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '248152002', 'label': 'Female'}, {'system': 'SNOMEDCT', 'code': '248153007', 'label': 'Male'}, {'system': 'SNOMEDCT', 'code': '184115007', 'label': 'Patient sex unknown'}, {'system': 'SNOMEDCT', 'code': '32570691000036108', 'label': 'Intersex'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:54123-5,AdministrativeGender Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:740604001,Deceased Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'draft', 'label': 'Pending'}, {'system': 'HL7FHIR', 'code': 'proposed', 'label': 'Proposed'}, {'system': 'HL7FHIR', 'code': 'active', 'label': 'Active'}, {'system': 'HL7FHIR', 'code': 'rejected', 'label': 'Rejected'}, {'system': 'HL7FHIR', 'code': 'inactive', 'label': 'Inactive'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}]",,,,,,,,HL7FHIR:309370004,Consent Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:consent_contact_research,Contact for Research Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:conset_data_reuse,Data Reuse Consent Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:123038009,Biological Sample Consent Value Set v2.0.0,,,,,,,,, +_section,codes,dataSpecification,dataType,description,elementCode,elementCodeSystem,elementName,fhirExpression_v4_0_1,id,label,namespace_iri,ordinal,phenopacketSchemaElement_v2_0,rd_cdm_date,rd_cdm_version,recommendedDataSpec_fhir,recommendedDataSpec_phenopackets,section,title,valueSet,version +_metadata,,,,,,,,,,,,,,2026-03-24,2.0.3,,,,,, +code_systems,,,,,,,,,SNOMEDCT,,http://purl.bioontology.org/ontology/SNOMEDCT/,,,,,,,,Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT),,2025AB +code_systems,,,,,,,,,LOINC,,http://loinc.org,,,,,,,,Logical Observation Identifiers Names and Codes (LOINC),,281 +code_systems,,,,,,,,,HP,,http://purl.obolibrary.org/obo/HP,,,,,,,,Human Phenotype Ontology (HPO),,2026-02-16 +code_systems,,,,,,,,,NCIT,,http://purl.obolibrary.org/obo/NCIT/,,,,,,,,NCI Thesaurus (NCIT) OBO Edition,,26.02d +code_systems,,,,,,,,,HL7FHIR,,http://hl7.org/fhir/,,,,,,,,"Health Level Seven Fast Healthcare Interoperability Resources, Release 4",,v4.0.1 +code_systems,,,,,,,,,GA4GH,,https://ga4gh.github.io/phenopacket-v2/,,,,,,,,Global Alliance for Genomics and Health Phenopackets Schema,,v2.0 +code_systems,,,,,,,,,CustomCode,,https://github.com/BIH-CEI/rd-cdm,,,,,,,,Custom Code System RD CDM v2.0,,v2.0 +code_systems,,,,,,,,,NCBITAXON,,http://purl.obolibrary.org/obo/NCBITAXON/,,,,,,,,NCBI organismal classification,,2025_04_10 +code_systems,,,,,,,,,GENO,,http://purl.obolibrary.org/obo/GENO/,,,,,,,,GENO – The Genotype Ontology,,2026-02-02 +code_systems,,,,,,,,,SO,,http://purl.obolibrary.org/obo/SO/,,,,,,,,Sequence Ontology,,2.6 +code_systems,,,,,,,,,UO,,http://purl.obolibrary.org/obo/UO/,,,,,,,,Units Ontology (UO),,2026-01-16 +code_systems,,,,,,,,,ECO,,http://purl.obolibrary.org/obo/ECO/,,,,,,,,Evidence & Conclusion Ontology (ECO),,releases/2025-06-23 +code_systems,,,,,,,,,ICD10CM,,http://purl.bioontology.org/ontology/ICD10CM/,,,,,,,,"International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)",,2026 +code_systems,,,,,,,,,MONDO,,http://purl.obolibrary.org/obo/MONDO/,,,,,,,,Mondo Disease Ontology,,2026-03-03 +code_systems,,,,,,,,,ORDO,,http://purl.obolibrary.org/obo/ORDO/,,,,,,,,Orphanet Rare Disease Ontology (ORDO),,4.8 +code_systems,,,,,,,,,HGNC,,http://identifiers.org/hgnc/,,,,,,,,HUGO Gene Nomenclature Committee (HGNC),,2024-08-23 +code_systems,,,,,,,,,OMIM,,http://purl.bioontology.org/ontology/OMIM/,,,,,,,,Online Mendelian Inheritance in Man (OMIM),,2025_08_04 +code_systems,,,,,,,,,HGVS,,https://varnomen.hgvs.org/,,,,,,,,Human Genome Variation Society Nomenclature,,21.0.0 +code_systems,,,,,,,,,ICD11,,http://id.who.int/icd/release/11/mms/,,,,,,,,"International Classification of Diseases, Eleventh Revision (ICD-11)",,2024-09-01 +code_systems,,,,,,,,,ISO3166,,https://www.iso.org/iso-3166-country-codes.html,,,,,,,,International Organization for Standardization – ISO 3166 Country Codes,,2020(en) +code_systems,,,,,,,,,ICF,,https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health,,,,,,,,"International Classification of Functioning, Disability and Health (ICF)",,1.0.2 +data_elements,,['n/a'],Identifier,The (local) patient-related identification code.,"{'system': 'SNOMEDCT', 'code': '422549004'}",SNOMEDCT,Pseudonym,Patient.identifier.value,,,,1.1,Individual.id,,,n/a,string,1. Formal Criteria,,, +data_elements,,['YYYY-MM-DD'],Date,The date of admission or data capture of the individual.,"{'system': 'SNOMEDCT', 'code': '399423000'}",SNOMEDCT,Date of Admission,Encounter.period.start,,,,1.2,Individual.time_at_last_encounter,,,n/a,TimeElement,1. Formal Criteria,,, +data_elements,,"['YYYY', 'YYYY-MM', 'YYYY-MM-DD']",Date,The individual's date of birth.,"{'system': 'SNOMEDCT', 'code': '184099003'}",SNOMEDCT,Date of Birth,Patient.birthDate,,,,2.1,Individual.date_of_birth,,,n/a,TimeElement,2. Personal Information,,, +data_elements,,"['VSe', 'VSc']",Code,The individual's sex that was assigned at birth.,"{'system': 'LOINC', 'code': '76689-9'}",LOINC,Sex at Birth,Patient.extension:individual-recordedSexOrGender,,,,2.2,Individual.sex,,,Recorded Sex Or Gender Type,Sex,2. Personal Information,,Sex at Birth Value Set v2.0.0, +data_elements,,['VSc'],Code,The chromosomal sex of an individual.,"{'system': 'SNOMEDCT', 'code': '1296886006'}",SNOMEDCT,Karyotypic Sex,Observation.value,,,,2.3,Individual.karyotypic_sex,,,n/a,Karyotypic Sex,2. Personal Information,,Karyotypic Sex Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,The self-assigned gender of the individual.,"{'system': 'SNOMEDCT', 'code': '263495000'}",SNOMEDCT,Gender Identity,Patient.extension:individual-genderIdentity,,,,2.4,Individual.gender,,,Gender Identity,OntologyClass,2. Personal Information,,Gender Identity Value Set v2.0.0, +data_elements,,['VS'],Code,The individual's country of birth.,"{'system': 'SNOMEDCT', 'code': '370159000'}",SNOMEDCT,Country of Birth,Patient.extension:patient-birthPlace,,,,2.5,n/a,,,DataType: Address,n/a,2. Personal Information,,, +data_elements,,"['VSe', 'VSc']",Code,The individual’s general clinical status orvital status.,"{'system': 'SNOMEDCT', 'code': '278844005'}",SNOMEDCT,Vital Status,Patient.deceased.deceasedBoolean|Observation.value,,,,3.1,Individual.VitalStatus.status,,,Boolean|Code,Value Set: VitalStatus.Status,3. Patient Status,,Vital Status Value Set v2.0.0, +data_elements,,"['YYYY', 'YYYY-MM', 'YYYY-MM-DD']",Date,"If deceased, the individual’s date of death.","{'system': 'SNOMEDCT', 'code': '398299004'}",SNOMEDCT,Time of Death,Patient.deceasedDateTime,,,,3.2,Individual.VitalStatus.time_of_death,,,DateTime,TimeElement,3. Patient Status,,, +data_elements,,['ICD-10CM'],Code,"If deceased, the individual’s primary cause of death.","{'system': 'SNOMEDCT', 'code': '184305005'}",SNOMEDCT,Cause of Death,Observation.value.coding.code,,,,3.3,Individual.VitalStatus.cause_of_death,,,Code|CodeableConcept,OntologyClass,3. Patient Status,,, +data_elements,,['VSe'],Code,The individual's age category at thetime of data capture.,"{'system': 'SNOMEDCT', 'code': '105727008'}",SNOMEDCT,Age Category,Observation.value.coding.code,,,,3.4,Individual.time_at_last_encounter,,,CodableConcept,TimeElement,3. Patient Status,,Age Category Value Set v2.0.0, +data_elements,,['XX+X'],String,"The duration of the pregnancy in weeks and days,formatted as XX+X (weeks+days).","{'system': 'SNOMEDCT', 'code': '412726003'}",SNOMEDCT,Length of Gestation at Birth [weeks+days],Observation.component:weeks.valueQuantity|Observation.component:days.valueQuantity,,,,3.5,n/a,,,Quantity,n/a,3. Patient Status,,, +data_elements,,['VSe'],Code,Identifies cases where an RD diagnosis has notbeen established.,"{'system': 'SNOMEDCT', 'code': '723663001'}",SNOMEDCT,Undiagnosed RD Case,(Condition.code),,,,3.6,(Disease.term),,,Code(e.g. ORDO:616874 - Rare disorderwithout a determined diagnosis afterfull investigation),(OntologyClass (e.g. ORDO:616874 - Rare disorder without a determineddiagnosis after full investigation)),3. Patient Status,,Undiagnosed RD Case Value Set v2.0.0, +data_elements,,['YYYY-MM-DD'],Date,The beginning of an encounter of the individual.,"{'system': 'HL7FHIR', 'code': 'encounter.period.start'}",HL7FHIR,Encounter Start,Encounter.period.start,,,,4.1,n/a,,,DateTime,n/a,4. Care Pathway,,, +data_elements,,['YYYY-MM-DD'],Date,The end of an encounter of the individual.,"{'system': 'HL7FHIR', 'code': 'encounter.period.end'}",HL7FHIR,Encounter End,Encounter.period.end,,,,4.2,n/a,,,DateTime,n/a,4. Care Pathway,,, +data_elements,,"['VSe', 'VSc']",Code,The status of an encounter of the individual at thetime of data capture.,"{'system': 'SNOMEDCT', 'code': '305058001'}",SNOMEDCT,Encounter Status,Encounter.status,,,,4.3,n/a,,,ValueSet: EncounterStatus,n/a,4. Care Pathway,,Encounter Status Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,The class of an encounter of the individualat the time of data capture.,"{'system': 'HL7FHIR', 'code': 'encounter.class'}",HL7FHIR,Encounter Class,Encounter.class,,,,4.4,n/a,,,ValueSet: EncounterClass,n/a,4. Care Pathway,,Encounter Class Value Set v2.0.0, +data_elements,,"['Ontology Class (MONDO, ORDO, ICD-10, ICD-11, OMIM_g, OMIM_p)']",Code,"A disease that the individual was affected by. If agenetic diagnosis or subtypes were diagnosed, please also provide the respective OMIM_g and OMIM_p codes.","{'system': 'SNOMEDCT', 'code': '64572001'}",SNOMEDCT,Disease,Condition.code,,,,5.1,Disease.term,,,Code,OntologyClass,5. Disease,,n/a, +data_elements,,['VS'],Code,The verification status of the disease.,"{'system': 'LOINC', 'code': '99498-8'}",LOINC,Verification Status,Condition.verificationStatus,,,,5.2,(Disease.excluded),,,ValueSet: Condition Verficication Status,boolean,5. Disease,,Verification Status Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,The age at the onset of the first symptomsor signs of the disease.,"{'system': 'SNOMEDCT', 'code': '424850005'}",SNOMEDCT,Age at Onset,Condition.onsetString orObservation.valueCodeableConcept,,,,5.3,Disease.onset,,,Disease.onset,Disease.onset,5. Disease,,Age at Onset Value Set v2.0.0, +data_elements,,['YYYY-MM-DD'],Date,The date at onset of first symptoms orsigns of the disease.,"{'system': 'SNOMEDCT', 'code': '298059007'}",SNOMEDCT,Date of Onset,Condition.onset,,,,5.4,Disease.onset,,,DateTime,TimeElement,5. Disease,,n/a, +data_elements,,"['VSe', 'VSc']",Code,The individual’s age when the diagnosis was made.,"{'system': 'SNOMEDCT', 'code': '423493009'}",SNOMEDCT,Age at Diagnosis,Observation.value,,,,5.5,(Disease.onset),,,CodeableConcept,(TimeElement),5. Disease,,Age at Diagnosis Value Set v2.0.0, +data_elements,,['YYYY-MM-DD'],Date,The date on which the disease was determined.,"{'system': 'SNOMEDCT', 'code': '432213005'}",SNOMEDCT,Date of Diagnosis,Condition.recordedDate,,,,5.6,(Disease.onset),,,DateTime,(TimeElement),5. Disease,,n/a, +data_elements,,['VS'],Code,The specific body site affected by disease is encodedusing all descendants of SCT Body Structure (123037004).,"{'system': 'SNOMEDCT', 'code': '363698007'}",SNOMEDCT,Body Site,Condition.bodySite.coding:SNOMEDCT-ct,,,,5.7,Disease.primary_site,,,CodeableConcept,OntologyClass,5. Disease,,Body Site Value Set v2.0.0, +data_elements,,['VS'],Code,"The clinical status of the disease indicates whetherit is active, inactive, or resolved.","{'system': 'SNOMEDCT', 'code': '263493007'}",SNOMEDCT,Clinical Status,Condition.clinicalStatus,,,,5.8,n/a,,,ValueSet: ClinicalStatus,n/a,5. Disease,,Clinical Status Value Set v2.0.0, +data_elements,,['VS'],Code,The severity of the disease is categorised byclinical evaluation.,"{'system': 'SNOMEDCT', 'code': '246112005'}",SNOMEDCT,Severity,Condition.severity,,,,5.9,n/a,,,ValueSet: ConditionSeverity,n/a,5. Disease,,Severity Value Set v2.0.0, +data_elements,,"['OMIM_p', 'MONDO']",Code,The genomic diagnoses can correspond to the diagnoseddisease in (5.1) if the same OMIM codes are used.,"{'system': 'SNOMEDCT', 'code': '106221001'}",SNOMEDCT,Genomic Diagnosis,Condition.code,,,,6.1.1,Interpretation.Diagnosis.disease,,,Code,OntologyClass,6. Genetic Findings,,n/a, +data_elements,,['VS'],Code,The interpretation has a ProgressStatus that refers tothe status of the attempted diagnosis.,"{'system': 'GA4GH', 'code': 'progress_status'}",GA4GH,Progress Status of Interpretation,Condition.extension,,,,6.1.2,Interpretation.progress_status,,,VS: GA4GH ProgressStatus,ValueSet: ProgressStatus,6. Genetic Findings,,Progress Status Value Set v2.0.0, +data_elements,,['VS'],Code,An enumeration that describes the conclusion made about the genomic interpretation.,"{'system': 'GA4GH', 'code': 'interpretation_status'}",GA4GH,Interpretation Status,Condition.extension,,,,6.1.3,GenomicInterpretation.interpretation_status,,,VS: GA4GH InterpretationStatus,ValueSet: InterpretationStatus,6. Genetic Findings,,Interpretation Status Value Set v2.0.0, +data_elements,,"['VS', 'LOINC']",Code,The method used to analyse structural variants in the genome.,"{'system': 'LOINC', 'code': '81304-8'}",LOINC,Structural Variant Analysis Method,Observation.method,,,,6.1.4,n/a,,,CodeableConcept,n/a,6. Genetic Findings,,Structural Variant Analysis Method Value Set v2.0.0, +data_elements,,['VS'],Code,The reference genome used for analysing the genetic variant.,"{'system': 'LOINC', 'code': '62374-4'}",LOINC,Reference Genome,Observation.component:reference-sequence-assembly,,,,6.1.5,n/a,,,CodeableConcept,n/a,6. Genetic Findings,,Reference Genome Value Set v2.0.0, +data_elements,,['n/a'],String,An unvalidated (HGVS) string that describes the variant change,"{'system': 'LOINC', 'code': 'LP7824-8'}",LOINC,Genetic Mutation String,Observation.component:Variant.valueString,,,,6.1.6,VariationDescriptor.Extension.value,,,string,string,6. Genetic Findings,,n/a, +data_elements,,['g.HGVS'],Code,The specific change in the genomic DNA sequence encoded with a validated g.HGVS expression.,"{'system': 'LOINC', 'code': '81290-9'}",LOINC,Genomic DNA Change,Observation.component:Variant.valueCode,,,,6.1.7,VariationDescriptor.Expression.value,,,Code,string,6. Genetic Findings,,n/a, +data_elements,,['c.HGVS'],Code,The specific change in the DNA sequence at the nucleotide level with a validated c.HGVS expression.,"{'system': 'LOINC', 'code': '48004-6'}",LOINC,Sequence DNA Change,Observation.component:Variant.valueCode,,,,6.1.8,VariationDescriptor.Expression.value,,,Code,string,6. Genetic Findings,,n/a, +data_elements,,['p.HGVS'],Code,The specific change in the amino acid sequence resulting from agenetic variant as a validated p.HGVS expression.,"{'system': 'LOINC', 'code': '48005-3'}",LOINC,Amino Acid Change,Observation.component:Variant.valueCode,,,,6.1.9,VariationDescriptor.Expression.value,,,Code,string,6. Genetic Findings,,n/a, +data_elements,,['HGNC'],Code,The specific gene or genes that were analysed or identified in the study.,"{'system': 'LOINC', 'code': '48018-6'}",LOINC,Gene,Observation.component:Gene,,,,6.1.10,GeneDescriptor.value_id,,,Code,string,6. Genetic Findings,,n/a, +data_elements,,"['VSe', 'VSc', 'LOINC']",Code,The zygosity of the genetic variant.,"{'system': 'LOINC', 'code': '53034-5'}",LOINC,Zygosity,Observation.component:geneticsAllele.State,,,,6.1.11,VariationDescriptor.allelic_state,,,VS: Allelic State,OntologyClass,6. Genetic Findings,,Zygosity Value Set v2.0.0, +data_elements,,['VS'],Code,"The classification of the genomic source, such as germline, somatic, or other origins.","{'system': 'LOINC', 'code': '48002-0'}",LOINC,Genomic Source Class,Observation.component:GenomicSourceClass,,,,6.1.12,n/a,,,CodeableConcept,n/a,6. Genetic Findings,,Genomic Source Class Value Set v2.0.0, +data_elements,,['VS'],Code,"The variant’s type of DNA change, such as point mutation, deletion, insertion, or other types.","{'system': 'LOINC', 'code': '48019-4'}",LOINC,DNA Change Type,Observation.component:Variant.Type,,,,6.1.13,n/a,,,Code,n/a,6. Genetic Findings,,DNA Change Type Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,"The clinical significance of the genetic variant, indicating its impact on health and disease.","{'system': 'LOINC', 'code': '53037-8'}",LOINC,Clinical Significance [ACMG],Observation.component:Variant.Interpretation,,,,6.1.14,VariantInterpretation.acmg_pathogenicity_classification,,,,ValueSet: AcmgPathogenicityClassification,6. Genetic Findings,,Clinical Significance ACMG Value Set v2.0.0, +data_elements,,['VS'],Code,"An enumeration flagging the variant as being a candidate for treatment or clinical intervention, which could improve the clinical outcome.","{'system': 'GA4GH', 'code': 'therapeutic_actionability'}",GA4GH,Therapeutic Actionability,n/a,,,,6.1.15,VariantInterpretation.therapeutic_actionability,,,n/a,ValueSet: TherapeuticActionability,6. Genetic Findings,,Therapeutic Actionability Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,The level of evidence supporting the clinical annotation of the genetic variant.,"{'system': 'LOINC', 'code': '93044-6'}",LOINC,Clinical Annotation Level Of Evidence,Observation.extension:Variant.Interpretation,,,,6.1.16,n/a,,,CodeableConcept,n/a,6. Genetic Findings,,Clinical Annotation Level Of Evidence Value Set v2.0.0, +data_elements,,['HPO'],Code,An observed physical and clinical characteristicencoded with HPO.,"{'system': 'SNOMEDCT', 'code': '8116006'}",SNOMEDCT,Phenotypic Feature,Observation.code,,,,6.2.1,PhenotypicFeature.type,,,Code,OntologyClass,6. Phenotypic Feature,,n/a, +data_elements,,"['VSe', 'VSc']",Code,"The current status of the phenotypic feature, indicating whether it is confirmed or refuted.","{'system': 'SNOMEDCT', 'code': '363778006'}",SNOMEDCT,Status,Observation.status,,,,6.2.2,PhenotypicFeature.excluded,,,ValueSet: ObservationStatus,boolean,6.2 Phenotypic Feature,,Phenotype Status Value Set v2.0.0, +data_elements,,['YYYY-MM-DD'],Date,The date on which the phenotypic feature was observed or recorded. We recommend capturing the time acharacteristic was observed.,"{'system': 'SNOMEDCT', 'code': '439272007:704321009=363778006'}",SNOMEDCT,Determination Date,Observation.effectiveDateTime,,,,6.2.3,PhenotypicFeature.onset,,,DateTime,TimeElement,6. Phenotypic Feature,,n/a, +data_elements,,['YYYY-MM-DD'],Date,Time at which the feature resolved or abated.,"{'system': 'HP', 'code': '0034382'}",HP,Resolution Date,Observation.effectiveDateTime,,,,6.2.4,PhenotypicFeature.resolution,,,DateTime,TimeElement,6.2 Phenotypic Feature,,n/a, +data_elements,,"['VSe', 'VSc']",Code,Time at which the feature was first observed within HPO onset categories.,"{'system': 'HP', 'code': '0003674'}",HP,Onset Category,Observation.category,,,,6.2.5,PhenotypicFeature.onset,,,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,Onset Category Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,The speed at which disease manifestations appear and develop.,"{'system': 'HP', 'code': '0011008'}",HP,Temporal Pattern,Observation.interpretation,,,,6.2.6,PhenotypicFeature.modifiers,,,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,Temporal Pattern Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,A description of the severity of the feature.,"{'system': 'HP', 'code': '0012824'}",HP,Severity,Observation.interpretation,,,,6.2.7,PhenotypicFeature.severity,,,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,Severity Value Set v2.0.0, +data_elements,,"['OntologyClass (HPO, NCBITAXON, SCT)']",Code,"Any number of additional modifiers describing a specific phenotypic feature further, such as severity (HP:0012824), clinical modifiers (HP:0012823), or linking causative infectious agents using the NCBITAXON Ontology.","{'system': 'GA4GH', 'code': 'phenotypicfeature.modifier'}",GA4GH,Modifiers,Suggested: Observation.extension,,,,6.2.8,PhenotypicFeature.modifiers,,,CodeableConcept,list of OntologyClass,6. Phenotypic Feature,,n/a, +data_elements,,['ECO'],Code,The evidence for an assertion of the observation of a type defined within the Evidence & Conclusion Ontology (ECO).,"{'system': 'GA4GH', 'code': 'phenotypicfeature.evidence'}",GA4GH,Evidence,Observation.method,,,,6.2.9,PhenotypicFeature.evidence,,,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,n/a, +data_elements,,['OntologyClass (e.g. LOINC)'],Code,A class that describes the assay used to producethe measurement.,"{'system': 'NCIT', 'code': 'C60819'}",NCIT,Assay,Observation.code,,,,6.3.1,Measurement.assay,,,Code,OntologyClass,6.3 Measurement,,n/a, +data_elements,,['float'],Value,The result of the measurement.,"{'system': 'NCIT', 'code': 'C25712'}",NCIT,Value,Observation.value[x],,,,6.3.2,Measurement.measurement_value,,,Quantity|integer,Quantity[double/float],6.3 Measurement,,n/a, +data_elements,,['UO'],Code,The unit of the result's measurement.,"{'system': 'NCIT', 'code': 'C92571'}",NCIT,Value Unit,Observation.value[x].unit,,,,6.3.3,Measurement.measurement_value,,,CodeableConcept,OntologyClass,6.3 Measurement,,n/a, +data_elements,,['NCIT'],Code,"The interpretation of the measurement (e.g.: Below/Within/Above age-related reference range, Absent/Low/Normal, or Positive/Negative).","{'system': 'NCIT', 'code': 'C41255'}",NCIT,Interpretation,Observation.interpretation,,,,6.3.4,n/a,,,n/a,n/a,6.3 Measurement,,n/a, +data_elements,,['YYYY-MM-DD'],Date,Time at which the measurement was performed.,"{'system': 'NCIT', 'code': 'C82577'}",NCIT,Time Observed,Observation.effectiveDateTime,,,,6.3.5,Measurement.time_observed,,,DateTime,TimeElement,6.3 Measurement,,n/a, +data_elements,,"['OntologyClass (e.g. NCIT, SNOMEDCT)']",Code,Clinical procedure performed to acquire the sample used for the measurement.,"{'system': 'SNOMEDCT', 'code': '122869004'}",SNOMEDCT,Procedure,Procedure.code,,,,6.3.6,Measurement.procedure,,,Measurement.procedure,Measurement.procedure,6.3 Measurement,,n/a, +data_elements,,['n/a'],Identifier,A unique identifier or local pseudonym for the familymember.,"{'system': 'CustomCode', 'code': 'family_member_id'}",CustomCode,Family Member Pseudonym,FamilyMemberHistory.identifier,,,,6.4.1,Family.Pedigree.Person.individual_id,,,Identifier,string,6.4 Family History,,n/a, +data_elements,,"['VSe', 'VSc']",Code,"Is the individual the first affected family member who seeks medical attention for a genetic disorder, leading to the diagnosis of other family members. Disclaimer: The SCT code for propositus (64245008) refers to any gender.","{'system': 'SNOMEDCT', 'code': '64245008'}",SNOMEDCT,Propositus/-a,n/a,,,,6.4.2,(Family.relatives → 1 Phenopacket per family member),,,n/a,(Family.relatives → 1 Phenopacket per family member),6.4 Family History,,Propositus Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,Specifies the familial relationship of the individual being evaluated to the propositus. Disclaimer: The SNOMEDCT code for propositus (64245008) refers to any gender.,"{'system': 'SNOMEDCT', 'code': '408732007'}",SNOMEDCT,Relationship of the Individual to the Propositus,n/a,,,,6.4.3,(Family.relatives → 1 Phenopacket per family member),,,n/a,(Family.relatives → 1 Phenopacket per family member),6.4 Family History,,Family Relationship To Index Case Value Set v2.0.0, +data_elements,,['VSe'],Code,"The presence of a biological relationship between parents who are related by blood, typically as first or second cousins.","{'system': 'SNOMEDCT', 'code': '842009'}",SNOMEDCT,Consanguinity,n/a,,,,6.4.4,Family.consanguinous_parents,,,n/a,boolean,6.4 Family History,,Consanguinity Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,Specifies the relationship of the selected family member to the patient.,"{'system': 'SNOMEDCT', 'code': '444018008'}",SNOMEDCT,Family Member Relationship,FamilyMemberHistory.relationship.coding,,,,6.4.5,Family.Pedigree.Person.individual_id,,,ValueSet: FamilyMember,string,6.4 Family History,,FamilyMember Value Set v2.0.0, +data_elements,,['VS'],Code,Specifies the record’s status of the family history of a specific family member.,"{'system': 'HL7FHIR', 'code': 'familymemberhistory.status'}",HL7FHIR,Family Member Record Status,FamilyMemberHistory.status,,,,6.4.6,n/a,,,,n/a,6.4 Family,,FamilyHistoryStatus Value Set v2.0.0, +data_elements,,"['VSe', 'VSc']",Code,"Specifies the sex (or gender) of the specific family member. If possible, the sex assigned at birth should be selected.","{'system': 'LOINC', 'code': '54123-5'}",LOINC,Family Member Sex,FamilyMemberHistory.sex,,,,6.4.7,Family.Pedigree.Person.sex,,,ValueSet: AdministrativeGender,ValueSet: Sex,6.4 Family,,AdministrativeGender Value Set v2.0.0, +data_elements,,['Integer'],Integer,Records the current age of the selected family member.,"{'system': 'LOINC', 'code': '54141-7'}",LOINC,Family Member Age,FamilyMemberHistory.ageAge,,,,6.4.8,(Family.relatives → 1 Phenopacket per family member),,,Age,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,n/a, +data_elements,,['YYYY-MM-DD'],Date,Records the date of birth of the selected family member.,"{'system': 'LOINC', 'code': '54124-3'}",LOINC,Family Member Date of Birth,FamilyMemberHistory.bornDate,,,,6.4.9,(Family.relatives → 1 Phenopacket per family member),,,DateTime,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,n/a, +data_elements,,['VSe'],Code,Indicates whether the selected family member is deceased.,"{'system': 'SNOMEDCT', 'code': '740604001'}",SNOMEDCT,Family Member Deceased,FamilyMemberHistory.deceased.deceasedBoolean,,,,6.4.10,(Family.relatives → 1 Phenopacket per family member),,,boolean,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,Deceased Value Set v2.0.0, +data_elements,,['ICD10CM'],Code,Records the cause of death of the selected deceasedfamily member.,"{'system': 'LOINC', 'code': '54112-8'}",LOINC,Family Member Cause of Death,FamilyMemberHistory.condition.code & FamilyMemberHistory.condition.contributedToDeath,,,,6.4.11,(Family.relatives → 1 Phenopacket per family member),,,Code,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,n/a, +data_elements,,['Integer'],Integer,Records the age at which the selected family member died.,"{'system': 'LOINC', 'code': '92662-6'}",LOINC,Family Member Deceased Age,FamilyMemberHistory.deceasedAge,,,,6.4.12,Family.relatives,,,Family.relatives,Family.relatives,6.4 Family,,n/a, +data_elements,,"['Ontology Class', 'ORDO', 'ICD-10-CM', 'ICD-11', 'MONDO', 'OMIM_p']",Code,Indicates whether the selected family member is affected by the same rare disease as the individual.,"{'system': 'LOINC', 'code': '75315-2'}",LOINC,Family Member Disease,FamilyMemberHistory.condition.code,,,,6.4.13,Family.relatives,,,Family.relatives,Family.relatives,6.4 Family,,n/a, +data_elements,,['VS'],Code,Indicates the current status of the consent.,"{'system': 'SNOMEDCT', 'code': '309370004'}",SNOMEDCT,Consent Status,Consent.status,,,,7.1,n/a,,,ValueSet: ConsentStatus,n/a,7. Consent,,Consent Status Value Set v2.0.0, +data_elements,,['YYYY-MM-DD'],Date,Records the date when the consent was given.,"{'system': 'HL7FHIR', 'code': 'consent.datetime'}",HL7FHIR,Consent Date,Consent.dateTime,,,,7.2,n/a,,,DateTime,n/a,7. Consent,,n/a, +data_elements,,['n/a'],String,References to the policies that are included in thisconsent scope.,"{'system': 'SNOMEDCT', 'code': '386318002'}",SNOMEDCT,Health Policy Monitoring,Consent.policy,,,,7.3,n/a,,,string,n/a,7. Consent,,n/a, +data_elements,,['VSe'],Code,Indicates whether the patient agrees to be contacted for research.,"{'system': 'CustomCode', 'code': 'consent_contact_research'}",CustomCode,Agreement to be Contacted for Research,Consent.scope.coding,,,,7.4,n/a,,,CodeableConcept,n/a,7. Consent,,Contact for Research Value Set v2.0.0, +data_elements,,['VSe'],Code,Indicates whether the patient consents to the reuse of their data.,"{'system': 'CustomCode', 'code': 'conset_data_reuse'}",CustomCode,Consent to the Reuse of Data,Consent.scope.coding,,,,7.5,n/a,,,CodeableConcept,n/a,7. Consent,,Data Reuse Consent Value Set v2.0.0, +data_elements,,['VSe'],Code,Indicates whether a patient's biological sample is available for research.,"{'system': 'SNOMEDCT', 'code': '123038009'}",SNOMEDCT,Biological Sample,n/a,,,,7.6,n/a,,,n/a,n/a,7. Consent,,Biological Sample Consent Value Set v2.0.0, +data_elements,,['n/a'],String,"If there is a biological sample, this data element indicates the link to the biobank of the individual's biological sample.","{'system': 'CustomCode', 'code': 'biobank_link'}",CustomCode,Link to a Biobank,n/a,,,,7.7,n/a,,,n/a,n/a,7. Consent,,n/a, +data_elements,,['ICF'],Code,"Specifies the classification of the individualss functioning or disability according to the International Classification of Functioning, Disability and Health (ICF).","{'system': 'CustomCode', 'code': 'icf_score'}",CustomCode,Classification of Functioning / Disability,n/a,,,,8.1,n/a,,,n/a,n/a,8. Disability,,n/a, +value_sets,"[{'system': 'SNOMEDCT', 'code': '248152002', 'label': 'Female'}, {'system': 'SNOMEDCT', 'code': '248153007', 'label': 'Male'}, {'system': 'SNOMEDCT', 'code': '184115007', 'label': 'Patient sex unknown'}, {'system': 'SNOMEDCT', 'code': '32570691000036108', 'label': 'Intersex'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:281053000,Sex at Birth Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '734875008', 'label': 'XX'}, {'system': 'SNOMEDCT', 'code': '734876009', 'label': 'XY'}, {'system': 'SNOMEDCT', 'code': '80427008', 'label': 'X0'}, {'system': 'SNOMEDCT', 'code': '65162001', 'label': 'XXY'}, {'system': 'SNOMEDCT', 'code': '35111009', 'label': 'XXX'}, {'system': 'SNOMEDCT', 'code': '403760006', 'label': 'XXYY'}, {'system': 'SNOMEDCT', 'code': '78317008', 'label': 'XXXY'}, {'system': 'SNOMEDCT', 'code': '10567003', 'label': 'XXXX'}, {'system': 'SNOMEDCT', 'code': '48930007', 'label': 'XYY'}, {'system': 'SNOMEDCT', 'code': '74964007', 'label': 'Other'}]",,,,,,,,SNOMEDCT:1296886006,Karyotypic Sex Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '446141000124107', 'label': 'Female gender identity'}, {'system': 'SNOMEDCT', 'code': '446151000124109', 'label': 'Male gender identity'}, {'system': 'SNOMEDCT', 'code': '394743007', 'label': 'Gender unknown'}, {'system': 'SNOMEDCT', 'code': '33791000087105', 'label': 'Identifies as nonbinary gender'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:263495000,Gender Identity Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '438949009', 'label': 'Alive'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '399307001', 'label': 'Unknown - Lost in follow-up'}, {'system': 'SNOMEDCT', 'code': '185924006', 'label': 'Unknown - Opted-out'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown - Other Reason'}]",,,,,,,,SNOMEDCT:278844005,Vital Status Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '3658006', 'label': 'Infancy'}, {'system': 'SNOMEDCT', 'code': '713153009', 'label': 'Toddler'}, {'system': 'SNOMEDCT', 'code': '255398004', 'label': 'Childhood'}, {'system': 'SNOMEDCT', 'code': '263659003', 'label': 'Adolescence'}, {'system': 'SNOMEDCT', 'code': '41847000', 'label': 'Adulthood'}, {'system': 'SNOMEDCT', 'code': '303112003', 'label': 'Fetal period'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:105727008,Age Category Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '438949009', 'label': 'Alive'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '399307001', 'label': 'Unknown - Lost in follow-up'}, {'system': 'SNOMEDCT', 'code': '185924006', 'label': 'Unknown - Opted-out'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown - Other Reason'}]",,,,,,,,SNOMEDCT:278844005,Vital Status Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '3658006', 'label': 'Infancy'}, {'system': 'SNOMEDCT', 'code': '713153009', 'label': 'Toddler'}, {'system': 'SNOMEDCT', 'code': '255398004', 'label': 'Childhood'}, {'system': 'SNOMEDCT', 'code': '263659003', 'label': 'Adolescence'}, {'system': 'SNOMEDCT', 'code': '41847000', 'label': 'Adulthood'}, {'system': 'SNOMEDCT', 'code': '303112003', 'label': 'Fetal period'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:105727008,Age Category Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}]",,,,,,,,SNOMEDCT:723663001,Undiagnosed RD Case Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'HL7FHIR', 'code': 'planned', 'label': 'Planned'}, {'system': 'HL7FHIR', 'code': 'arrived', 'label': 'Arrived'}, {'system': 'HL7FHIR', 'code': 'triaged', 'label': 'Triaged'}, {'system': 'HL7FHIR', 'code': 'in-progress', 'label': 'In Progress'}, {'system': 'HL7FHIR', 'code': 'onleave', 'label': 'On Leave'}, {'system': 'HL7FHIR', 'code': 'finished', 'label': 'Finished'}, {'system': 'HL7FHIR', 'code': 'cancelled', 'label': 'Cancelled'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}, {'system': 'HL7FHIR', 'code': 'unknown', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:305058001,Encounter Status Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'HL7FHIR', 'code': 'AMB', 'label': 'Ambulatory'}, {'system': 'HL7FHIR', 'code': 'IMP', 'label': 'Inpatient'}, {'system': 'HL7FHIR', 'code': 'OBSENC', 'label': 'Observation'}, {'system': 'HL7FHIR', 'code': 'EMER', 'label': 'Emergency'}, {'system': 'HL7FHIR', 'code': 'VR', 'label': 'Virtual'}, {'system': 'HL7FHIR', 'code': 'HH', 'label': 'Home Health'}, {'system': 'CustomCode', 'code': 'RDC', 'label': 'RD Specialist Center'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,HL7FHIR:encounter.class,Encounter Class Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'HL7FHIR', 'code': 'unconfirmed', 'label': 'Unconfirmed'}, {'system': 'HL7FHIR', 'code': 'provisional', 'label': 'Provisional'}, {'system': 'HL7FHIR', 'code': 'differential', 'label': 'Differential'}, {'system': 'HL7FHIR', 'code': 'confirmed', 'label': 'Confirmed'}, {'system': 'HL7FHIR', 'code': 'refuted', 'label': 'Refuted'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}]",,,,,,,,HL7FHIR:99498-8,Verification Status Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '118189007', 'label': 'Prenatal'}, {'system': 'SNOMEDCT', 'code': '3950001', 'label': 'Birth'}, {'system': 'SNOMEDCT', 'code': '410672004', 'label': 'Date'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:424850005,Age at Onset Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '118189007', 'label': 'Prenatal'}, {'system': 'SNOMEDCT', 'code': '3950001', 'label': 'Birth'}, {'system': 'SNOMEDCT', 'code': '410672004', 'label': 'Date'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:423493009,Age at Diagnosis Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '442083009', 'label': 'Anatomical or acquired body structure'}]",,,,,,,,SNOMEDCT:363698007,Body Site Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'HL7FHIR', 'code': 'active', 'label': 'Active'}, {'system': 'HL7FHIR', 'code': 'recurrence', 'label': 'Recurrence'}, {'system': 'HL7FHIR', 'code': 'relapse', 'label': 'Relapse'}, {'system': 'HL7FHIR', 'code': 'inactive', 'label': 'Inactive'}, {'system': 'HL7FHIR', 'code': 'remission', 'label': 'Remission'}, {'system': 'HL7FHIR', 'code': 'resolved', 'label': 'Resolved'}]",,,,,,,,SNOMEDCT:263493007,Clinical Status Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '24484000', 'label': 'Severe'}, {'system': 'SNOMEDCT', 'code': '6736007', 'label': 'Moderate severity'}, {'system': 'SNOMEDCT', 'code': '255604002', 'label': 'Mild'}]",,,,,,,,SNOMEDCT:246112005,Severity Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'GA4GH', 'code': 'UNKNOWN_PROGRESS', 'label': 'No information is available aboutthe diagnosis'}, {'system': 'GA4GH', 'code': 'IN_PROGRESS', 'label': 'No diagnosis has been found to date but additional differential diagnostic work is in progress.'}, {'system': 'GA4GH', 'code': 'COMPLETED', 'label': 'The work on the interpretation is complete.'}, {'system': 'GA4GH', 'code': 'SOLVED', 'label': 'The interpretation is complete and also considered to be a definitive diagnosis.'}, {'system': 'GA4GH', 'code': 'UNSOLVED', 'label': 'The interpretation is complete but no definitive diagnosiswas found.'}]",,,,,,,,GA4GH:progress_status,Progress Status Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'GA4GH', 'code': 'UNKNOWN_STATUS', 'label': 'No information is available about the status'}, {'system': 'GA4GH', 'code': 'REJECTED', 'label': 'The variant or gene reported here is interpreted not to be related to the diagnosis.'}, {'system': 'GA4GH', 'code': 'CANDIDATE', 'label': 'The variant or gene reported here is interpreted to possibly be related to the diagnosis.'}, {'system': 'GA4GH', 'code': 'CONTRIBUTORY', 'label': 'The variant or gene reported here is interpreted to be related to the diagnosis.'}, {'system': 'GA4GH', 'code': 'CAUSATIVE', 'label': 'The variant or gene reported here is interpreted to be causative of the diagnosis.'}]",,,,,,,,GA4GH:interpretation_status,Interpretation Status Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'LOINC', 'code': 'LA26406-1', 'label': 'Karyotyping'}, {'system': 'LOINC', 'code': 'LA26404-6', 'label': 'FISH'}, {'system': 'LOINC', 'code': 'LA26418-6', 'label': 'PCR'}, {'system': 'LOINC', 'code': 'LA26419-4', 'label': 'qPCR (real-time PCR)'}, {'system': 'LOINC', 'code': 'LA26400-4', 'label': 'SNP array'}, {'system': 'LOINC', 'code': 'LA26813-8', 'label': 'Restriction fragment length polymorphism (RFLP)'}, {'system': 'LOINC', 'code': 'LA26810-4', 'label': 'DNA hybridization'}, {'system': 'LOINC', 'code': 'LA26398-0', 'label': 'Sequencing'}, {'system': 'LOINC', 'code': 'LA26415-2', 'label': 'MLPA'}, {'system': 'LOINC', 'code': 'LA46-8', 'label': 'Other'}]",,,,,,,,LOINC:81304-8,Structural Variant Analysis Method Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'LOINC', 'code': 'LA14032-9', 'label': 'NCBI Build 34 (hg16)'}, {'system': 'LOINC', 'code': 'LA14029-5', 'label': 'GRCh37 (hg19)'}, {'system': 'LOINC', 'code': 'LA14030-3', 'label': 'NCBI Build 36.1 (hg18)'}, {'system': 'LOINC', 'code': 'LA14031-1', 'label': 'NCBI Build 35 (hg17)'}, {'system': 'LOINC', 'code': 'LA26806-2', 'label': 'GRCh38 (hg38)'}]",,,,,,,,LOINC:62374-4,Reference Genome Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'LOINC', 'code': 'LA6705-3', 'label': 'Homozygous'}, {'system': 'LOINC', 'code': 'LA6706-1', 'label': 'Heterozygous'}, {'system': 'LOINC', 'code': 'LA26217-2', 'label': 'Compound heterozygous'}, {'system': 'LOINC', 'code': 'LA26220-6', 'label': 'Double heterozygous'}, {'system': 'LOINC', 'code': 'LA6707-9', 'label': 'Hemizygous'}, {'system': 'LOINC', 'code': 'LA6703-8', 'label': 'Heteroplasmic'}, {'system': 'LOINC', 'code': 'LA6704-6', 'label': 'Homoplasmic'}, {'system': 'LOINC', 'code': 'LA46-8', 'label': 'Other'}]",,,,,,,,LOINC:53034-5,Zygosity Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'LOINC', 'code': 'LA6683-2', 'label': 'Germline'}, {'system': 'LOINC', 'code': 'LA6684-0', 'label': 'Somatic'}, {'system': 'LOINC', 'code': 'LA10429-1', 'label': 'Fetal'}, {'system': 'LOINC', 'code': 'LA18194-3', 'label': 'Likely germline'}, {'system': 'LOINC', 'code': 'LA18195-0', 'label': 'Likely somatic'}, {'system': 'LOINC', 'code': 'LA18196-8', 'label': 'Likely fetal'}, {'system': 'LOINC', 'code': 'LA18197-6', 'label': 'Unknown genomic origin'}, {'system': 'LOINC', 'code': 'LA26807-0', 'label': 'De novo'}]",,,,,,,,LOINC:48002-0,Genomic Source Class Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'LOINC', 'code': 'LA9658-1', 'label': 'Wild type'}, {'system': 'LOINC', 'code': 'LA6692-3', 'label': 'Deletion'}, {'system': 'LOINC', 'code': 'LA6686-5', 'label': 'Duplication'}, {'system': 'LOINC', 'code': 'LA6687-3', 'label': 'Insertion'}, {'system': 'LOINC', 'code': 'LA6688-1', 'label': 'Insertion/Deletion'}, {'system': 'LOINC', 'code': 'LA6689-9', 'label': 'Inversion'}, {'system': 'LOINC', 'code': 'LA6690-7', 'label': 'Substitution'}]",,,,,,,,LOINC:48019-4,DNA Change Type Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'LOINC', 'code': 'LA6668-3', 'label': 'Pathogenic'}, {'system': 'LOINC', 'code': 'LA26332-9', 'label': 'Likely pathogenic'}, {'system': 'LOINC', 'code': 'LA26333-7', 'label': 'Uncertain significance'}, {'system': 'LOINC', 'code': 'LA26334-5', 'label': 'Likely benign'}, {'system': 'LOINC', 'code': 'LA6675-8', 'label': 'Benign'}, {'system': 'LOINC', 'code': 'LA4489-6', 'label': 'Unknown'}]",,,,,,,,LOINC:53037-8,Clinical Significance ACMG Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'GA4GH', 'code': 'UNKNOWN_ACTIONABILITY', 'label': 'There is not enough information at this time to support any therapeutic actionability for this variant.'}, {'system': 'GA4GH', 'code': 'NOT_ACTIONABLE', 'label': 'This variant has no therapeutic actionability.'}, {'system': 'GA4GH', 'code': 'ACTIONABLE', 'label': 'This variant is known to be therapeuticallyactionalbe.'}]",,,,,,,,GA4GH:therapeutic_actionability,Therapeutic Actionability Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'LOINC', 'code': 'LA30200-2', 'label': 'Very strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30201-0', 'label': 'Strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30202-8', 'label': 'Moderate evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30203-6', 'label': 'Supporting evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30204-4', 'label': 'Supporting evidence benign'}, {'system': 'LOINC', 'code': 'LA30205-1', 'label': 'Strong evidence benign'}, {'system': 'LOINC', 'code': 'LA30206-9', 'label': 'Stand-alone evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30207-7', 'label': 'Stand-alone evidence benign'}, {'system': 'LOINC', 'code': 'LA26333-7', 'label': 'Uncertain significance'}]",,,,,,,,LOINC:93044-6,Clinical Annotation Level Of Evidence Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '410605003', 'label': 'Confirmed present'}, {'system': 'SNOMEDCT', 'code': '723511001', 'label': 'Refuted'}]",,,,,,,,CustomCode:phenotypicfeature.excluded,Phenotype Status Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'HP', 'code': '0011460', 'label': 'Embryonal onset'}, {'system': 'HP', 'code': '0011461', 'label': 'Fetal onset'}, {'system': 'HP', 'code': '0003577', 'label': 'Congenital onset'}, {'system': 'HP', 'code': '0003623', 'label': 'Neonatal onset'}, {'system': 'HP', 'code': '0003593', 'label': 'Infantile onset'}, {'system': 'HP', 'code': '0011463', 'label': 'Childhood onset'}, {'system': 'HP', 'code': '0003621', 'label': 'Juvenile onset'}, {'system': 'HP', 'code': '0011462', 'label': 'Young adult onset'}, {'system': 'HP', 'code': '0003596', 'label': 'Middle age onset'}, {'system': 'HP', 'code': '0003584', 'label': 'Late onset'}]",,,,,,,,HP:0003674,Onset Category Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'HP', 'code': '0011009', 'label': 'Acute'}, {'system': 'HP', 'code': '0011010', 'label': 'Chronic'}, {'system': 'HP', 'code': '0031914', 'label': 'Fluctuating'}, {'system': 'HP', 'code': '0025297', 'label': 'Prolonged'}, {'system': 'HP', 'code': '0031796', 'label': 'Recurrent'}, {'system': 'HP', 'code': '0031915', 'label': 'Stable'}, {'system': 'HP', 'code': '0011011', 'label': 'Subacute'}, {'system': 'HP', 'code': '0025153', 'label': 'Transient'}]",,,,,,,,HP:0011008,Temporal Pattern Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'HP', 'code': '0012827', 'label': 'Borderline'}, {'system': 'HP', 'code': '0012825', 'label': 'Mild'}, {'system': 'HP', 'code': '0012826', 'label': 'Moderate'}, {'system': 'HP', 'code': '0012829', 'label': 'Profound'}, {'system': 'HP', 'code': '0012828', 'label': 'Severe'}]",,,,,,,,HP:0012824,Severity Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:64245008,Propositus Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '65656005', 'label': 'Natural mother'}, {'system': 'SNOMEDCT', 'code': '9947008', 'label': 'Natural father'}, {'system': 'SNOMEDCT', 'code': '83420006', 'label': 'Natural daughter'}, {'system': 'SNOMEDCT', 'code': '113160008', 'label': 'Natural son'}, {'system': 'SNOMEDCT', 'code': '60614009', 'label': 'Natural brother'}, {'system': 'SNOMEDCT', 'code': '73678001', 'label': 'Natural sister'}, {'system': 'SNOMEDCT', 'code': '11286003', 'label': 'Twin sibling'}, {'system': 'SNOMEDCT', 'code': '45929001', 'label': 'Half-brother'}, {'system': 'SNOMEDCT', 'code': '2272004', 'label': 'Half-sister'}, {'system': 'SNOMEDCT', 'code': '62296006', 'label': 'Natural grandfather'}, {'system': 'SNOMEDCT', 'code': '17945006', 'label': 'Natural grandmother'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:408732007,Family Relationship To Index Case Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:842009,Consanguinity Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '65656005', 'label': 'Natural mother'}, {'system': 'SNOMEDCT', 'code': '9947008', 'label': 'Natural father'}, {'system': 'SNOMEDCT', 'code': '83420006', 'label': 'Natural daughter'}, {'system': 'SNOMEDCT', 'code': '113160008', 'label': 'Natural son'}, {'system': 'SNOMEDCT', 'code': '60614009', 'label': 'Natural brother'}, {'system': 'SNOMEDCT', 'code': '73678001', 'label': 'Natural sister'}, {'system': 'SNOMEDCT', 'code': '11286003', 'label': 'Twin sibling'}, {'system': 'SNOMEDCT', 'code': '45929001', 'label': 'Half-brother'}, {'system': 'SNOMEDCT', 'code': '2272004', 'label': 'Half-sister'}, {'system': 'SNOMEDCT', 'code': '62296006', 'label': 'Natural grandfather'}, {'system': 'SNOMEDCT', 'code': '17945006', 'label': 'Natural grandmother'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:444018008,FamilyMember Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'HL7FHIR', 'code': 'partial', 'label': 'Partial'}, {'system': 'HL7FHIR', 'code': 'completed', 'label': 'Completed'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}, {'system': 'HL7FHIR', 'code': 'health-unknown', 'label': 'Health Unknown'}]",,,,,,,,HL7FHIR:familymemberhistory.status,FamilyHistoryStatus Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '248152002', 'label': 'Female'}, {'system': 'SNOMEDCT', 'code': '248153007', 'label': 'Male'}, {'system': 'SNOMEDCT', 'code': '184115007', 'label': 'Patient sex unknown'}, {'system': 'SNOMEDCT', 'code': '32570691000036108', 'label': 'Intersex'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:54123-5,AdministrativeGender Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:740604001,Deceased Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'HL7FHIR', 'code': 'draft', 'label': 'Pending'}, {'system': 'HL7FHIR', 'code': 'proposed', 'label': 'Proposed'}, {'system': 'HL7FHIR', 'code': 'active', 'label': 'Active'}, {'system': 'HL7FHIR', 'code': 'rejected', 'label': 'Rejected'}, {'system': 'HL7FHIR', 'code': 'inactive', 'label': 'Inactive'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}]",,,,,,,,HL7FHIR:309370004,Consent Status Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:consent_contact_research,Contact for Research Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:conset_data_reuse,Data Reuse Consent Value Set v2.0.0,,,,,,,,,,, +value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:123038009,Biological Sample Consent Value Set v2.0.0,,,,,,,,,,, diff --git a/src/rd_cdm/instances/v2_0_2/csvs/value_sets.csv b/src/rd_cdm/instances/csvs/value_sets.csv similarity index 99% rename from src/rd_cdm/instances/v2_0_2/csvs/value_sets.csv rename to src/rd_cdm/instances/csvs/value_sets.csv index a377632..c0e1532 100644 --- a/src/rd_cdm/instances/v2_0_2/csvs/value_sets.csv +++ b/src/rd_cdm/instances/csvs/value_sets.csv @@ -21,10 +21,10 @@ codes,id,label "[{'system': 'LOINC', 'code': 'LA14032-9', 'label': 'NCBI Build 34 (hg16)'}, {'system': 'LOINC', 'code': 'LA14029-5', 'label': 'GRCh37 (hg19)'}, {'system': 'LOINC', 'code': 'LA14030-3', 'label': 'NCBI Build 36.1 (hg18)'}, {'system': 'LOINC', 'code': 'LA14031-1', 'label': 'NCBI Build 35 (hg17)'}, {'system': 'LOINC', 'code': 'LA26806-2', 'label': 'GRCh38 (hg38)'}]",LOINC:62374-4,Reference Genome Value Set v2.0.0 "[{'system': 'LOINC', 'code': 'LA6705-3', 'label': 'Homozygous'}, {'system': 'LOINC', 'code': 'LA6706-1', 'label': 'Heterozygous'}, {'system': 'LOINC', 'code': 'LA26217-2', 'label': 'Compound heterozygous'}, {'system': 'LOINC', 'code': 'LA26220-6', 'label': 'Double heterozygous'}, {'system': 'LOINC', 'code': 'LA6707-9', 'label': 'Hemizygous'}, {'system': 'LOINC', 'code': 'LA6703-8', 'label': 'Heteroplasmic'}, {'system': 'LOINC', 'code': 'LA6704-6', 'label': 'Homoplasmic'}, {'system': 'LOINC', 'code': 'LA46-8', 'label': 'Other'}]",LOINC:53034-5,Zygosity Value Set v2.0.0 "[{'system': 'LOINC', 'code': 'LA6683-2', 'label': 'Germline'}, {'system': 'LOINC', 'code': 'LA6684-0', 'label': 'Somatic'}, {'system': 'LOINC', 'code': 'LA10429-1', 'label': 'Fetal'}, {'system': 'LOINC', 'code': 'LA18194-3', 'label': 'Likely germline'}, {'system': 'LOINC', 'code': 'LA18195-0', 'label': 'Likely somatic'}, {'system': 'LOINC', 'code': 'LA18196-8', 'label': 'Likely fetal'}, {'system': 'LOINC', 'code': 'LA18197-6', 'label': 'Unknown genomic origin'}, {'system': 'LOINC', 'code': 'LA26807-0', 'label': 'De novo'}]",LOINC:48002-0,Genomic Source Class Value Set v2.0.0 -"[{'system': 'LOINC', 'code': 'LA9658-1', 'label': 'Wild Type'}, {'system': 'LOINC', 'code': 'LA6692-3', 'label': 'Deletion'}, {'system': 'LOINC', 'code': 'LA6686-5', 'label': 'Duplication'}, {'system': 'LOINC', 'code': 'LA6687-3', 'label': 'Insertion'}, {'system': 'LOINC', 'code': 'LA6688-1', 'label': 'Insertion/Deletion'}, {'system': 'LOINC', 'code': 'LA6689-9', 'label': 'Inversion'}, {'system': 'LOINC', 'code': 'LA6690-7', 'label': 'Substitution'}]",LOINC:48019-4,DNA Change Type Value Set v2.0.0 +"[{'system': 'LOINC', 'code': 'LA9658-1', 'label': 'Wild type'}, {'system': 'LOINC', 'code': 'LA6692-3', 'label': 'Deletion'}, {'system': 'LOINC', 'code': 'LA6686-5', 'label': 'Duplication'}, {'system': 'LOINC', 'code': 'LA6687-3', 'label': 'Insertion'}, {'system': 'LOINC', 'code': 'LA6688-1', 'label': 'Insertion/Deletion'}, {'system': 'LOINC', 'code': 'LA6689-9', 'label': 'Inversion'}, {'system': 'LOINC', 'code': 'LA6690-7', 'label': 'Substitution'}]",LOINC:48019-4,DNA Change Type Value Set v2.0.0 "[{'system': 'LOINC', 'code': 'LA6668-3', 'label': 'Pathogenic'}, {'system': 'LOINC', 'code': 'LA26332-9', 'label': 'Likely pathogenic'}, {'system': 'LOINC', 'code': 'LA26333-7', 'label': 'Uncertain significance'}, {'system': 'LOINC', 'code': 'LA26334-5', 'label': 'Likely benign'}, {'system': 'LOINC', 'code': 'LA6675-8', 'label': 'Benign'}, {'system': 'LOINC', 'code': 'LA4489-6', 'label': 'Unknown'}]",LOINC:53037-8,Clinical Significance ACMG Value Set v2.0.0 "[{'system': 'GA4GH', 'code': 'UNKNOWN_ACTIONABILITY', 'label': 'There is not enough information at this time to support any therapeutic actionability for this variant.'}, {'system': 'GA4GH', 'code': 'NOT_ACTIONABLE', 'label': 'This variant has no therapeutic actionability.'}, {'system': 'GA4GH', 'code': 'ACTIONABLE', 'label': 'This variant is known to be therapeuticallyactionalbe.'}]",GA4GH:therapeutic_actionability,Therapeutic Actionability Value Set v2.0.0 -"[{'system': 'LOINC', 'code': 'LA30200-2', 'label': 'Very Strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30201-0', 'label': 'Strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30202-8', 'label': 'Moderate evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30203-6', 'label': 'Supporting evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30204-4', 'label': 'Supporting evidence benign'}, {'system': 'LOINC', 'code': 'LA30205-1', 'label': 'Strong evidence benign'}, {'system': 'LOINC', 'code': 'LA30206-9', 'label': 'Stand-alone evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30207-7', 'label': 'Stand-alone evidence benign'}, {'system': 'LOINC', 'code': 'LA26333-7', 'label': 'Uncertain significance'}]",LOINC:93044-6,Clinical Annotation Level Of Evidence Value Set v2.0.0 +"[{'system': 'LOINC', 'code': 'LA30200-2', 'label': 'Very strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30201-0', 'label': 'Strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30202-8', 'label': 'Moderate evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30203-6', 'label': 'Supporting evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30204-4', 'label': 'Supporting evidence benign'}, {'system': 'LOINC', 'code': 'LA30205-1', 'label': 'Strong evidence benign'}, {'system': 'LOINC', 'code': 'LA30206-9', 'label': 'Stand-alone evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30207-7', 'label': 'Stand-alone evidence benign'}, {'system': 'LOINC', 'code': 'LA26333-7', 'label': 'Uncertain significance'}]",LOINC:93044-6,Clinical Annotation Level Of Evidence Value Set v2.0.0 "[{'system': 'SNOMEDCT', 'code': '410605003', 'label': 'Confirmed present'}, {'system': 'SNOMEDCT', 'code': '723511001', 'label': 'Refuted'}]",CustomCode:phenotypicfeature.excluded,Phenotype Status Value Set v2.0.0 "[{'system': 'HP', 'code': '0011460', 'label': 'Embryonal onset'}, {'system': 'HP', 'code': '0011461', 'label': 'Fetal onset'}, {'system': 'HP', 'code': '0003577', 'label': 'Congenital onset'}, {'system': 'HP', 'code': '0003623', 'label': 'Neonatal onset'}, {'system': 'HP', 'code': '0003593', 'label': 'Infantile onset'}, {'system': 'HP', 'code': '0011463', 'label': 'Childhood onset'}, {'system': 'HP', 'code': '0003621', 'label': 'Juvenile onset'}, {'system': 'HP', 'code': '0011462', 'label': 'Young adult onset'}, {'system': 'HP', 'code': '0003596', 'label': 'Middle age onset'}, {'system': 'HP', 'code': '0003584', 'label': 'Late onset'}]",HP:0003674,Onset Category Value Set v2.0.0 "[{'system': 'HP', 'code': '0011009', 'label': 'Acute'}, {'system': 'HP', 'code': '0011010', 'label': 'Chronic'}, {'system': 'HP', 'code': '0031914', 'label': 'Fluctuating'}, {'system': 'HP', 'code': '0025297', 'label': 'Prolonged'}, {'system': 'HP', 'code': '0031796', 'label': 'Recurrent'}, {'system': 'HP', 'code': '0031915', 'label': 'Stable'}, {'system': 'HP', 'code': '0011011', 'label': 'Subacute'}, {'system': 'HP', 'code': '0025153', 'label': 'Transient'}]",HP:0011008,Temporal Pattern Value Set v2.0.0 diff --git a/src/rd_cdm/instances/v2_0_2/data_elements.yaml b/src/rd_cdm/instances/data_elements.yaml similarity index 99% rename from src/rd_cdm/instances/v2_0_2/data_elements.yaml rename to src/rd_cdm/instances/data_elements.yaml index a0cd2f2..146d7af 100644 --- a/src/rd_cdm/instances/v2_0_2/data_elements.yaml +++ b/src/rd_cdm/instances/data_elements.yaml @@ -53,9 +53,9 @@ data_elements: section: 2. Personal Information elementName: Sex at Birth elementCode: - system: SNOMEDCT - code: '281053000' - elementCodeSystem: SNOMEDCT + system: LOINC + code: '76689-9' + elementCodeSystem: LOINC dataType: Code dataSpecification: - VSe diff --git a/src/rd_cdm/instances/v2_0_2/jsons/code_systems.json b/src/rd_cdm/instances/jsons/code_systems.json similarity index 88% rename from src/rd_cdm/instances/v2_0_2/jsons/code_systems.json rename to src/rd_cdm/instances/jsons/code_systems.json index 9990939..85b7332 100644 --- a/src/rd_cdm/instances/v2_0_2/jsons/code_systems.json +++ b/src/rd_cdm/instances/jsons/code_systems.json @@ -3,25 +3,25 @@ { "id": "SNOMEDCT", "namespace_iri": "http://purl.bioontology.org/ontology/SNOMEDCT/", - "version": "SNOMEDCT_US_2024_09_01", + "version": "2025AB", "title": "Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT)" }, { "id": "LOINC", "namespace_iri": "http://loinc.org", - "version": "LNC278", + "version": "281", "title": "Logical Observation Identifiers Names and Codes (LOINC)" }, { "id": "HP", "namespace_iri": "http://purl.obolibrary.org/obo/HP", - "version": "2025-05-06", + "version": "2026-02-16", "title": "Human Phenotype Ontology (HPO)" }, { "id": "NCIT", "namespace_iri": "http://purl.obolibrary.org/obo/NCIT/", - "version": "24.01e", + "version": "26.02d", "title": "NCI Thesaurus (NCIT) OBO Edition" }, { @@ -39,19 +39,19 @@ { "id": "CustomCode", "namespace_iri": "https://github.com/BIH-CEI/rd-cdm", - "version": "v2.0.0", - "title": "Custom Code System RD CDM v2.0.0" + "version": "v2.0", + "title": "Custom Code System RD CDM v2.0" }, { "id": "NCBITAXON", "namespace_iri": "http://purl.obolibrary.org/obo/NCBITAXON/", - "version": "NCBI2024_04_02", + "version": "2025_04_10", "title": "NCBI organismal classification" }, { "id": "GENO", "namespace_iri": "http://purl.obolibrary.org/obo/GENO/", - "version": "2023-10-08", + "version": "2026-02-02", "title": "GENO – The Genotype Ontology" }, { @@ -63,31 +63,31 @@ { "id": "UO", "namespace_iri": "http://purl.obolibrary.org/obo/UO/", - "version": "2023-05-25", + "version": "2026-01-16", "title": "Units Ontology (UO)" }, { "id": "ECO", "namespace_iri": "http://purl.obolibrary.org/obo/ECO/", - "version": "2025-06-23", + "version": "releases/2025-06-23", "title": "Evidence & Conclusion Ontology (ECO)" }, { "id": "ICD10CM", "namespace_iri": "http://purl.bioontology.org/ontology/ICD10CM/", - "version": "CD10CM_2025", + "version": "2026", "title": "International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)" }, { "id": "MONDO", "namespace_iri": "http://purl.obolibrary.org/obo/MONDO/", - "version": "2025-06-03", + "version": "2026-03-03", "title": "Mondo Disease Ontology" }, { "id": "ORDO", "namespace_iri": "http://purl.obolibrary.org/obo/ORDO/", - "version": "4.7", + "version": "4.8", "title": "Orphanet Rare Disease Ontology (ORDO)" }, { @@ -99,7 +99,7 @@ { "id": "OMIM", "namespace_iri": "http://purl.bioontology.org/ontology/OMIM/", - "version": "OMIM2024_08_09", + "version": "2025_08_04", "title": "Online Mendelian Inheritance in Man (OMIM)" }, { diff --git a/src/rd_cdm/instances/v2_0_2/jsons/data_elements.json b/src/rd_cdm/instances/jsons/data_elements.json similarity index 99% rename from src/rd_cdm/instances/v2_0_2/jsons/data_elements.json rename to src/rd_cdm/instances/jsons/data_elements.json index 552c62f..da68d42 100644 --- a/src/rd_cdm/instances/v2_0_2/jsons/data_elements.json +++ b/src/rd_cdm/instances/jsons/data_elements.json @@ -63,10 +63,10 @@ "ordinal": "2.2", "elementName": "Sex at Birth", "elementCode": { - "system": "SNOMEDCT", - "code": "281053000" + "system": "LOINC", + "code": "76689-9" }, - "elementCodeSystem": "SNOMEDCT", + "elementCodeSystem": "LOINC", "section": "2. Personal Information", "dataType": "Code", "dataSpecification": [ diff --git a/src/rd_cdm/instances/jsons/rd_cdm.json b/src/rd_cdm/instances/jsons/rd_cdm.json new file mode 100644 index 0000000..ee78843 --- /dev/null +++ b/src/rd_cdm/instances/jsons/rd_cdm.json @@ -0,0 +1,3166 @@ +{ + "rd_cdm_version": "2.0.3", + "rd_cdm_date": "2026-03-24", + "code_systems": [ + { + "id": "SNOMEDCT", + "namespace_iri": "http://purl.bioontology.org/ontology/SNOMEDCT/", + "version": "2025AB", + "title": "Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT)" + }, + { + "id": "LOINC", + "namespace_iri": "http://loinc.org", + "version": "281", + "title": "Logical Observation Identifiers Names and Codes (LOINC)" + }, + { + "id": "HP", + "namespace_iri": "http://purl.obolibrary.org/obo/HP", + "version": "2026-02-16", + "title": "Human Phenotype Ontology (HPO)" + }, + { + "id": "NCIT", + "namespace_iri": "http://purl.obolibrary.org/obo/NCIT/", + "version": "26.02d", + "title": "NCI Thesaurus (NCIT) OBO Edition" + }, + { + "id": "HL7FHIR", + "namespace_iri": "http://hl7.org/fhir/", + "version": "v4.0.1", + "title": "Health Level Seven Fast Healthcare Interoperability Resources, Release 4" + }, + { + "id": "GA4GH", + "namespace_iri": "https://ga4gh.github.io/phenopacket-v2/", + "version": "v2.0", + "title": "Global Alliance for Genomics and Health Phenopackets Schema" + }, + { + "id": "CustomCode", + "namespace_iri": "https://github.com/BIH-CEI/rd-cdm", + "version": "v2.0", + "title": "Custom Code System RD CDM v2.0" + }, + { + "id": "NCBITAXON", + "namespace_iri": "http://purl.obolibrary.org/obo/NCBITAXON/", + "version": "2025_04_10", + "title": "NCBI organismal classification" + }, + { + "id": "GENO", + "namespace_iri": "http://purl.obolibrary.org/obo/GENO/", + "version": "2026-02-02", + "title": "GENO – The Genotype Ontology" + }, + { + "id": "SO", + "namespace_iri": "http://purl.obolibrary.org/obo/SO/", + "version": "2.6", + "title": "Sequence Ontology" + }, + { + "id": "UO", + "namespace_iri": "http://purl.obolibrary.org/obo/UO/", + "version": "2026-01-16", + "title": "Units Ontology (UO)" + }, + { + "id": "ECO", + "namespace_iri": "http://purl.obolibrary.org/obo/ECO/", + "version": "releases/2025-06-23", + "title": "Evidence & Conclusion Ontology (ECO)" + }, + { + "id": "ICD10CM", + "namespace_iri": "http://purl.bioontology.org/ontology/ICD10CM/", + "version": "2026", + "title": "International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)" + }, + { + "id": "MONDO", + "namespace_iri": "http://purl.obolibrary.org/obo/MONDO/", + "version": "2026-03-03", + "title": "Mondo Disease Ontology" + }, + { + "id": "ORDO", + "namespace_iri": "http://purl.obolibrary.org/obo/ORDO/", + "version": "4.8", + "title": "Orphanet Rare Disease Ontology (ORDO)" + }, + { + "id": "HGNC", + "namespace_iri": "http://identifiers.org/hgnc/", + "version": "2024-08-23", + "title": "HUGO Gene Nomenclature Committee (HGNC)" + }, + { + "id": "OMIM", + "namespace_iri": "http://purl.bioontology.org/ontology/OMIM/", + "version": "2025_08_04", + "title": "Online Mendelian Inheritance in Man (OMIM)" + }, + { + "id": "HGVS", + "namespace_iri": "https://varnomen.hgvs.org/", + "version": "21.0.0", + "title": "Human Genome Variation Society Nomenclature" + }, + { + "id": "ICD11", + "namespace_iri": "http://id.who.int/icd/release/11/mms/", + "version": "2024-09-01", + "title": "International Classification of Diseases, Eleventh Revision (ICD-11)" + }, + { + "id": "ISO3166", + "namespace_iri": "https://www.iso.org/iso-3166-country-codes.html", + "version": "2020(en)", + "title": "International Organization for Standardization – ISO 3166 Country Codes" + }, + { + "id": "ICF", + "namespace_iri": "https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health", + "version": "1.0.2", + "title": "International Classification of Functioning, Disability and Health (ICF)" + } + ], + "data_elements": [ + { + "ordinal": "1.1", + "section": "1. Formal Criteria", + "elementName": "Pseudonym", + "elementCode": { + "system": "SNOMEDCT", + "code": "422549004" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Identifier", + "dataSpecification": [ + "n/a" + ], + "valueSet": null, + "fhirExpression_v4_0_1": "Patient.identifier.value", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "Individual.id", + "recommendedDataSpec_phenopackets": "string", + "description": "The (local) patient-related identification code." + }, + { + "ordinal": "1.2", + "section": "1. Formal Criteria", + "elementName": "Date of Admission", + "elementCode": { + "system": "SNOMEDCT", + "code": "399423000" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": null, + "fhirExpression_v4_0_1": "Encounter.period.start", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "Individual.time_at_last_encounter", + "recommendedDataSpec_phenopackets": "TimeElement", + "description": "The date of admission or data capture of the individual." + }, + { + "ordinal": "2.1", + "section": "2. Personal Information", + "elementName": "Date of Birth", + "elementCode": { + "system": "SNOMEDCT", + "code": "184099003" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Date", + "dataSpecification": [ + "YYYY", + "YYYY-MM", + "YYYY-MM-DD" + ], + "valueSet": null, + "fhirExpression_v4_0_1": "Patient.birthDate", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "Individual.date_of_birth", + "recommendedDataSpec_phenopackets": "TimeElement", + "description": "The individual's date of birth." + }, + { + "ordinal": "2.2", + "section": "2. Personal Information", + "elementName": "Sex at Birth", + "elementCode": { + "system": "LOINC", + "code": "76689-9" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Sex at Birth Value Set v2.0.0", + "fhirExpression_v4_0_1": "Patient.extension:individual-recordedSexOrGender", + "recommendedDataSpec_fhir": "Recorded Sex Or Gender Type", + "phenopacketSchemaElement_v2_0": "Individual.sex", + "recommendedDataSpec_phenopackets": "Sex", + "description": "The individual's sex that was assigned at birth." + }, + { + "ordinal": "2.3", + "section": "2. Personal Information", + "elementName": "Karyotypic Sex", + "elementCode": { + "system": "SNOMEDCT", + "code": "1296886006" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSc" + ], + "valueSet": "Karyotypic Sex Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.value", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "Individual.karyotypic_sex", + "recommendedDataSpec_phenopackets": "Karyotypic Sex", + "description": "The chromosomal sex of an individual." + }, + { + "ordinal": "2.4", + "section": "2. Personal Information", + "elementName": "Gender Identity", + "elementCode": { + "system": "SNOMEDCT", + "code": "263495000" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Gender Identity Value Set v2.0.0", + "fhirExpression_v4_0_1": "Patient.extension:individual-genderIdentity", + "recommendedDataSpec_fhir": "Gender Identity", + "phenopacketSchemaElement_v2_0": "Individual.gender", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "The self-assigned gender of the individual." + }, + { + "ordinal": "2.5", + "section": "2. Personal Information", + "elementName": "Country of Birth", + "elementCode": { + "system": "SNOMEDCT", + "code": "370159000" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": null, + "fhirExpression_v4_0_1": "Patient.extension:patient-birthPlace", + "recommendedDataSpec_fhir": "DataType: Address", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The individual's country of birth." + }, + { + "ordinal": "3.1", + "section": "3. Patient Status", + "elementName": "Vital Status", + "elementCode": { + "system": "SNOMEDCT", + "code": "278844005" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Vital Status Value Set v2.0.0", + "fhirExpression_v4_0_1": "Patient.deceased.deceasedBoolean|Observation.value", + "recommendedDataSpec_fhir": "Boolean|Code", + "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.status", + "recommendedDataSpec_phenopackets": "Value Set: VitalStatus.Status", + "description": "The individual’s general clinical status orvital status." + }, + { + "ordinal": "3.2", + "section": "3. Patient Status", + "elementName": "Time of Death", + "elementCode": { + "system": "SNOMEDCT", + "code": "398299004" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Date", + "dataSpecification": [ + "YYYY", + "YYYY-MM", + "YYYY-MM-DD" + ], + "valueSet": null, + "fhirExpression_v4_0_1": "Patient.deceasedDateTime", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.time_of_death", + "recommendedDataSpec_phenopackets": "TimeElement", + "description": "If deceased, the individual’s date of death." + }, + { + "ordinal": "3.3", + "section": "3. Patient Status", + "elementName": "Cause of Death", + "elementCode": { + "system": "SNOMEDCT", + "code": "184305005" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "ICD-10CM" + ], + "valueSet": null, + "fhirExpression_v4_0_1": "Observation.value.coding.code", + "recommendedDataSpec_fhir": "Code|CodeableConcept", + "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.cause_of_death", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "If deceased, the individual’s primary cause of death." + }, + { + "ordinal": "3.4", + "section": "3. Patient Status", + "elementName": "Age Category", + "elementCode": { + "system": "SNOMEDCT", + "code": "105727008" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe" + ], + "valueSet": "Age Category Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.value.coding.code", + "recommendedDataSpec_fhir": "CodableConcept", + "phenopacketSchemaElement_v2_0": "Individual.time_at_last_encounter", + "recommendedDataSpec_phenopackets": "TimeElement", + "description": "The individual's age category at thetime of data capture." + }, + { + "ordinal": "3.5", + "section": "3. Patient Status", + "elementName": "Length of Gestation at Birth [weeks+days]", + "elementCode": { + "system": "SNOMEDCT", + "code": "412726003" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "String", + "dataSpecification": [ + "XX+X" + ], + "valueSet": null, + "fhirExpression_v4_0_1": "Observation.component:weeks.valueQuantity|Observation.component:days.valueQuantity", + "recommendedDataSpec_fhir": "Quantity", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The duration of the pregnancy in weeks and days,formatted as XX+X (weeks+days)." + }, + { + "ordinal": "3.6", + "section": "3. Patient Status", + "elementName": "Undiagnosed RD Case", + "elementCode": { + "system": "SNOMEDCT", + "code": "723663001" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe" + ], + "valueSet": "Undiagnosed RD Case Value Set v2.0.0", + "fhirExpression_v4_0_1": "(Condition.code)", + "recommendedDataSpec_fhir": "Code(e.g. ORDO:616874 - Rare disorderwithout a determined diagnosis afterfull investigation)", + "phenopacketSchemaElement_v2_0": "(Disease.term)", + "recommendedDataSpec_phenopackets": "(OntologyClass (e.g. ORDO:616874 - Rare disorder without a determineddiagnosis after full investigation))", + "description": "Identifies cases where an RD diagnosis has notbeen established." + }, + { + "ordinal": "4.1", + "section": "4. Care Pathway", + "elementName": "Encounter Start", + "elementCode": { + "system": "HL7FHIR", + "code": "encounter.period.start" + }, + "elementCodeSystem": "HL7FHIR", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": null, + "fhirExpression_v4_0_1": "Encounter.period.start", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The beginning of an encounter of the individual." + }, + { + "ordinal": "4.2", + "section": "4. Care Pathway", + "elementName": "Encounter End", + "elementCode": { + "system": "HL7FHIR", + "code": "encounter.period.end" + }, + "elementCodeSystem": "HL7FHIR", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": null, + "fhirExpression_v4_0_1": "Encounter.period.end", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The end of an encounter of the individual." + }, + { + "ordinal": "4.3", + "section": "4. Care Pathway", + "elementName": "Encounter Status", + "elementCode": { + "system": "SNOMEDCT", + "code": "305058001" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Encounter Status Value Set v2.0.0", + "fhirExpression_v4_0_1": "Encounter.status", + "recommendedDataSpec_fhir": "ValueSet: EncounterStatus", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The status of an encounter of the individual at thetime of data capture." + }, + { + "ordinal": "4.4", + "section": "4. Care Pathway", + "elementName": "Encounter Class", + "elementCode": { + "system": "HL7FHIR", + "code": "encounter.class" + }, + "elementCodeSystem": "HL7FHIR", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Encounter Class Value Set v2.0.0", + "fhirExpression_v4_0_1": "Encounter.class", + "recommendedDataSpec_fhir": "ValueSet: EncounterClass", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The class of an encounter of the individualat the time of data capture." + }, + { + "ordinal": "5.1", + "section": "5. Disease", + "elementName": "Disease", + "elementCode": { + "system": "SNOMEDCT", + "code": "64572001" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "Ontology Class (MONDO, ORDO, ICD-10, ICD-11, OMIM_g, OMIM_p)" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Condition.code", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "Disease.term", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "A disease that the individual was affected by. If agenetic diagnosis or subtypes were diagnosed, please also provide the respective OMIM_g and OMIM_p codes." + }, + { + "ordinal": "5.2", + "section": "5. Disease", + "elementName": "Verification Status", + "elementCode": { + "system": "LOINC", + "code": "99498-8" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Verification Status Value Set v2.0.0", + "fhirExpression_v4_0_1": "Condition.verificationStatus", + "recommendedDataSpec_fhir": "ValueSet: Condition Verficication Status", + "phenopacketSchemaElement_v2_0": "(Disease.excluded)", + "recommendedDataSpec_phenopackets": "boolean", + "description": "The verification status of the disease." + }, + { + "ordinal": "5.3", + "section": "5. Disease", + "elementName": "Age at Onset", + "elementCode": { + "system": "SNOMEDCT", + "code": "424850005" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Age at Onset Value Set v2.0.0", + "fhirExpression_v4_0_1": "Condition.onsetString orObservation.valueCodeableConcept", + "recommendedDataSpec_fhir": "Disease.onset", + "phenopacketSchemaElement_v2_0": "Disease.onset", + "recommendedDataSpec_phenopackets": "Disease.onset", + "description": "The age at the onset of the first symptomsor signs of the disease." + }, + { + "ordinal": "5.4", + "section": "5. Disease", + "elementName": "Date of Onset", + "elementCode": { + "system": "SNOMEDCT", + "code": "298059007" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Condition.onset", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "Disease.onset", + "recommendedDataSpec_phenopackets": "TimeElement", + "description": "The date at onset of first symptoms orsigns of the disease." + }, + { + "ordinal": "5.5", + "section": "5. Disease", + "elementName": "Age at Diagnosis", + "elementCode": { + "system": "SNOMEDCT", + "code": "423493009" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Age at Diagnosis Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.value", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "(Disease.onset)", + "recommendedDataSpec_phenopackets": "(TimeElement)", + "description": "The individual’s age when the diagnosis was made." + }, + { + "ordinal": "5.6", + "section": "5. Disease", + "elementName": "Date of Diagnosis", + "elementCode": { + "system": "SNOMEDCT", + "code": "432213005" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Condition.recordedDate", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "(Disease.onset)", + "recommendedDataSpec_phenopackets": "(TimeElement)", + "description": "The date on which the disease was determined." + }, + { + "ordinal": "5.7", + "section": "5. Disease", + "elementName": "Body Site", + "elementCode": { + "system": "SNOMEDCT", + "code": "363698007" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Body Site Value Set v2.0.0", + "fhirExpression_v4_0_1": "Condition.bodySite.coding:SNOMEDCT-ct", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "Disease.primary_site", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "The specific body site affected by disease is encodedusing all descendants of SCT Body Structure (123037004)." + }, + { + "ordinal": "5.8", + "section": "5. Disease", + "elementName": "Clinical Status", + "elementCode": { + "system": "SNOMEDCT", + "code": "263493007" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Clinical Status Value Set v2.0.0", + "fhirExpression_v4_0_1": "Condition.clinicalStatus", + "recommendedDataSpec_fhir": "ValueSet: ClinicalStatus", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The clinical status of the disease indicates whetherit is active, inactive, or resolved." + }, + { + "ordinal": "5.9", + "section": "5. Disease", + "elementName": "Severity", + "elementCode": { + "system": "SNOMEDCT", + "code": "246112005" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Severity Value Set v2.0.0", + "fhirExpression_v4_0_1": "Condition.severity", + "recommendedDataSpec_fhir": "ValueSet: ConditionSeverity", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The severity of the disease is categorised byclinical evaluation." + }, + { + "ordinal": "6.1.1", + "section": "6. Genetic Findings", + "elementName": "Genomic Diagnosis", + "elementCode": { + "system": "SNOMEDCT", + "code": "106221001" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "OMIM_p", + "MONDO" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Condition.code", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "Interpretation.Diagnosis.disease", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "The genomic diagnoses can correspond to the diagnoseddisease in (5.1) if the same OMIM codes are used." + }, + { + "ordinal": "6.1.2", + "section": "6. Genetic Findings", + "elementName": "Progress Status of Interpretation", + "elementCode": { + "system": "GA4GH", + "code": "progress_status" + }, + "elementCodeSystem": "GA4GH", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Progress Status Value Set v2.0.0", + "fhirExpression_v4_0_1": "Condition.extension", + "recommendedDataSpec_fhir": "VS: GA4GH ProgressStatus", + "phenopacketSchemaElement_v2_0": "Interpretation.progress_status", + "recommendedDataSpec_phenopackets": "ValueSet: ProgressStatus", + "description": "The interpretation has a ProgressStatus that refers tothe status of the attempted diagnosis." + }, + { + "ordinal": "6.1.3", + "section": "6. Genetic Findings", + "elementName": "Interpretation Status", + "elementCode": { + "system": "GA4GH", + "code": "interpretation_status" + }, + "elementCodeSystem": "GA4GH", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Interpretation Status Value Set v2.0.0", + "fhirExpression_v4_0_1": "Condition.extension", + "recommendedDataSpec_fhir": "VS: GA4GH InterpretationStatus", + "phenopacketSchemaElement_v2_0": "GenomicInterpretation.interpretation_status", + "recommendedDataSpec_phenopackets": "ValueSet: InterpretationStatus", + "description": "An enumeration that describes the conclusion made about the genomic interpretation." + }, + { + "ordinal": "6.1.4", + "section": "6. Genetic Findings", + "elementName": "Structural Variant Analysis Method", + "elementCode": { + "system": "LOINC", + "code": "81304-8" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VS", + "LOINC" + ], + "valueSet": "Structural Variant Analysis Method Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.method", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The method used to analyse structural variants in the genome." + }, + { + "ordinal": "6.1.5", + "section": "6. Genetic Findings", + "elementName": "Reference Genome", + "elementCode": { + "system": "LOINC", + "code": "62374-4" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Reference Genome Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.component:reference-sequence-assembly", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The reference genome used for analysing the genetic variant." + }, + { + "ordinal": "6.1.6", + "section": "6. Genetic Findings", + "elementName": "Genetic Mutation String", + "elementCode": { + "system": "LOINC", + "code": "LP7824-8" + }, + "elementCodeSystem": "LOINC", + "dataType": "String", + "dataSpecification": [ + "n/a" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.component:Variant.valueString", + "recommendedDataSpec_fhir": "string", + "phenopacketSchemaElement_v2_0": "VariationDescriptor.Extension.value", + "recommendedDataSpec_phenopackets": "string", + "description": "An unvalidated (HGVS) string that describes the variant change" + }, + { + "ordinal": "6.1.7", + "section": "6. Genetic Findings", + "elementName": "Genomic DNA Change", + "elementCode": { + "system": "LOINC", + "code": "81290-9" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "g.HGVS" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.component:Variant.valueCode", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "VariationDescriptor.Expression.value", + "recommendedDataSpec_phenopackets": "string", + "description": "The specific change in the genomic DNA sequence encoded with a validated g.HGVS expression." + }, + { + "ordinal": "6.1.8", + "section": "6. Genetic Findings", + "elementName": "Sequence DNA Change", + "elementCode": { + "system": "LOINC", + "code": "48004-6" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "c.HGVS" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.component:Variant.valueCode", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "VariationDescriptor.Expression.value", + "recommendedDataSpec_phenopackets": "string", + "description": "The specific change in the DNA sequence at the nucleotide level with a validated c.HGVS expression." + }, + { + "ordinal": "6.1.9", + "section": "6. Genetic Findings", + "elementName": "Amino Acid Change", + "elementCode": { + "system": "LOINC", + "code": "48005-3" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "p.HGVS" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.component:Variant.valueCode", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "VariationDescriptor.Expression.value", + "recommendedDataSpec_phenopackets": "string", + "description": "The specific change in the amino acid sequence resulting from agenetic variant as a validated p.HGVS expression." + }, + { + "ordinal": "6.1.10", + "section": "6. Genetic Findings", + "elementName": "Gene", + "elementCode": { + "system": "LOINC", + "code": "48018-6" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "HGNC" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.component:Gene", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "GeneDescriptor.value_id", + "recommendedDataSpec_phenopackets": "string", + "description": "The specific gene or genes that were analysed or identified in the study." + }, + { + "ordinal": "6.1.11", + "section": "6. Genetic Findings", + "elementName": "Zygosity", + "elementCode": { + "system": "LOINC", + "code": "53034-5" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc", + "LOINC" + ], + "valueSet": "Zygosity Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.component:geneticsAllele.State", + "recommendedDataSpec_fhir": "VS: Allelic State", + "phenopacketSchemaElement_v2_0": "VariationDescriptor.allelic_state", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "The zygosity of the genetic variant." + }, + { + "ordinal": "6.1.12", + "section": "6. Genetic Findings", + "elementName": "Genomic Source Class", + "elementCode": { + "system": "LOINC", + "code": "48002-0" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Genomic Source Class Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.component:GenomicSourceClass", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The classification of the genomic source, such as germline, somatic, or other origins." + }, + { + "ordinal": "6.1.13", + "section": "6. Genetic Findings", + "elementName": "DNA Change Type", + "elementCode": { + "system": "LOINC", + "code": "48019-4" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "DNA Change Type Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.component:Variant.Type", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The variant’s type of DNA change, such as point mutation, deletion, insertion, or other types." + }, + { + "ordinal": "6.1.14", + "section": "6. Genetic Findings", + "elementName": "Clinical Significance [ACMG]", + "elementCode": { + "system": "LOINC", + "code": "53037-8" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Clinical Significance ACMG Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.component:Variant.Interpretation", + "recommendedDataSpec_fhir": "", + "phenopacketSchemaElement_v2_0": "VariantInterpretation.acmg_pathogenicity_classification", + "recommendedDataSpec_phenopackets": "ValueSet: AcmgPathogenicityClassification", + "description": "The clinical significance of the genetic variant, indicating its impact on health and disease." + }, + { + "ordinal": "6.1.15", + "section": "6. Genetic Findings", + "elementName": "Therapeutic Actionability", + "elementCode": { + "system": "GA4GH", + "code": "therapeutic_actionability" + }, + "elementCodeSystem": "GA4GH", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Therapeutic Actionability Value Set v2.0.0", + "fhirExpression_v4_0_1": "n/a", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "VariantInterpretation.therapeutic_actionability", + "recommendedDataSpec_phenopackets": "ValueSet: TherapeuticActionability", + "description": "An enumeration flagging the variant as being a candidate for treatment or clinical intervention, which could improve the clinical outcome." + }, + { + "ordinal": "6.1.16", + "section": "6. Genetic Findings", + "elementName": "Clinical Annotation Level Of Evidence", + "elementCode": { + "system": "LOINC", + "code": "93044-6" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Clinical Annotation Level Of Evidence Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.extension:Variant.Interpretation", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The level of evidence supporting the clinical annotation of the genetic variant." + }, + { + "ordinal": "6.2.1", + "section": "6. Phenotypic Feature", + "elementName": "Phenotypic Feature", + "elementCode": { + "system": "SNOMEDCT", + "code": "8116006" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "HPO" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.code", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "PhenotypicFeature.type", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "An observed physical and clinical characteristicencoded with HPO." + }, + { + "ordinal": "6.2.2", + "section": "6.2 Phenotypic Feature", + "elementName": "Status", + "elementCode": { + "system": "SNOMEDCT", + "code": "363778006" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Phenotype Status Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.status", + "recommendedDataSpec_fhir": "ValueSet: ObservationStatus", + "phenopacketSchemaElement_v2_0": "PhenotypicFeature.excluded", + "recommendedDataSpec_phenopackets": "boolean", + "description": "The current status of the phenotypic feature, indicating whether it is confirmed or refuted." + }, + { + "ordinal": "6.2.3", + "section": "6. Phenotypic Feature", + "elementName": "Determination Date", + "elementCode": { + "system": "SNOMEDCT", + "code": "439272007:704321009=363778006" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.effectiveDateTime", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "PhenotypicFeature.onset", + "recommendedDataSpec_phenopackets": "TimeElement", + "description": "The date on which the phenotypic feature was observed or recorded. We recommend capturing the time acharacteristic was observed." + }, + { + "ordinal": "6.2.4", + "section": "6.2 Phenotypic Feature", + "elementName": "Resolution Date", + "elementCode": { + "system": "HP", + "code": "0034382" + }, + "elementCodeSystem": "HP", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.effectiveDateTime", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "PhenotypicFeature.resolution", + "recommendedDataSpec_phenopackets": "TimeElement", + "description": "Time at which the feature resolved or abated." + }, + { + "ordinal": "6.2.5", + "section": "6.2 Phenotypic Feature", + "elementName": "Onset Category", + "elementCode": { + "system": "HP", + "code": "0003674" + }, + "elementCodeSystem": "HP", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Onset Category Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.category", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "PhenotypicFeature.onset", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "Time at which the feature was first observed within HPO onset categories." + }, + { + "ordinal": "6.2.6", + "section": "6.2 Phenotypic Feature", + "elementName": "Temporal Pattern", + "elementCode": { + "system": "HP", + "code": "0011008" + }, + "elementCodeSystem": "HP", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Temporal Pattern Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.interpretation", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "PhenotypicFeature.modifiers", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "The speed at which disease manifestations appear and develop." + }, + { + "ordinal": "6.2.7", + "section": "6.2 Phenotypic Feature", + "elementName": "Severity", + "elementCode": { + "system": "HP", + "code": "0012824" + }, + "elementCodeSystem": "HP", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Severity Value Set v2.0.0", + "fhirExpression_v4_0_1": "Observation.interpretation", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "PhenotypicFeature.severity", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "A description of the severity of the feature." + }, + { + "ordinal": "6.2.8", + "section": "6. Phenotypic Feature", + "elementName": "Modifiers", + "elementCode": { + "system": "GA4GH", + "code": "phenotypicfeature.modifier" + }, + "elementCodeSystem": "GA4GH", + "dataType": "Code", + "dataSpecification": [ + "OntologyClass (HPO, NCBITAXON, SCT)" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Suggested: Observation.extension", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "PhenotypicFeature.modifiers", + "recommendedDataSpec_phenopackets": "list of OntologyClass", + "description": "Any number of additional modifiers describing a specific phenotypic feature further, such as severity (HP:0012824), clinical modifiers (HP:0012823), or linking causative infectious agents using the NCBITAXON Ontology." + }, + { + "ordinal": "6.2.9", + "section": "6.2 Phenotypic Feature", + "elementName": "Evidence", + "elementCode": { + "system": "GA4GH", + "code": "phenotypicfeature.evidence" + }, + "elementCodeSystem": "GA4GH", + "dataType": "Code", + "dataSpecification": [ + "ECO" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.method", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "PhenotypicFeature.evidence", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "The evidence for an assertion of the observation of a type defined within the Evidence & Conclusion Ontology (ECO)." + }, + { + "ordinal": "6.3.1", + "section": "6.3 Measurement", + "elementName": "Assay", + "elementCode": { + "system": "NCIT", + "code": "C60819" + }, + "elementCodeSystem": "NCIT", + "dataType": "Code", + "dataSpecification": [ + "OntologyClass (e.g. LOINC)" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.code", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "Measurement.assay", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "A class that describes the assay used to producethe measurement." + }, + { + "ordinal": "6.3.2", + "section": "6.3 Measurement", + "elementName": "Value", + "elementCode": { + "system": "NCIT", + "code": "C25712" + }, + "elementCodeSystem": "NCIT", + "dataType": "Value", + "dataSpecification": [ + "float" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.value[x]", + "recommendedDataSpec_fhir": "Quantity|integer", + "phenopacketSchemaElement_v2_0": "Measurement.measurement_value", + "recommendedDataSpec_phenopackets": "Quantity[double/float]", + "description": "The result of the measurement." + }, + { + "ordinal": "6.3.3", + "section": "6.3 Measurement", + "elementName": "Value Unit", + "elementCode": { + "system": "NCIT", + "code": "C92571" + }, + "elementCodeSystem": "NCIT", + "dataType": "Code", + "dataSpecification": [ + "UO" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.value[x].unit", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "Measurement.measurement_value", + "recommendedDataSpec_phenopackets": "OntologyClass", + "description": "The unit of the result's measurement." + }, + { + "ordinal": "6.3.4", + "section": "6.3 Measurement", + "elementName": "Interpretation", + "elementCode": { + "system": "NCIT", + "code": "C41255" + }, + "elementCodeSystem": "NCIT", + "dataType": "Code", + "dataSpecification": [ + "NCIT" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.interpretation", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "The interpretation of the measurement (e.g.: Below/Within/Above age-related reference range, Absent/Low/Normal, or Positive/Negative)." + }, + { + "ordinal": "6.3.5", + "section": "6.3 Measurement", + "elementName": "Time Observed", + "elementCode": { + "system": "NCIT", + "code": "C82577" + }, + "elementCodeSystem": "NCIT", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Observation.effectiveDateTime", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "Measurement.time_observed", + "recommendedDataSpec_phenopackets": "TimeElement", + "description": "Time at which the measurement was performed." + }, + { + "ordinal": "6.3.6", + "section": "6.3 Measurement", + "elementName": "Procedure", + "elementCode": { + "system": "SNOMEDCT", + "code": "122869004" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "OntologyClass (e.g. NCIT, SNOMEDCT)" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Procedure.code", + "recommendedDataSpec_fhir": "Measurement.procedure", + "phenopacketSchemaElement_v2_0": "Measurement.procedure", + "recommendedDataSpec_phenopackets": "Measurement.procedure", + "description": "Clinical procedure performed to acquire the sample used for the measurement." + }, + { + "ordinal": "6.4.1", + "section": "6.4 Family History", + "elementName": "Family Member Pseudonym", + "elementCode": { + "system": "CustomCode", + "code": "family_member_id" + }, + "elementCodeSystem": "CustomCode", + "dataType": "Identifier", + "dataSpecification": [ + "n/a" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "FamilyMemberHistory.identifier", + "recommendedDataSpec_fhir": "Identifier", + "phenopacketSchemaElement_v2_0": "Family.Pedigree.Person.individual_id", + "recommendedDataSpec_phenopackets": "string", + "description": "A unique identifier or local pseudonym for the familymember." + }, + { + "ordinal": "6.4.2", + "section": "6.4 Family History", + "elementName": "Propositus/-a", + "elementCode": { + "system": "SNOMEDCT", + "code": "64245008" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Propositus Value Set v2.0.0", + "fhirExpression_v4_0_1": "n/a", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", + "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", + "description": "Is the individual the first affected family member who seeks medical attention for a genetic disorder, leading to the diagnosis of other family members. Disclaimer: The SCT code for propositus (64245008) refers to any gender." + }, + { + "ordinal": "6.4.3", + "section": "6.4 Family History", + "elementName": "Relationship of the Individual to the Propositus", + "elementCode": { + "system": "SNOMEDCT", + "code": "408732007" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "Family Relationship To Index Case Value Set v2.0.0", + "fhirExpression_v4_0_1": "n/a", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", + "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", + "description": "Specifies the familial relationship of the individual being evaluated to the propositus. Disclaimer: The SNOMEDCT code for propositus (64245008) refers to any gender." + }, + { + "ordinal": "6.4.4", + "section": "6.4 Family History", + "elementName": "Consanguinity", + "elementCode": { + "system": "SNOMEDCT", + "code": "842009" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe" + ], + "valueSet": "Consanguinity Value Set v2.0.0", + "fhirExpression_v4_0_1": "n/a", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "Family.consanguinous_parents", + "recommendedDataSpec_phenopackets": "boolean", + "description": "The presence of a biological relationship between parents who are related by blood, typically as first or second cousins." + }, + { + "ordinal": "6.4.5", + "section": "6.4 Family History", + "elementName": "Family Member Relationship", + "elementCode": { + "system": "SNOMEDCT", + "code": "444018008" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "FamilyMember Value Set v2.0.0", + "fhirExpression_v4_0_1": "FamilyMemberHistory.relationship.coding", + "recommendedDataSpec_fhir": "ValueSet: FamilyMember", + "phenopacketSchemaElement_v2_0": "Family.Pedigree.Person.individual_id", + "recommendedDataSpec_phenopackets": "string", + "description": "Specifies the relationship of the selected family member to the patient." + }, + { + "ordinal": "6.4.6", + "section": "6.4 Family", + "elementName": "Family Member Record Status", + "elementCode": { + "system": "HL7FHIR", + "code": "familymemberhistory.status" + }, + "elementCodeSystem": "HL7FHIR", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "FamilyHistoryStatus Value Set v2.0.0", + "fhirExpression_v4_0_1": "FamilyMemberHistory.status", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "Specifies the record’s status of the family history of a specific family member." + }, + { + "ordinal": "6.4.7", + "section": "6.4 Family", + "elementName": "Family Member Sex", + "elementCode": { + "system": "LOINC", + "code": "54123-5" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "VSe", + "VSc" + ], + "valueSet": "AdministrativeGender Value Set v2.0.0", + "fhirExpression_v4_0_1": "FamilyMemberHistory.sex", + "recommendedDataSpec_fhir": "ValueSet: AdministrativeGender", + "phenopacketSchemaElement_v2_0": "Family.Pedigree.Person.sex", + "recommendedDataSpec_phenopackets": "ValueSet: Sex", + "description": "Specifies the sex (or gender) of the specific family member. If possible, the sex assigned at birth should be selected." + }, + { + "ordinal": "6.4.8", + "section": "6.4 Family", + "elementName": "Family Member Age", + "elementCode": { + "system": "LOINC", + "code": "54141-7" + }, + "elementCodeSystem": "LOINC", + "dataType": "Integer", + "dataSpecification": [ + "Integer" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "FamilyMemberHistory.ageAge", + "recommendedDataSpec_fhir": "Age", + "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", + "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", + "description": "Records the current age of the selected family member." + }, + { + "ordinal": "6.4.9", + "section": "6.4 Family", + "elementName": "Family Member Date of Birth", + "elementCode": { + "system": "LOINC", + "code": "54124-3" + }, + "elementCodeSystem": "LOINC", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "FamilyMemberHistory.bornDate", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", + "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", + "description": "Records the date of birth of the selected family member." + }, + { + "ordinal": "6.4.10", + "section": "6.4 Family", + "elementName": "Family Member Deceased", + "elementCode": { + "system": "SNOMEDCT", + "code": "740604001" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe" + ], + "valueSet": "Deceased Value Set v2.0.0", + "fhirExpression_v4_0_1": "FamilyMemberHistory.deceased.deceasedBoolean", + "recommendedDataSpec_fhir": "boolean", + "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", + "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", + "description": "Indicates whether the selected family member is deceased." + }, + { + "ordinal": "6.4.11", + "section": "6.4 Family", + "elementName": "Family Member Cause of Death", + "elementCode": { + "system": "LOINC", + "code": "54112-8" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "ICD10CM" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "FamilyMemberHistory.condition.code & FamilyMemberHistory.condition.contributedToDeath", + "recommendedDataSpec_fhir": "Code", + "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", + "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", + "description": "Records the cause of death of the selected deceasedfamily member." + }, + { + "ordinal": "6.4.12", + "section": "6.4 Family", + "elementName": "Family Member Deceased Age", + "elementCode": { + "system": "LOINC", + "code": "92662-6" + }, + "elementCodeSystem": "LOINC", + "dataType": "Integer", + "dataSpecification": [ + "Integer" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "FamilyMemberHistory.deceasedAge", + "recommendedDataSpec_fhir": "Family.relatives", + "phenopacketSchemaElement_v2_0": "Family.relatives", + "recommendedDataSpec_phenopackets": "Family.relatives", + "description": "Records the age at which the selected family member died." + }, + { + "ordinal": "6.4.13", + "section": "6.4 Family", + "elementName": "Family Member Disease", + "elementCode": { + "system": "LOINC", + "code": "75315-2" + }, + "elementCodeSystem": "LOINC", + "dataType": "Code", + "dataSpecification": [ + "Ontology Class", + "ORDO", + "ICD-10-CM", + "ICD-11", + "MONDO", + "OMIM_p" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "FamilyMemberHistory.condition.code", + "recommendedDataSpec_fhir": "Family.relatives", + "phenopacketSchemaElement_v2_0": "Family.relatives", + "recommendedDataSpec_phenopackets": "Family.relatives", + "description": "Indicates whether the selected family member is affected by the same rare disease as the individual." + }, + { + "ordinal": "7.1", + "section": "7. Consent", + "elementName": "Consent Status", + "elementCode": { + "system": "SNOMEDCT", + "code": "309370004" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VS" + ], + "valueSet": "Consent Status Value Set v2.0.0", + "fhirExpression_v4_0_1": "Consent.status", + "recommendedDataSpec_fhir": "ValueSet: ConsentStatus", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "Indicates the current status of the consent." + }, + { + "ordinal": "7.2", + "section": "7. Consent", + "elementName": "Consent Date", + "elementCode": { + "system": "HL7FHIR", + "code": "consent.datetime" + }, + "elementCodeSystem": "HL7FHIR", + "dataType": "Date", + "dataSpecification": [ + "YYYY-MM-DD" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Consent.dateTime", + "recommendedDataSpec_fhir": "DateTime", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "Records the date when the consent was given." + }, + { + "ordinal": "7.3", + "section": "7. Consent", + "elementName": "Health Policy Monitoring", + "elementCode": { + "system": "SNOMEDCT", + "code": "386318002" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "String", + "dataSpecification": [ + "n/a" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "Consent.policy", + "recommendedDataSpec_fhir": "string", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "References to the policies that are included in thisconsent scope." + }, + { + "ordinal": "7.4", + "section": "7. Consent", + "elementName": "Agreement to be Contacted for Research", + "elementCode": { + "system": "CustomCode", + "code": "consent_contact_research" + }, + "elementCodeSystem": "CustomCode", + "dataType": "Code", + "dataSpecification": [ + "VSe" + ], + "valueSet": "Contact for Research Value Set v2.0.0", + "fhirExpression_v4_0_1": "Consent.scope.coding", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "Indicates whether the patient agrees to be contacted for research." + }, + { + "ordinal": "7.5", + "section": "7. Consent", + "elementName": "Consent to the Reuse of Data", + "elementCode": { + "system": "CustomCode", + "code": "conset_data_reuse" + }, + "elementCodeSystem": "CustomCode", + "dataType": "Code", + "dataSpecification": [ + "VSe" + ], + "valueSet": "Data Reuse Consent Value Set v2.0.0", + "fhirExpression_v4_0_1": "Consent.scope.coding", + "recommendedDataSpec_fhir": "CodeableConcept", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "Indicates whether the patient consents to the reuse of their data." + }, + { + "ordinal": "7.6", + "section": "7. Consent", + "elementName": "Biological Sample", + "elementCode": { + "system": "SNOMEDCT", + "code": "123038009" + }, + "elementCodeSystem": "SNOMEDCT", + "dataType": "Code", + "dataSpecification": [ + "VSe" + ], + "valueSet": "Biological Sample Consent Value Set v2.0.0", + "fhirExpression_v4_0_1": "n/a", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "Indicates whether a patient's biological sample is available for research." + }, + { + "ordinal": "7.7", + "section": "7. Consent", + "elementName": "Link to a Biobank", + "elementCode": { + "system": "CustomCode", + "code": "biobank_link" + }, + "elementCodeSystem": "CustomCode", + "dataType": "String", + "dataSpecification": [ + "n/a" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "n/a", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "If there is a biological sample, this data element indicates the link to the biobank of the individual's biological sample." + }, + { + "ordinal": "8.1", + "section": "8. Disability", + "elementName": "Classification of Functioning / Disability", + "elementCode": { + "system": "CustomCode", + "code": "icf_score" + }, + "elementCodeSystem": "CustomCode", + "dataType": "Code", + "dataSpecification": [ + "ICF" + ], + "valueSet": "n/a", + "fhirExpression_v4_0_1": "n/a", + "recommendedDataSpec_fhir": "n/a", + "phenopacketSchemaElement_v2_0": "n/a", + "recommendedDataSpec_phenopackets": "n/a", + "description": "Specifies the classification of the individualss functioning or disability according to the International Classification of Functioning, Disability and Health (ICF)." + } + ], + "value_sets": [ + { + "id": "SNOMEDCT:281053000", + "label": "Sex at Birth Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "248152002", + "label": "Female" + }, + { + "system": "SNOMEDCT", + "code": "248153007", + "label": "Male" + }, + { + "system": "SNOMEDCT", + "code": "184115007", + "label": "Patient sex unknown" + }, + { + "system": "SNOMEDCT", + "code": "32570691000036108", + "label": "Intersex" + }, + { + "system": "SNOMEDCT", + "code": "1220561009", + "label": "Not recorded" + } + ] + }, + { + "id": "SNOMEDCT:1296886006", + "label": "Karyotypic Sex Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "734875008", + "label": "XX" + }, + { + "system": "SNOMEDCT", + "code": "734876009", + "label": "XY" + }, + { + "system": "SNOMEDCT", + "code": "80427008", + "label": "X0" + }, + { + "system": "SNOMEDCT", + "code": "65162001", + "label": "XXY" + }, + { + "system": "SNOMEDCT", + "code": "35111009", + "label": "XXX" + }, + { + "system": "SNOMEDCT", + "code": "403760006", + "label": "XXYY" + }, + { + "system": "SNOMEDCT", + "code": "78317008", + "label": "XXXY" + }, + { + "system": "SNOMEDCT", + "code": "10567003", + "label": "XXXX" + }, + { + "system": "SNOMEDCT", + "code": "48930007", + "label": "XYY" + }, + { + "system": "SNOMEDCT", + "code": "74964007", + "label": "Other" + } + ] + }, + { + "id": "SNOMEDCT:263495000", + "label": "Gender Identity Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "446141000124107", + "label": "Female gender identity" + }, + { + "system": "SNOMEDCT", + "code": "446151000124109", + "label": "Male gender identity" + }, + { + "system": "SNOMEDCT", + "code": "394743007", + "label": "Gender unknown" + }, + { + "system": "SNOMEDCT", + "code": "33791000087105", + "label": "Identifies as nonbinary gender" + }, + { + "system": "SNOMEDCT", + "code": "1220561009", + "label": "Not recorded" + } + ] + }, + { + "id": "SNOMEDCT:278844005", + "label": "Vital Status Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "438949009", + "label": "Alive" + }, + { + "system": "SNOMEDCT", + "code": "419099009", + "label": "Dead" + }, + { + "system": "SNOMEDCT", + "code": "399307001", + "label": "Unknown - Lost in follow-up" + }, + { + "system": "SNOMEDCT", + "code": "185924006", + "label": "Unknown - Opted-out" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown - Other Reason" + } + ] + }, + { + "id": "SNOMEDCT:105727008", + "label": "Age Category Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "3658006", + "label": "Infancy" + }, + { + "system": "SNOMEDCT", + "code": "713153009", + "label": "Toddler" + }, + { + "system": "SNOMEDCT", + "code": "255398004", + "label": "Childhood" + }, + { + "system": "SNOMEDCT", + "code": "263659003", + "label": "Adolescence" + }, + { + "system": "SNOMEDCT", + "code": "41847000", + "label": "Adulthood" + }, + { + "system": "SNOMEDCT", + "code": "303112003", + "label": "Fetal period" + }, + { + "system": "SNOMEDCT", + "code": "419099009", + "label": "Dead" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + } + ] + }, + { + "id": "SNOMEDCT:278844005", + "label": "Vital Status Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "438949009", + "label": "Alive" + }, + { + "system": "SNOMEDCT", + "code": "419099009", + "label": "Dead" + }, + { + "system": "SNOMEDCT", + "code": "399307001", + "label": "Unknown - Lost in follow-up" + }, + { + "system": "SNOMEDCT", + "code": "185924006", + "label": "Unknown - Opted-out" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown - Other Reason" + } + ] + }, + { + "id": "SNOMEDCT:105727008", + "label": "Age Category Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "3658006", + "label": "Infancy" + }, + { + "system": "SNOMEDCT", + "code": "713153009", + "label": "Toddler" + }, + { + "system": "SNOMEDCT", + "code": "255398004", + "label": "Childhood" + }, + { + "system": "SNOMEDCT", + "code": "263659003", + "label": "Adolescence" + }, + { + "system": "SNOMEDCT", + "code": "41847000", + "label": "Adulthood" + }, + { + "system": "SNOMEDCT", + "code": "303112003", + "label": "Fetal period" + }, + { + "system": "SNOMEDCT", + "code": "419099009", + "label": "Dead" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + } + ] + }, + { + "id": "SNOMEDCT:723663001", + "label": "Undiagnosed RD Case Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "373066001", + "label": "Yes" + }, + { + "system": "SNOMEDCT", + "code": "373067005", + "label": "No" + } + ] + }, + { + "id": "SNOMEDCT:305058001", + "label": "Encounter Status Value Set v2.0.0", + "codes": [ + { + "system": "HL7FHIR", + "code": "planned", + "label": "Planned" + }, + { + "system": "HL7FHIR", + "code": "arrived", + "label": "Arrived" + }, + { + "system": "HL7FHIR", + "code": "triaged", + "label": "Triaged" + }, + { + "system": "HL7FHIR", + "code": "in-progress", + "label": "In Progress" + }, + { + "system": "HL7FHIR", + "code": "onleave", + "label": "On Leave" + }, + { + "system": "HL7FHIR", + "code": "finished", + "label": "Finished" + }, + { + "system": "HL7FHIR", + "code": "cancelled", + "label": "Cancelled" + }, + { + "system": "HL7FHIR", + "code": "entered-in-error", + "label": "Entered in Error" + }, + { + "system": "HL7FHIR", + "code": "unknown", + "label": "Unknown" + } + ] + }, + { + "id": "HL7FHIR:encounter.class", + "label": "Encounter Class Value Set v2.0.0", + "codes": [ + { + "system": "HL7FHIR", + "code": "AMB", + "label": "Ambulatory" + }, + { + "system": "HL7FHIR", + "code": "IMP", + "label": "Inpatient" + }, + { + "system": "HL7FHIR", + "code": "OBSENC", + "label": "Observation" + }, + { + "system": "HL7FHIR", + "code": "EMER", + "label": "Emergency" + }, + { + "system": "HL7FHIR", + "code": "VR", + "label": "Virtual" + }, + { + "system": "HL7FHIR", + "code": "HH", + "label": "Home Health" + }, + { + "system": "CustomCode", + "code": "RDC", + "label": "RD Specialist Center" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + } + ] + }, + { + "id": "HL7FHIR:99498-8", + "label": "Verification Status Value Set v2.0.0", + "codes": [ + { + "system": "HL7FHIR", + "code": "unconfirmed", + "label": "Unconfirmed" + }, + { + "system": "HL7FHIR", + "code": "provisional", + "label": "Provisional" + }, + { + "system": "HL7FHIR", + "code": "differential", + "label": "Differential" + }, + { + "system": "HL7FHIR", + "code": "confirmed", + "label": "Confirmed" + }, + { + "system": "HL7FHIR", + "code": "refuted", + "label": "Refuted" + }, + { + "system": "HL7FHIR", + "code": "entered-in-error", + "label": "Entered in Error" + } + ] + }, + { + "id": "SNOMEDCT:424850005", + "label": "Age at Onset Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "118189007", + "label": "Prenatal" + }, + { + "system": "SNOMEDCT", + "code": "3950001", + "label": "Birth" + }, + { + "system": "SNOMEDCT", + "code": "410672004", + "label": "Date" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + } + ] + }, + { + "id": "SNOMEDCT:423493009", + "label": "Age at Diagnosis Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "118189007", + "label": "Prenatal" + }, + { + "system": "SNOMEDCT", + "code": "3950001", + "label": "Birth" + }, + { + "system": "SNOMEDCT", + "code": "410672004", + "label": "Date" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + } + ] + }, + { + "id": "SNOMEDCT:363698007", + "label": "Body Site Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "442083009", + "label": "Anatomical or acquired body structure" + } + ] + }, + { + "id": "SNOMEDCT:263493007", + "label": "Clinical Status Value Set v2.0.0", + "codes": [ + { + "system": "HL7FHIR", + "code": "active", + "label": "Active" + }, + { + "system": "HL7FHIR", + "code": "recurrence", + "label": "Recurrence" + }, + { + "system": "HL7FHIR", + "code": "relapse", + "label": "Relapse" + }, + { + "system": "HL7FHIR", + "code": "inactive", + "label": "Inactive" + }, + { + "system": "HL7FHIR", + "code": "remission", + "label": "Remission" + }, + { + "system": "HL7FHIR", + "code": "resolved", + "label": "Resolved" + } + ] + }, + { + "id": "SNOMEDCT:246112005", + "label": "Severity Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "24484000", + "label": "Severe" + }, + { + "system": "SNOMEDCT", + "code": "6736007", + "label": "Moderate severity" + }, + { + "system": "SNOMEDCT", + "code": "255604002", + "label": "Mild" + } + ] + }, + { + "id": "GA4GH:progress_status", + "label": "Progress Status Value Set v2.0.0", + "codes": [ + { + "system": "GA4GH", + "code": "UNKNOWN_PROGRESS", + "label": "No information is available aboutthe diagnosis" + }, + { + "system": "GA4GH", + "code": "IN_PROGRESS", + "label": "No diagnosis has been found to date but additional differential diagnostic work is in progress." + }, + { + "system": "GA4GH", + "code": "COMPLETED", + "label": "The work on the interpretation is complete." + }, + { + "system": "GA4GH", + "code": "SOLVED", + "label": "The interpretation is complete and also considered to be a definitive diagnosis." + }, + { + "system": "GA4GH", + "code": "UNSOLVED", + "label": "The interpretation is complete but no definitive diagnosiswas found." + } + ] + }, + { + "id": "GA4GH:interpretation_status", + "label": "Interpretation Status Value Set v2.0.0", + "codes": [ + { + "system": "GA4GH", + "code": "UNKNOWN_STATUS", + "label": "No information is available about the status" + }, + { + "system": "GA4GH", + "code": "REJECTED", + "label": "The variant or gene reported here is interpreted not to be related to the diagnosis." + }, + { + "system": "GA4GH", + "code": "CANDIDATE", + "label": "The variant or gene reported here is interpreted to possibly be related to the diagnosis." + }, + { + "system": "GA4GH", + "code": "CONTRIBUTORY", + "label": "The variant or gene reported here is interpreted to be related to the diagnosis." + }, + { + "system": "GA4GH", + "code": "CAUSATIVE", + "label": "The variant or gene reported here is interpreted to be causative of the diagnosis." + } + ] + }, + { + "id": "LOINC:81304-8", + "label": "Structural Variant Analysis Method Value Set v2.0.0", + "codes": [ + { + "system": "LOINC", + "code": "LA26406-1", + "label": "Karyotyping" + }, + { + "system": "LOINC", + "code": "LA26404-6", + "label": "FISH" + }, + { + "system": "LOINC", + "code": "LA26418-6", + "label": "PCR" + }, + { + "system": "LOINC", + "code": "LA26419-4", + "label": "qPCR (real-time PCR)" + }, + { + "system": "LOINC", + "code": "LA26400-4", + "label": "SNP array" + }, + { + "system": "LOINC", + "code": "LA26813-8", + "label": "Restriction fragment length polymorphism (RFLP)" + }, + { + "system": "LOINC", + "code": "LA26810-4", + "label": "DNA hybridization" + }, + { + "system": "LOINC", + "code": "LA26398-0", + "label": "Sequencing" + }, + { + "system": "LOINC", + "code": "LA26415-2", + "label": "MLPA" + }, + { + "system": "LOINC", + "code": "LA46-8", + "label": "Other" + } + ] + }, + { + "id": "LOINC:62374-4", + "label": "Reference Genome Value Set v2.0.0", + "codes": [ + { + "system": "LOINC", + "code": "LA14032-9", + "label": "NCBI Build 34 (hg16)" + }, + { + "system": "LOINC", + "code": "LA14029-5", + "label": "GRCh37 (hg19)" + }, + { + "system": "LOINC", + "code": "LA14030-3", + "label": "NCBI Build 36.1 (hg18)" + }, + { + "system": "LOINC", + "code": "LA14031-1", + "label": "NCBI Build 35 (hg17)" + }, + { + "system": "LOINC", + "code": "LA26806-2", + "label": "GRCh38 (hg38)" + } + ] + }, + { + "id": "LOINC:53034-5", + "label": "Zygosity Value Set v2.0.0", + "codes": [ + { + "system": "LOINC", + "code": "LA6705-3", + "label": "Homozygous" + }, + { + "system": "LOINC", + "code": "LA6706-1", + "label": "Heterozygous" + }, + { + "system": "LOINC", + "code": "LA26217-2", + "label": "Compound heterozygous" + }, + { + "system": "LOINC", + "code": "LA26220-6", + "label": "Double heterozygous" + }, + { + "system": "LOINC", + "code": "LA6707-9", + "label": "Hemizygous" + }, + { + "system": "LOINC", + "code": "LA6703-8", + "label": "Heteroplasmic" + }, + { + "system": "LOINC", + "code": "LA6704-6", + "label": "Homoplasmic" + }, + { + "system": "LOINC", + "code": "LA46-8", + "label": "Other" + } + ] + }, + { + "id": "LOINC:48002-0", + "label": "Genomic Source Class Value Set v2.0.0", + "codes": [ + { + "system": "LOINC", + "code": "LA6683-2", + "label": "Germline" + }, + { + "system": "LOINC", + "code": "LA6684-0", + "label": "Somatic" + }, + { + "system": "LOINC", + "code": "LA10429-1", + "label": "Fetal" + }, + { + "system": "LOINC", + "code": "LA18194-3", + "label": "Likely germline" + }, + { + "system": "LOINC", + "code": "LA18195-0", + "label": "Likely somatic" + }, + { + "system": "LOINC", + "code": "LA18196-8", + "label": "Likely fetal" + }, + { + "system": "LOINC", + "code": "LA18197-6", + "label": "Unknown genomic origin" + }, + { + "system": "LOINC", + "code": "LA26807-0", + "label": "De novo" + } + ] + }, + { + "id": "LOINC:48019-4", + "label": "DNA Change Type Value Set v2.0.0", + "codes": [ + { + "system": "LOINC", + "code": "LA9658-1", + "label": "Wild type" + }, + { + "system": "LOINC", + "code": "LA6692-3", + "label": "Deletion" + }, + { + "system": "LOINC", + "code": "LA6686-5", + "label": "Duplication" + }, + { + "system": "LOINC", + "code": "LA6687-3", + "label": "Insertion" + }, + { + "system": "LOINC", + "code": "LA6688-1", + "label": "Insertion/Deletion" + }, + { + "system": "LOINC", + "code": "LA6689-9", + "label": "Inversion" + }, + { + "system": "LOINC", + "code": "LA6690-7", + "label": "Substitution" + } + ] + }, + { + "id": "LOINC:53037-8", + "label": "Clinical Significance ACMG Value Set v2.0.0", + "codes": [ + { + "system": "LOINC", + "code": "LA6668-3", + "label": "Pathogenic" + }, + { + "system": "LOINC", + "code": "LA26332-9", + "label": "Likely pathogenic" + }, + { + "system": "LOINC", + "code": "LA26333-7", + "label": "Uncertain significance" + }, + { + "system": "LOINC", + "code": "LA26334-5", + "label": "Likely benign" + }, + { + "system": "LOINC", + "code": "LA6675-8", + "label": "Benign" + }, + { + "system": "LOINC", + "code": "LA4489-6", + "label": "Unknown" + } + ] + }, + { + "id": "GA4GH:therapeutic_actionability", + "label": "Therapeutic Actionability Value Set v2.0.0", + "codes": [ + { + "system": "GA4GH", + "code": "UNKNOWN_ACTIONABILITY", + "label": "There is not enough information at this time to support any therapeutic actionability for this variant." + }, + { + "system": "GA4GH", + "code": "NOT_ACTIONABLE", + "label": "This variant has no therapeutic actionability." + }, + { + "system": "GA4GH", + "code": "ACTIONABLE", + "label": "This variant is known to be therapeuticallyactionalbe." + } + ] + }, + { + "id": "LOINC:93044-6", + "label": "Clinical Annotation Level Of Evidence Value Set v2.0.0", + "codes": [ + { + "system": "LOINC", + "code": "LA30200-2", + "label": "Very strong evidence pathogenic" + }, + { + "system": "LOINC", + "code": "LA30201-0", + "label": "Strong evidence pathogenic" + }, + { + "system": "LOINC", + "code": "LA30202-8", + "label": "Moderate evidence pathogenic" + }, + { + "system": "LOINC", + "code": "LA30203-6", + "label": "Supporting evidence pathogenic" + }, + { + "system": "LOINC", + "code": "LA30204-4", + "label": "Supporting evidence benign" + }, + { + "system": "LOINC", + "code": "LA30205-1", + "label": "Strong evidence benign" + }, + { + "system": "LOINC", + "code": "LA30206-9", + "label": "Stand-alone evidence pathogenic" + }, + { + "system": "LOINC", + "code": "LA30207-7", + "label": "Stand-alone evidence benign" + }, + { + "system": "LOINC", + "code": "LA26333-7", + "label": "Uncertain significance" + } + ] + }, + { + "id": "CustomCode:phenotypicfeature.excluded", + "label": "Phenotype Status Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "410605003", + "label": "Confirmed present" + }, + { + "system": "SNOMEDCT", + "code": "723511001", + "label": "Refuted" + } + ] + }, + { + "id": "HP:0003674", + "label": "Onset Category Value Set v2.0.0", + "codes": [ + { + "system": "HP", + "code": "0011460", + "label": "Embryonal onset" + }, + { + "system": "HP", + "code": "0011461", + "label": "Fetal onset" + }, + { + "system": "HP", + "code": "0003577", + "label": "Congenital onset" + }, + { + "system": "HP", + "code": "0003623", + "label": "Neonatal onset" + }, + { + "system": "HP", + "code": "0003593", + "label": "Infantile onset" + }, + { + "system": "HP", + "code": "0011463", + "label": "Childhood onset" + }, + { + "system": "HP", + "code": "0003621", + "label": "Juvenile onset" + }, + { + "system": "HP", + "code": "0011462", + "label": "Young adult onset" + }, + { + "system": "HP", + "code": "0003596", + "label": "Middle age onset" + }, + { + "system": "HP", + "code": "0003584", + "label": "Late onset" + } + ] + }, + { + "id": "HP:0011008", + "label": "Temporal Pattern Value Set v2.0.0", + "codes": [ + { + "system": "HP", + "code": "0011009", + "label": "Acute" + }, + { + "system": "HP", + "code": "0011010", + "label": "Chronic" + }, + { + "system": "HP", + "code": "0031914", + "label": "Fluctuating" + }, + { + "system": "HP", + "code": "0025297", + "label": "Prolonged" + }, + { + "system": "HP", + "code": "0031796", + "label": "Recurrent" + }, + { + "system": "HP", + "code": "0031915", + "label": "Stable" + }, + { + "system": "HP", + "code": "0011011", + "label": "Subacute" + }, + { + "system": "HP", + "code": "0025153", + "label": "Transient" + } + ] + }, + { + "id": "HP:0012824", + "label": "Severity Value Set v2.0.0", + "codes": [ + { + "system": "HP", + "code": "0012827", + "label": "Borderline" + }, + { + "system": "HP", + "code": "0012825", + "label": "Mild" + }, + { + "system": "HP", + "code": "0012826", + "label": "Moderate" + }, + { + "system": "HP", + "code": "0012829", + "label": "Profound" + }, + { + "system": "HP", + "code": "0012828", + "label": "Severe" + } + ] + }, + { + "id": "SNOMEDCT:64245008", + "label": "Propositus Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "373066001", + "label": "Yes" + }, + { + "system": "SNOMEDCT", + "code": "373067005", + "label": "No" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + }, + { + "system": "SNOMEDCT", + "code": "1220561009", + "label": "Not recorded" + } + ] + }, + { + "id": "SNOMEDCT:408732007", + "label": "Family Relationship To Index Case Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "65656005", + "label": "Natural mother" + }, + { + "system": "SNOMEDCT", + "code": "9947008", + "label": "Natural father" + }, + { + "system": "SNOMEDCT", + "code": "83420006", + "label": "Natural daughter" + }, + { + "system": "SNOMEDCT", + "code": "113160008", + "label": "Natural son" + }, + { + "system": "SNOMEDCT", + "code": "60614009", + "label": "Natural brother" + }, + { + "system": "SNOMEDCT", + "code": "73678001", + "label": "Natural sister" + }, + { + "system": "SNOMEDCT", + "code": "11286003", + "label": "Twin sibling" + }, + { + "system": "SNOMEDCT", + "code": "45929001", + "label": "Half-brother" + }, + { + "system": "SNOMEDCT", + "code": "2272004", + "label": "Half-sister" + }, + { + "system": "SNOMEDCT", + "code": "62296006", + "label": "Natural grandfather" + }, + { + "system": "SNOMEDCT", + "code": "17945006", + "label": "Natural grandmother" + }, + { + "system": "SNOMEDCT", + "code": "1220561009", + "label": "Not recorded" + } + ] + }, + { + "id": "SNOMEDCT:842009", + "label": "Consanguinity Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "373066001", + "label": "Yes" + }, + { + "system": "SNOMEDCT", + "code": "373067005", + "label": "No" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + }, + { + "system": "SNOMEDCT", + "code": "1220561009", + "label": "Not recorded" + } + ] + }, + { + "id": "SNOMEDCT:444018008", + "label": "FamilyMember Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "65656005", + "label": "Natural mother" + }, + { + "system": "SNOMEDCT", + "code": "9947008", + "label": "Natural father" + }, + { + "system": "SNOMEDCT", + "code": "83420006", + "label": "Natural daughter" + }, + { + "system": "SNOMEDCT", + "code": "113160008", + "label": "Natural son" + }, + { + "system": "SNOMEDCT", + "code": "60614009", + "label": "Natural brother" + }, + { + "system": "SNOMEDCT", + "code": "73678001", + "label": "Natural sister" + }, + { + "system": "SNOMEDCT", + "code": "11286003", + "label": "Twin sibling" + }, + { + "system": "SNOMEDCT", + "code": "45929001", + "label": "Half-brother" + }, + { + "system": "SNOMEDCT", + "code": "2272004", + "label": "Half-sister" + }, + { + "system": "SNOMEDCT", + "code": "62296006", + "label": "Natural grandfather" + }, + { + "system": "SNOMEDCT", + "code": "17945006", + "label": "Natural grandmother" + }, + { + "system": "SNOMEDCT", + "code": "1220561009", + "label": "Not recorded" + } + ] + }, + { + "id": "HL7FHIR:familymemberhistory.status", + "label": "FamilyHistoryStatus Value Set v2.0.0", + "codes": [ + { + "system": "HL7FHIR", + "code": "partial", + "label": "Partial" + }, + { + "system": "HL7FHIR", + "code": "completed", + "label": "Completed" + }, + { + "system": "HL7FHIR", + "code": "entered-in-error", + "label": "Entered in Error" + }, + { + "system": "HL7FHIR", + "code": "health-unknown", + "label": "Health Unknown" + } + ] + }, + { + "id": "SNOMEDCT:54123-5", + "label": "AdministrativeGender Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "248152002", + "label": "Female" + }, + { + "system": "SNOMEDCT", + "code": "248153007", + "label": "Male" + }, + { + "system": "SNOMEDCT", + "code": "184115007", + "label": "Patient sex unknown" + }, + { + "system": "SNOMEDCT", + "code": "32570691000036108", + "label": "Intersex" + }, + { + "system": "SNOMEDCT", + "code": "1220561009", + "label": "Not recorded" + } + ] + }, + { + "id": "SNOMEDCT:740604001", + "label": "Deceased Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "373066001", + "label": "Yes" + }, + { + "system": "SNOMEDCT", + "code": "373067005", + "label": "No" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + } + ] + }, + { + "id": "HL7FHIR:309370004", + "label": "Consent Status Value Set v2.0.0", + "codes": [ + { + "system": "HL7FHIR", + "code": "draft", + "label": "Pending" + }, + { + "system": "HL7FHIR", + "code": "proposed", + "label": "Proposed" + }, + { + "system": "HL7FHIR", + "code": "active", + "label": "Active" + }, + { + "system": "HL7FHIR", + "code": "rejected", + "label": "Rejected" + }, + { + "system": "HL7FHIR", + "code": "inactive", + "label": "Inactive" + }, + { + "system": "HL7FHIR", + "code": "entered-in-error", + "label": "Entered in Error" + } + ] + }, + { + "id": "SNOMEDCT:consent_contact_research", + "label": "Contact for Research Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "373066001", + "label": "Yes" + }, + { + "system": "SNOMEDCT", + "code": "373067005", + "label": "No" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + } + ] + }, + { + "id": "SNOMEDCT:conset_data_reuse", + "label": "Data Reuse Consent Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "373066001", + "label": "Yes" + }, + { + "system": "SNOMEDCT", + "code": "373067005", + "label": "No" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + } + ] + }, + { + "id": "SNOMEDCT:123038009", + "label": "Biological Sample Consent Value Set v2.0.0", + "codes": [ + { + "system": "SNOMEDCT", + "code": "373066001", + "label": "Yes" + }, + { + "system": "SNOMEDCT", + "code": "373067005", + "label": "No" + }, + { + "system": "SNOMEDCT", + "code": "261665006", + "label": "Unknown" + } + ] + } + ] +} \ No newline at end of file diff --git a/src/rd_cdm/instances/v2_0_2/jsons/value_sets.json b/src/rd_cdm/instances/jsons/value_sets.json similarity index 100% rename from src/rd_cdm/instances/v2_0_2/jsons/value_sets.json rename to src/rd_cdm/instances/jsons/value_sets.json diff --git a/src/rd_cdm/instances/v2_0_2/rd_cdm_v2_0_1.yaml b/src/rd_cdm/instances/rd_cdm.yaml similarity index 99% rename from src/rd_cdm/instances/v2_0_2/rd_cdm_v2_0_1.yaml rename to src/rd_cdm/instances/rd_cdm.yaml index 0b85150..cf21a09 100644 --- a/src/rd_cdm/instances/v2_0_2/rd_cdm_v2_0_1.yaml +++ b/src/rd_cdm/instances/rd_cdm.yaml @@ -1,23 +1,25 @@ +rd_cdm_version: 2.0.3 +rd_cdm_date: 2026-03-24 code_systems: # Codesystems that encode elements and value set items - id: SNOMEDCT namespace_iri: http://purl.bioontology.org/ontology/SNOMEDCT/ - version: "SNOMEDCT_US_2024_09_01" + version: "2025AB" title: "Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT)" - id: LOINC namespace_iri: http://loinc.org - version: "LNC278" + version: "281" title: "Logical Observation Identifiers Names and Codes (LOINC)" - id: HP namespace_iri: http://purl.obolibrary.org/obo/HP - version: "2025-05-06" + version: "2026-02-16" title: "Human Phenotype Ontology (HPO)" - id: NCIT namespace_iri: http://purl.obolibrary.org/obo/NCIT/ - version: "24.01e" + version: "26.02d" title: "NCI Thesaurus (NCIT) OBO Edition" - id: HL7FHIR @@ -32,18 +34,18 @@ code_systems: - id: CustomCode namespace_iri: https://github.com/BIH-CEI/rd-cdm - version: "v2.0.0" - title: "Custom Code System RD CDM v2.0.0" + version: "v2.0" + title: "Custom Code System RD CDM v2.0" # Codesystems that can encode values of data elements - id: NCBITAXON namespace_iri: http://purl.obolibrary.org/obo/NCBITAXON/ - version: "NCBI2024_04_02" + version: "2025_04_10" title: "NCBI organismal classification" - id: GENO namespace_iri: http://purl.obolibrary.org/obo/GENO/ - version: "2023-10-08" + version: "2026-02-02" title: "GENO – The Genotype Ontology" - id: SO @@ -53,27 +55,27 @@ code_systems: - id: UO namespace_iri: http://purl.obolibrary.org/obo/UO/ - version: "2023-05-25" + version: "2026-01-16" title: "Units Ontology (UO)" - id: ECO namespace_iri: http://purl.obolibrary.org/obo/ECO/ - version: "2025-06-23" + version: "releases/2025-06-23" title: "Evidence & Conclusion Ontology (ECO)" - id: ICD10CM namespace_iri: http://purl.bioontology.org/ontology/ICD10CM/ - version: "CD10CM_2025" + version: "2026" title: "International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)" - id: MONDO namespace_iri: http://purl.obolibrary.org/obo/MONDO/ - version: "2025-06-03" + version: "2026-03-03" title: "Mondo Disease Ontology" - id: ORDO namespace_iri: http://purl.obolibrary.org/obo/ORDO/ - version: "4.7" + version: "4.8" title: "Orphanet Rare Disease Ontology (ORDO)" - id: HGNC @@ -83,7 +85,7 @@ code_systems: - id: OMIM namespace_iri: http://purl.bioontology.org/ontology/OMIM/ - version: "OMIM2024_08_09" + version: "2025_08_04" title: "Online Mendelian Inheritance in Man (OMIM)" - id: HGVS @@ -161,9 +163,9 @@ data_elements: section: 2. Personal Information elementName: Sex at Birth elementCode: - system: SNOMEDCT - code: '281053000' - elementCodeSystem: SNOMEDCT + system: LOINC + code: '76689-9' + elementCodeSystem: LOINC dataType: Code dataSpecification: - VSe @@ -1910,7 +1912,7 @@ value_sets: codes: - system: LOINC code: 'LA9658-1' - label: Wild Type + label: Wild type - system: LOINC code: 'LA6692-3' label: Deletion @@ -1968,7 +1970,7 @@ value_sets: codes: - system: LOINC code: 'LA30200-2' - label: Very Strong evidence pathogenic + label: Very strong evidence pathogenic - system: LOINC code: 'LA30201-0' label: Strong evidence pathogenic diff --git a/src/rd_cdm/instances/v2_0_2/csvs/rd_cdm_v2_0_2.csv b/src/rd_cdm/instances/v2_0_2/csvs/rd_cdm_v2_0_2.csv deleted file mode 100644 index 7dc6b43..0000000 --- a/src/rd_cdm/instances/v2_0_2/csvs/rd_cdm_v2_0_2.csv +++ /dev/null @@ -1,141 +0,0 @@ -_section,codes,dataSpecification,dataType,description,elementCode,elementCodeSystem,elementName,fhirExpression_v4_0_1,id,label,namespace_iri,ordinal,phenopacketSchemaElement_v2_0,recommendedDataSpec_fhir,recommendedDataSpec_phenopackets,section,title,valueSet,version -code_systems,,,,,,,,,SNOMEDCT,,http://purl.bioontology.org/ontology/SNOMEDCT/,,,,,,Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT),,SNOMEDCT_US_2024_09_01 -code_systems,,,,,,,,,LOINC,,http://loinc.org,,,,,,Logical Observation Identifiers Names and Codes (LOINC),,LNC278 -code_systems,,,,,,,,,HP,,http://purl.obolibrary.org/obo/HP,,,,,,Human Phenotype Ontology (HPO),,2025-05-06 -code_systems,,,,,,,,,NCIT,,http://purl.obolibrary.org/obo/NCIT/,,,,,,NCI Thesaurus (NCIT) OBO Edition,,24.01e -code_systems,,,,,,,,,HL7FHIR,,http://hl7.org/fhir/,,,,,,"Health Level Seven Fast Healthcare Interoperability Resources, Release 4",,v4.0.1 -code_systems,,,,,,,,,GA4GH,,https://ga4gh.github.io/phenopacket-v2/,,,,,,Global Alliance for Genomics and Health Phenopackets Schema,,v2.0 -code_systems,,,,,,,,,CustomCode,,https://github.com/BIH-CEI/rd-cdm,,,,,,Custom Code System RD CDM v2.0.0,,v2.0.0 -code_systems,,,,,,,,,NCBITAXON,,http://purl.obolibrary.org/obo/NCBITAXON/,,,,,,NCBI organismal classification,,NCBI2024_04_02 -code_systems,,,,,,,,,GENO,,http://purl.obolibrary.org/obo/GENO/,,,,,,GENO – The Genotype Ontology,,2023-10-08 -code_systems,,,,,,,,,SO,,http://purl.obolibrary.org/obo/SO/,,,,,,Sequence Ontology,,2.6 -code_systems,,,,,,,,,UO,,http://purl.obolibrary.org/obo/UO/,,,,,,Units Ontology (UO),,2023-05-25 -code_systems,,,,,,,,,ECO,,http://purl.obolibrary.org/obo/ECO/,,,,,,Evidence & Conclusion Ontology (ECO),,2025-06-23 -code_systems,,,,,,,,,ICD10CM,,http://purl.bioontology.org/ontology/ICD10CM/,,,,,,"International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)",,CD10CM_2025 -code_systems,,,,,,,,,MONDO,,http://purl.obolibrary.org/obo/MONDO/,,,,,,Mondo Disease Ontology,,2025-06-03 -code_systems,,,,,,,,,ORDO,,http://purl.obolibrary.org/obo/ORDO/,,,,,,Orphanet Rare Disease Ontology (ORDO),,4.7 -code_systems,,,,,,,,,HGNC,,http://identifiers.org/hgnc/,,,,,,HUGO Gene Nomenclature Committee (HGNC),,2024-08-23 -code_systems,,,,,,,,,OMIM,,http://purl.bioontology.org/ontology/OMIM/,,,,,,Online Mendelian Inheritance in Man (OMIM),,OMIM2024_08_09 -code_systems,,,,,,,,,HGVS,,https://varnomen.hgvs.org/,,,,,,Human Genome Variation Society Nomenclature,,21.0.0 -code_systems,,,,,,,,,ICD11,,http://id.who.int/icd/release/11/mms/,,,,,,"International Classification of Diseases, Eleventh Revision (ICD-11)",,2024-09-01 -code_systems,,,,,,,,,ISO3166,,https://www.iso.org/iso-3166-country-codes.html,,,,,,International Organization for Standardization – ISO 3166 Country Codes,,2020(en) -code_systems,,,,,,,,,ICF,,https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health,,,,,,"International Classification of Functioning, Disability and Health (ICF)",,1.0.2 -data_elements,,['n/a'],Identifier,The (local) patient-related identification code.,"{'system': 'SNOMEDCT', 'code': '422549004'}",SNOMEDCT,Pseudonym,Patient.identifier.value,,,,1.1,Individual.id,n/a,string,1. Formal Criteria,,, -data_elements,,['YYYY-MM-DD'],Date,The date of admission or data capture of the individual.,"{'system': 'SNOMEDCT', 'code': '399423000'}",SNOMEDCT,Date of Admission,Encounter.period.start,,,,1.2,Individual.time_at_last_encounter,n/a,TimeElement,1. Formal Criteria,,, -data_elements,,"['YYYY', 'YYYY-MM', 'YYYY-MM-DD']",Date,The individual's date of birth.,"{'system': 'SNOMEDCT', 'code': '184099003'}",SNOMEDCT,Date of Birth,Patient.birthDate,,,,2.1,Individual.date_of_birth,n/a,TimeElement,2. Personal Information,,, -data_elements,,"['VSe', 'VSc']",Code,The individual's sex that was assigned at birth.,"{'system': 'SNOMEDCT', 'code': '281053000'}",SNOMEDCT,Sex at Birth,Patient.extension:individual-recordedSexOrGender,,,,2.2,Individual.sex,Recorded Sex Or Gender Type,Sex,2. Personal Information,,Sex at Birth Value Set v2.0.0, -data_elements,,['VSc'],Code,The chromosomal sex of an individual.,"{'system': 'SNOMEDCT', 'code': '1296886006'}",SNOMEDCT,Karyotypic Sex,Observation.value,,,,2.3,Individual.karyotypic_sex,n/a,Karyotypic Sex,2. Personal Information,,Karyotypic Sex Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The self-assigned gender of the individual.,"{'system': 'SNOMEDCT', 'code': '263495000'}",SNOMEDCT,Gender Identity,Patient.extension:individual-genderIdentity,,,,2.4,Individual.gender,Gender Identity,OntologyClass,2. Personal Information,,Gender Identity Value Set v2.0.0, -data_elements,,['VS'],Code,The individual's country of birth.,"{'system': 'SNOMEDCT', 'code': '370159000'}",SNOMEDCT,Country of Birth,Patient.extension:patient-birthPlace,,,,2.5,n/a,DataType: Address,n/a,2. Personal Information,,, -data_elements,,"['VSe', 'VSc']",Code,The individual’s general clinical status orvital status.,"{'system': 'SNOMEDCT', 'code': '278844005'}",SNOMEDCT,Vital Status,Patient.deceased.deceasedBoolean|Observation.value,,,,3.1,Individual.VitalStatus.status,Boolean|Code,Value Set: VitalStatus.Status,3. Patient Status,,Vital Status Value Set v2.0.0, -data_elements,,"['YYYY', 'YYYY-MM', 'YYYY-MM-DD']",Date,"If deceased, the individual’s date of death.","{'system': 'SNOMEDCT', 'code': '398299004'}",SNOMEDCT,Time of Death,Patient.deceasedDateTime,,,,3.2,Individual.VitalStatus.time_of_death,DateTime,TimeElement,3. Patient Status,,, -data_elements,,['ICD-10CM'],Code,"If deceased, the individual’s primary cause of death.","{'system': 'SNOMEDCT', 'code': '184305005'}",SNOMEDCT,Cause of Death,Observation.value.coding.code,,,,3.3,Individual.VitalStatus.cause_of_death,Code|CodeableConcept,OntologyClass,3. Patient Status,,, -data_elements,,['VSe'],Code,The individual's age category at thetime of data capture.,"{'system': 'SNOMEDCT', 'code': '105727008'}",SNOMEDCT,Age Category,Observation.value.coding.code,,,,3.4,Individual.time_at_last_encounter,CodableConcept,TimeElement,3. Patient Status,,Age Category Value Set v2.0.0, -data_elements,,['XX+X'],String,"The duration of the pregnancy in weeks and days,formatted as XX+X (weeks+days).","{'system': 'SNOMEDCT', 'code': '412726003'}",SNOMEDCT,Length of Gestation at Birth [weeks+days],Observation.component:weeks.valueQuantity|Observation.component:days.valueQuantity,,,,3.5,n/a,Quantity,n/a,3. Patient Status,,, -data_elements,,['VSe'],Code,Identifies cases where an RD diagnosis has notbeen established.,"{'system': 'SNOMEDCT', 'code': '723663001'}",SNOMEDCT,Undiagnosed RD Case,(Condition.code),,,,3.6,(Disease.term),Code(e.g. ORDO:616874 - Rare disorderwithout a determined diagnosis afterfull investigation),(OntologyClass (e.g. ORDO:616874 - Rare disorder without a determineddiagnosis after full investigation)),3. Patient Status,,Undiagnosed RD Case Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,The beginning of an encounter of the individual.,"{'system': 'HL7FHIR', 'code': 'encounter.period.start'}",HL7FHIR,Encounter Start,Encounter.period.start,,,,4.1,n/a,DateTime,n/a,4. Care Pathway,,, -data_elements,,['YYYY-MM-DD'],Date,The end of an encounter of the individual.,"{'system': 'HL7FHIR', 'code': 'encounter.period.end'}",HL7FHIR,Encounter End,Encounter.period.end,,,,4.2,n/a,DateTime,n/a,4. Care Pathway,,, -data_elements,,"['VSe', 'VSc']",Code,The status of an encounter of the individual at thetime of data capture.,"{'system': 'SNOMEDCT', 'code': '305058001'}",SNOMEDCT,Encounter Status,Encounter.status,,,,4.3,n/a,ValueSet: EncounterStatus,n/a,4. Care Pathway,,Encounter Status Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The class of an encounter of the individualat the time of data capture.,"{'system': 'HL7FHIR', 'code': 'encounter.class'}",HL7FHIR,Encounter Class,Encounter.class,,,,4.4,n/a,ValueSet: EncounterClass,n/a,4. Care Pathway,,Encounter Class Value Set v2.0.0, -data_elements,,"['Ontology Class (MONDO, ORDO, ICD-10, ICD-11, OMIM_g, OMIM_p)']",Code,"A disease that the individual was affected by. If agenetic diagnosis or subtypes were diagnosed, please also provide the respective OMIM_g and OMIM_p codes.","{'system': 'SNOMEDCT', 'code': '64572001'}",SNOMEDCT,Disease,Condition.code,,,,5.1,Disease.term,Code,OntologyClass,5. Disease,,n/a, -data_elements,,['VS'],Code,The verification status of the disease.,"{'system': 'LOINC', 'code': '99498-8'}",LOINC,Verification Status,Condition.verificationStatus,,,,5.2,(Disease.excluded),ValueSet: Condition Verficication Status,boolean,5. Disease,,Verification Status Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The age at the onset of the first symptomsor signs of the disease.,"{'system': 'SNOMEDCT', 'code': '424850005'}",SNOMEDCT,Age at Onset,Condition.onsetString orObservation.valueCodeableConcept,,,,5.3,Disease.onset,Disease.onset,Disease.onset,5. Disease,,Age at Onset Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,The date at onset of first symptoms orsigns of the disease.,"{'system': 'SNOMEDCT', 'code': '298059007'}",SNOMEDCT,Date of Onset,Condition.onset,,,,5.4,Disease.onset,DateTime,TimeElement,5. Disease,,n/a, -data_elements,,"['VSe', 'VSc']",Code,The individual’s age when the diagnosis was made.,"{'system': 'SNOMEDCT', 'code': '423493009'}",SNOMEDCT,Age at Diagnosis,Observation.value,,,,5.5,(Disease.onset),CodeableConcept,(TimeElement),5. Disease,,Age at Diagnosis Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,The date on which the disease was determined.,"{'system': 'SNOMEDCT', 'code': '432213005'}",SNOMEDCT,Date of Diagnosis,Condition.recordedDate,,,,5.6,(Disease.onset),DateTime,(TimeElement),5. Disease,,n/a, -data_elements,,['VS'],Code,The specific body site affected by disease is encodedusing all descendants of SCT Body Structure (123037004).,"{'system': 'SNOMEDCT', 'code': '363698007'}",SNOMEDCT,Body Site,Condition.bodySite.coding:SNOMEDCT-ct,,,,5.7,Disease.primary_site,CodeableConcept,OntologyClass,5. Disease,,Body Site Value Set v2.0.0, -data_elements,,['VS'],Code,"The clinical status of the disease indicates whetherit is active, inactive, or resolved.","{'system': 'SNOMEDCT', 'code': '263493007'}",SNOMEDCT,Clinical Status,Condition.clinicalStatus,,,,5.8,n/a,ValueSet: ClinicalStatus,n/a,5. Disease,,Clinical Status Value Set v2.0.0, -data_elements,,['VS'],Code,The severity of the disease is categorised byclinical evaluation.,"{'system': 'SNOMEDCT', 'code': '246112005'}",SNOMEDCT,Severity,Condition.severity,,,,5.9,n/a,ValueSet: ConditionSeverity,n/a,5. Disease,,Severity Value Set v2.0.0, -data_elements,,"['OMIM_p', 'MONDO']",Code,The genomic diagnoses can correspond to the diagnoseddisease in (5.1) if the same OMIM codes are used.,"{'system': 'SNOMEDCT', 'code': '106221001'}",SNOMEDCT,Genomic Diagnosis,Condition.code,,,,6.1.1,Interpretation.Diagnosis.disease,Code,OntologyClass,6. Genetic Findings,,n/a, -data_elements,,['VS'],Code,The interpretation has a ProgressStatus that refers tothe status of the attempted diagnosis.,"{'system': 'GA4GH', 'code': 'progress_status'}",GA4GH,Progress Status of Interpretation,Condition.extension,,,,6.1.2,Interpretation.progress_status,VS: GA4GH ProgressStatus,ValueSet: ProgressStatus,6. Genetic Findings,,Progress Status Value Set v2.0.0, -data_elements,,['VS'],Code,An enumeration that describes the conclusion made about the genomic interpretation.,"{'system': 'GA4GH', 'code': 'interpretation_status'}",GA4GH,Interpretation Status,Condition.extension,,,,6.1.3,GenomicInterpretation.interpretation_status,VS: GA4GH InterpretationStatus,ValueSet: InterpretationStatus,6. Genetic Findings,,Interpretation Status Value Set v2.0.0, -data_elements,,"['VS', 'LOINC']",Code,The method used to analyse structural variants in the genome.,"{'system': 'LOINC', 'code': '81304-8'}",LOINC,Structural Variant Analysis Method,Observation.method,,,,6.1.4,n/a,CodeableConcept,n/a,6. Genetic Findings,,Structural Variant Analysis Method Value Set v2.0.0, -data_elements,,['VS'],Code,The reference genome used for analysing the genetic variant.,"{'system': 'LOINC', 'code': '62374-4'}",LOINC,Reference Genome,Observation.component:reference-sequence-assembly,,,,6.1.5,n/a,CodeableConcept,n/a,6. Genetic Findings,,Reference Genome Value Set v2.0.0, -data_elements,,['n/a'],String,An unvalidated (HGVS) string that describes the variant change,"{'system': 'LOINC', 'code': 'LP7824-8'}",LOINC,Genetic Mutation String,Observation.component:Variant.valueString,,,,6.1.6,VariationDescriptor.Extension.value,string,string,6. Genetic Findings,,n/a, -data_elements,,['g.HGVS'],Code,The specific change in the genomic DNA sequence encoded with a validated g.HGVS expression.,"{'system': 'LOINC', 'code': '81290-9'}",LOINC,Genomic DNA Change,Observation.component:Variant.valueCode,,,,6.1.7,VariationDescriptor.Expression.value,Code,string,6. Genetic Findings,,n/a, -data_elements,,['c.HGVS'],Code,The specific change in the DNA sequence at the nucleotide level with a validated c.HGVS expression.,"{'system': 'LOINC', 'code': '48004-6'}",LOINC,Sequence DNA Change,Observation.component:Variant.valueCode,,,,6.1.8,VariationDescriptor.Expression.value,Code,string,6. Genetic Findings,,n/a, -data_elements,,['p.HGVS'],Code,The specific change in the amino acid sequence resulting from agenetic variant as a validated p.HGVS expression.,"{'system': 'LOINC', 'code': '48005-3'}",LOINC,Amino Acid Change,Observation.component:Variant.valueCode,,,,6.1.9,VariationDescriptor.Expression.value,Code,string,6. Genetic Findings,,n/a, -data_elements,,['HGNC'],Code,The specific gene or genes that were analysed or identified in the study.,"{'system': 'LOINC', 'code': '48018-6'}",LOINC,Gene,Observation.component:Gene,,,,6.1.10,GeneDescriptor.value_id,Code,string,6. Genetic Findings,,n/a, -data_elements,,"['VSe', 'VSc', 'LOINC']",Code,The zygosity of the genetic variant.,"{'system': 'LOINC', 'code': '53034-5'}",LOINC,Zygosity,Observation.component:geneticsAllele.State,,,,6.1.11,VariationDescriptor.allelic_state,VS: Allelic State,OntologyClass,6. Genetic Findings,,Zygosity Value Set v2.0.0, -data_elements,,['VS'],Code,"The classification of the genomic source, such as germline, somatic, or other origins.","{'system': 'LOINC', 'code': '48002-0'}",LOINC,Genomic Source Class,Observation.component:GenomicSourceClass,,,,6.1.12,n/a,CodeableConcept,n/a,6. Genetic Findings,,Genomic Source Class Value Set v2.0.0, -data_elements,,['VS'],Code,"The variant’s type of DNA change, such as point mutation, deletion, insertion, or other types.","{'system': 'LOINC', 'code': '48019-4'}",LOINC,DNA Change Type,Observation.component:Variant.Type,,,,6.1.13,n/a,Code,n/a,6. Genetic Findings,,DNA Change Type Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,"The clinical significance of the genetic variant, indicating its impact on health and disease.","{'system': 'LOINC', 'code': '53037-8'}",LOINC,Clinical Significance [ACMG],Observation.component:Variant.Interpretation,,,,6.1.14,VariantInterpretation.acmg_pathogenicity_classification,,ValueSet: AcmgPathogenicityClassification,6. Genetic Findings,,Clinical Significance ACMG Value Set v2.0.0, -data_elements,,['VS'],Code,"An enumeration flagging the variant as being a candidate for treatment or clinical intervention, which could improve the clinical outcome.","{'system': 'GA4GH', 'code': 'therapeutic_actionability'}",GA4GH,Therapeutic Actionability,n/a,,,,6.1.15,VariantInterpretation.therapeutic_actionability,n/a,ValueSet: TherapeuticActionability,6. Genetic Findings,,Therapeutic Actionability Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The level of evidence supporting the clinical annotation of the genetic variant.,"{'system': 'LOINC', 'code': '93044-6'}",LOINC,Clinical Annotation Level Of Evidence,Observation.extension:Variant.Interpretation,,,,6.1.16,n/a,CodeableConcept,n/a,6. Genetic Findings,,Clinical Annotation Level Of Evidence Value Set v2.0.0, -data_elements,,['HPO'],Code,An observed physical and clinical characteristicencoded with HPO.,"{'system': 'SNOMEDCT', 'code': '8116006'}",SNOMEDCT,Phenotypic Feature,Observation.code,,,,6.2.1,PhenotypicFeature.type,Code,OntologyClass,6. Phenotypic Feature,,n/a, -data_elements,,"['VSe', 'VSc']",Code,"The current status of the phenotypic feature, indicating whether it is confirmed or refuted.","{'system': 'SNOMEDCT', 'code': '363778006'}",SNOMEDCT,Status,Observation.status,,,,6.2.2,PhenotypicFeature.excluded,ValueSet: ObservationStatus,boolean,6.2 Phenotypic Feature,,Phenotype Status Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,The date on which the phenotypic feature was observed or recorded. We recommend capturing the time acharacteristic was observed.,"{'system': 'SNOMEDCT', 'code': '439272007:704321009=363778006'}",SNOMEDCT,Determination Date,Observation.effectiveDateTime,,,,6.2.3,PhenotypicFeature.onset,DateTime,TimeElement,6. Phenotypic Feature,,n/a, -data_elements,,['YYYY-MM-DD'],Date,Time at which the feature resolved or abated.,"{'system': 'HP', 'code': '0034382'}",HP,Resolution Date,Observation.effectiveDateTime,,,,6.2.4,PhenotypicFeature.resolution,DateTime,TimeElement,6.2 Phenotypic Feature,,n/a, -data_elements,,"['VSe', 'VSc']",Code,Time at which the feature was first observed within HPO onset categories.,"{'system': 'HP', 'code': '0003674'}",HP,Onset Category,Observation.category,,,,6.2.5,PhenotypicFeature.onset,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,Onset Category Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,The speed at which disease manifestations appear and develop.,"{'system': 'HP', 'code': '0011008'}",HP,Temporal Pattern,Observation.interpretation,,,,6.2.6,PhenotypicFeature.modifiers,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,Temporal Pattern Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,A description of the severity of the feature.,"{'system': 'HP', 'code': '0012824'}",HP,Severity,Observation.interpretation,,,,6.2.7,PhenotypicFeature.severity,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,Severity Value Set v2.0.0, -data_elements,,"['OntologyClass (HPO, NCBITAXON, SCT)']",Code,"Any number of additional modifiers describing a specific phenotypic feature further, such as severity (HP:0012824), clinical modifiers (HP:0012823), or linking causative infectious agents using the NCBITAXON Ontology.","{'system': 'GA4GH', 'code': 'phenotypicfeature.modifier'}",GA4GH,Modifiers,Suggested: Observation.extension,,,,6.2.8,PhenotypicFeature.modifiers,CodeableConcept,list of OntologyClass,6. Phenotypic Feature,,n/a, -data_elements,,['ECO'],Code,The evidence for an assertion of the observation of a type defined within the Evidence & Conclusion Ontology (ECO).,"{'system': 'GA4GH', 'code': 'phenotypicfeature.evidence'}",GA4GH,Evidence,Observation.method,,,,6.2.9,PhenotypicFeature.evidence,CodeableConcept,OntologyClass,6.2 Phenotypic Feature,,n/a, -data_elements,,['OntologyClass (e.g. LOINC)'],Code,A class that describes the assay used to producethe measurement.,"{'system': 'NCIT', 'code': 'C60819'}",NCIT,Assay,Observation.code,,,,6.3.1,Measurement.assay,Code,OntologyClass,6.3 Measurement,,n/a, -data_elements,,['float'],Value,The result of the measurement.,"{'system': 'NCIT', 'code': 'C25712'}",NCIT,Value,Observation.value[x],,,,6.3.2,Measurement.measurement_value,Quantity|integer,Quantity[double/float],6.3 Measurement,,n/a, -data_elements,,['UO'],Code,The unit of the result's measurement.,"{'system': 'NCIT', 'code': 'C92571'}",NCIT,Value Unit,Observation.value[x].unit,,,,6.3.3,Measurement.measurement_value,CodeableConcept,OntologyClass,6.3 Measurement,,n/a, -data_elements,,['NCIT'],Code,"The interpretation of the measurement (e.g.: Below/Within/Above age-related reference range, Absent/Low/Normal, or Positive/Negative).","{'system': 'NCIT', 'code': 'C41255'}",NCIT,Interpretation,Observation.interpretation,,,,6.3.4,n/a,n/a,n/a,6.3 Measurement,,n/a, -data_elements,,['YYYY-MM-DD'],Date,Time at which the measurement was performed.,"{'system': 'NCIT', 'code': 'C82577'}",NCIT,Time Observed,Observation.effectiveDateTime,,,,6.3.5,Measurement.time_observed,DateTime,TimeElement,6.3 Measurement,,n/a, -data_elements,,"['OntologyClass (e.g. NCIT, SNOMEDCT)']",Code,Clinical procedure performed to acquire the sample used for the measurement.,"{'system': 'SNOMEDCT', 'code': '122869004'}",SNOMEDCT,Procedure,Procedure.code,,,,6.3.6,Measurement.procedure,Measurement.procedure,Measurement.procedure,6.3 Measurement,,n/a, -data_elements,,['n/a'],Identifier,A unique identifier or local pseudonym for the familymember.,"{'system': 'CustomCode', 'code': 'family_member_id'}",CustomCode,Family Member Pseudonym,FamilyMemberHistory.identifier,,,,6.4.1,Family.Pedigree.Person.individual_id,Identifier,string,6.4 Family History,,n/a, -data_elements,,"['VSe', 'VSc']",Code,"Is the individual the first affected family member who seeks medical attention for a genetic disorder, leading to the diagnosis of other family members. Disclaimer: The SCT code for propositus (64245008) refers to any gender.","{'system': 'SNOMEDCT', 'code': '64245008'}",SNOMEDCT,Propositus/-a,n/a,,,,6.4.2,(Family.relatives → 1 Phenopacket per family member),n/a,(Family.relatives → 1 Phenopacket per family member),6.4 Family History,,Propositus Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,Specifies the familial relationship of the individual being evaluated to the propositus. Disclaimer: The SNOMEDCT code for propositus (64245008) refers to any gender.,"{'system': 'SNOMEDCT', 'code': '408732007'}",SNOMEDCT,Relationship of the Individual to the Propositus,n/a,,,,6.4.3,(Family.relatives → 1 Phenopacket per family member),n/a,(Family.relatives → 1 Phenopacket per family member),6.4 Family History,,Family Relationship To Index Case Value Set v2.0.0, -data_elements,,['VSe'],Code,"The presence of a biological relationship between parents who are related by blood, typically as first or second cousins.","{'system': 'SNOMEDCT', 'code': '842009'}",SNOMEDCT,Consanguinity,n/a,,,,6.4.4,Family.consanguinous_parents,n/a,boolean,6.4 Family History,,Consanguinity Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,Specifies the relationship of the selected family member to the patient.,"{'system': 'SNOMEDCT', 'code': '444018008'}",SNOMEDCT,Family Member Relationship,FamilyMemberHistory.relationship.coding,,,,6.4.5,Family.Pedigree.Person.individual_id,ValueSet: FamilyMember,string,6.4 Family History,,FamilyMember Value Set v2.0.0, -data_elements,,['VS'],Code,Specifies the record’s status of the family history of a specific family member.,"{'system': 'HL7FHIR', 'code': 'familymemberhistory.status'}",HL7FHIR,Family Member Record Status,FamilyMemberHistory.status,,,,6.4.6,n/a,,n/a,6.4 Family,,FamilyHistoryStatus Value Set v2.0.0, -data_elements,,"['VSe', 'VSc']",Code,"Specifies the sex (or gender) of the specific family member. If possible, the sex assigned at birth should be selected.","{'system': 'LOINC', 'code': '54123-5'}",LOINC,Family Member Sex,FamilyMemberHistory.sex,,,,6.4.7,Family.Pedigree.Person.sex,ValueSet: AdministrativeGender,ValueSet: Sex,6.4 Family,,AdministrativeGender Value Set v2.0.0, -data_elements,,['Integer'],Integer,Records the current age of the selected family member.,"{'system': 'LOINC', 'code': '54141-7'}",LOINC,Family Member Age,FamilyMemberHistory.ageAge,,,,6.4.8,(Family.relatives → 1 Phenopacket per family member),Age,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,n/a, -data_elements,,['YYYY-MM-DD'],Date,Records the date of birth of the selected family member.,"{'system': 'LOINC', 'code': '54124-3'}",LOINC,Family Member Date of Birth,FamilyMemberHistory.bornDate,,,,6.4.9,(Family.relatives → 1 Phenopacket per family member),DateTime,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,n/a, -data_elements,,['VSe'],Code,Indicates whether the selected family member is deceased.,"{'system': 'SNOMEDCT', 'code': '740604001'}",SNOMEDCT,Family Member Deceased,FamilyMemberHistory.deceased.deceasedBoolean,,,,6.4.10,(Family.relatives → 1 Phenopacket per family member),boolean,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,Deceased Value Set v2.0.0, -data_elements,,['ICD10CM'],Code,Records the cause of death of the selected deceasedfamily member.,"{'system': 'LOINC', 'code': '54112-8'}",LOINC,Family Member Cause of Death,FamilyMemberHistory.condition.code & FamilyMemberHistory.condition.contributedToDeath,,,,6.4.11,(Family.relatives → 1 Phenopacket per family member),Code,(Family.relatives → 1 Phenopacket per family member),6.4 Family,,n/a, -data_elements,,['Integer'],Integer,Records the age at which the selected family member died.,"{'system': 'LOINC', 'code': '92662-6'}",LOINC,Family Member Deceased Age,FamilyMemberHistory.deceasedAge,,,,6.4.12,Family.relatives,Family.relatives,Family.relatives,6.4 Family,,n/a, -data_elements,,"['Ontology Class', 'ORDO', 'ICD-10-CM', 'ICD-11', 'MONDO', 'OMIM_p']",Code,Indicates whether the selected family member is affected by the same rare disease as the individual.,"{'system': 'LOINC', 'code': '75315-2'}",LOINC,Family Member Disease,FamilyMemberHistory.condition.code,,,,6.4.13,Family.relatives,Family.relatives,Family.relatives,6.4 Family,,n/a, -data_elements,,['VS'],Code,Indicates the current status of the consent.,"{'system': 'SNOMEDCT', 'code': '309370004'}",SNOMEDCT,Consent Status,Consent.status,,,,7.1,n/a,ValueSet: ConsentStatus,n/a,7. Consent,,Consent Status Value Set v2.0.0, -data_elements,,['YYYY-MM-DD'],Date,Records the date when the consent was given.,"{'system': 'HL7FHIR', 'code': 'consent.datetime'}",HL7FHIR,Consent Date,Consent.dateTime,,,,7.2,n/a,DateTime,n/a,7. Consent,,n/a, -data_elements,,['n/a'],String,References to the policies that are included in thisconsent scope.,"{'system': 'SNOMEDCT', 'code': '386318002'}",SNOMEDCT,Health Policy Monitoring,Consent.policy,,,,7.3,n/a,string,n/a,7. Consent,,n/a, -data_elements,,['VSe'],Code,Indicates whether the patient agrees to be contacted for research.,"{'system': 'CustomCode', 'code': 'consent_contact_research'}",CustomCode,Agreement to be Contacted for Research,Consent.scope.coding,,,,7.4,n/a,CodeableConcept,n/a,7. Consent,,Contact for Research Value Set v2.0.0, -data_elements,,['VSe'],Code,Indicates whether the patient consents to the reuse of their data.,"{'system': 'CustomCode', 'code': 'conset_data_reuse'}",CustomCode,Consent to the Reuse of Data,Consent.scope.coding,,,,7.5,n/a,CodeableConcept,n/a,7. Consent,,Data Reuse Consent Value Set v2.0.0, -data_elements,,['VSe'],Code,Indicates whether a patient's biological sample is available for research.,"{'system': 'SNOMEDCT', 'code': '123038009'}",SNOMEDCT,Biological Sample,n/a,,,,7.6,n/a,n/a,n/a,7. Consent,,Biological Sample Consent Value Set v2.0.0, -data_elements,,['n/a'],String,"If there is a biological sample, this data element indicates the link to the biobank of the individual's biological sample.","{'system': 'CustomCode', 'code': 'biobank_link'}",CustomCode,Link to a Biobank,n/a,,,,7.7,n/a,n/a,n/a,7. Consent,,n/a, -data_elements,,['ICF'],Code,"Specifies the classification of the individualss functioning or disability according to the International Classification of Functioning, Disability and Health (ICF).","{'system': 'CustomCode', 'code': 'icf_score'}",CustomCode,Classification of Functioning / Disability,n/a,,,,8.1,n/a,n/a,n/a,8. Disability,,n/a, -value_sets,"[{'system': 'SNOMEDCT', 'code': '248152002', 'label': 'Female'}, {'system': 'SNOMEDCT', 'code': '248153007', 'label': 'Male'}, {'system': 'SNOMEDCT', 'code': '184115007', 'label': 'Patient sex unknown'}, {'system': 'SNOMEDCT', 'code': '32570691000036108', 'label': 'Intersex'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:281053000,Sex at Birth Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '734875008', 'label': 'XX'}, {'system': 'SNOMEDCT', 'code': '734876009', 'label': 'XY'}, {'system': 'SNOMEDCT', 'code': '80427008', 'label': 'X0'}, {'system': 'SNOMEDCT', 'code': '65162001', 'label': 'XXY'}, {'system': 'SNOMEDCT', 'code': '35111009', 'label': 'XXX'}, {'system': 'SNOMEDCT', 'code': '403760006', 'label': 'XXYY'}, {'system': 'SNOMEDCT', 'code': '78317008', 'label': 'XXXY'}, {'system': 'SNOMEDCT', 'code': '10567003', 'label': 'XXXX'}, {'system': 'SNOMEDCT', 'code': '48930007', 'label': 'XYY'}, {'system': 'SNOMEDCT', 'code': '74964007', 'label': 'Other'}]",,,,,,,,SNOMEDCT:1296886006,Karyotypic Sex Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '446141000124107', 'label': 'Female gender identity'}, {'system': 'SNOMEDCT', 'code': '446151000124109', 'label': 'Male gender identity'}, {'system': 'SNOMEDCT', 'code': '394743007', 'label': 'Gender unknown'}, {'system': 'SNOMEDCT', 'code': '33791000087105', 'label': 'Identifies as nonbinary gender'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:263495000,Gender Identity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '438949009', 'label': 'Alive'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '399307001', 'label': 'Unknown - Lost in follow-up'}, {'system': 'SNOMEDCT', 'code': '185924006', 'label': 'Unknown - Opted-out'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown - Other Reason'}]",,,,,,,,SNOMEDCT:278844005,Vital Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '3658006', 'label': 'Infancy'}, {'system': 'SNOMEDCT', 'code': '713153009', 'label': 'Toddler'}, {'system': 'SNOMEDCT', 'code': '255398004', 'label': 'Childhood'}, {'system': 'SNOMEDCT', 'code': '263659003', 'label': 'Adolescence'}, {'system': 'SNOMEDCT', 'code': '41847000', 'label': 'Adulthood'}, {'system': 'SNOMEDCT', 'code': '303112003', 'label': 'Fetal period'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:105727008,Age Category Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '438949009', 'label': 'Alive'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '399307001', 'label': 'Unknown - Lost in follow-up'}, {'system': 'SNOMEDCT', 'code': '185924006', 'label': 'Unknown - Opted-out'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown - Other Reason'}]",,,,,,,,SNOMEDCT:278844005,Vital Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '3658006', 'label': 'Infancy'}, {'system': 'SNOMEDCT', 'code': '713153009', 'label': 'Toddler'}, {'system': 'SNOMEDCT', 'code': '255398004', 'label': 'Childhood'}, {'system': 'SNOMEDCT', 'code': '263659003', 'label': 'Adolescence'}, {'system': 'SNOMEDCT', 'code': '41847000', 'label': 'Adulthood'}, {'system': 'SNOMEDCT', 'code': '303112003', 'label': 'Fetal period'}, {'system': 'SNOMEDCT', 'code': '419099009', 'label': 'Dead'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:105727008,Age Category Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}]",,,,,,,,SNOMEDCT:723663001,Undiagnosed RD Case Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'planned', 'label': 'Planned'}, {'system': 'HL7FHIR', 'code': 'arrived', 'label': 'Arrived'}, {'system': 'HL7FHIR', 'code': 'triaged', 'label': 'Triaged'}, {'system': 'HL7FHIR', 'code': 'in-progress', 'label': 'In Progress'}, {'system': 'HL7FHIR', 'code': 'onleave', 'label': 'On Leave'}, {'system': 'HL7FHIR', 'code': 'finished', 'label': 'Finished'}, {'system': 'HL7FHIR', 'code': 'cancelled', 'label': 'Cancelled'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}, {'system': 'HL7FHIR', 'code': 'unknown', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:305058001,Encounter Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'AMB', 'label': 'Ambulatory'}, {'system': 'HL7FHIR', 'code': 'IMP', 'label': 'Inpatient'}, {'system': 'HL7FHIR', 'code': 'OBSENC', 'label': 'Observation'}, {'system': 'HL7FHIR', 'code': 'EMER', 'label': 'Emergency'}, {'system': 'HL7FHIR', 'code': 'VR', 'label': 'Virtual'}, {'system': 'HL7FHIR', 'code': 'HH', 'label': 'Home Health'}, {'system': 'CustomCode', 'code': 'RDC', 'label': 'RD Specialist Center'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,HL7FHIR:encounter.class,Encounter Class Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'unconfirmed', 'label': 'Unconfirmed'}, {'system': 'HL7FHIR', 'code': 'provisional', 'label': 'Provisional'}, {'system': 'HL7FHIR', 'code': 'differential', 'label': 'Differential'}, {'system': 'HL7FHIR', 'code': 'confirmed', 'label': 'Confirmed'}, {'system': 'HL7FHIR', 'code': 'refuted', 'label': 'Refuted'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}]",,,,,,,,HL7FHIR:99498-8,Verification Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '118189007', 'label': 'Prenatal'}, {'system': 'SNOMEDCT', 'code': '3950001', 'label': 'Birth'}, {'system': 'SNOMEDCT', 'code': '410672004', 'label': 'Date'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:424850005,Age at Onset Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '118189007', 'label': 'Prenatal'}, {'system': 'SNOMEDCT', 'code': '3950001', 'label': 'Birth'}, {'system': 'SNOMEDCT', 'code': '410672004', 'label': 'Date'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:423493009,Age at Diagnosis Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '442083009', 'label': 'Anatomical or acquired body structure'}]",,,,,,,,SNOMEDCT:363698007,Body Site Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'active', 'label': 'Active'}, {'system': 'HL7FHIR', 'code': 'recurrence', 'label': 'Recurrence'}, {'system': 'HL7FHIR', 'code': 'relapse', 'label': 'Relapse'}, {'system': 'HL7FHIR', 'code': 'inactive', 'label': 'Inactive'}, {'system': 'HL7FHIR', 'code': 'remission', 'label': 'Remission'}, {'system': 'HL7FHIR', 'code': 'resolved', 'label': 'Resolved'}]",,,,,,,,SNOMEDCT:263493007,Clinical Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '24484000', 'label': 'Severe'}, {'system': 'SNOMEDCT', 'code': '6736007', 'label': 'Moderate severity'}, {'system': 'SNOMEDCT', 'code': '255604002', 'label': 'Mild'}]",,,,,,,,SNOMEDCT:246112005,Severity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'GA4GH', 'code': 'UNKNOWN_PROGRESS', 'label': 'No information is available aboutthe diagnosis'}, {'system': 'GA4GH', 'code': 'IN_PROGRESS', 'label': 'No diagnosis has been found to date but additional differential diagnostic work is in progress.'}, {'system': 'GA4GH', 'code': 'COMPLETED', 'label': 'The work on the interpretation is complete.'}, {'system': 'GA4GH', 'code': 'SOLVED', 'label': 'The interpretation is complete and also considered to be a definitive diagnosis.'}, {'system': 'GA4GH', 'code': 'UNSOLVED', 'label': 'The interpretation is complete but no definitive diagnosiswas found.'}]",,,,,,,,GA4GH:progress_status,Progress Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'GA4GH', 'code': 'UNKNOWN_STATUS', 'label': 'No information is available about the status'}, {'system': 'GA4GH', 'code': 'REJECTED', 'label': 'The variant or gene reported here is interpreted not to be related to the diagnosis.'}, {'system': 'GA4GH', 'code': 'CANDIDATE', 'label': 'The variant or gene reported here is interpreted to possibly be related to the diagnosis.'}, {'system': 'GA4GH', 'code': 'CONTRIBUTORY', 'label': 'The variant or gene reported here is interpreted to be related to the diagnosis.'}, {'system': 'GA4GH', 'code': 'CAUSATIVE', 'label': 'The variant or gene reported here is interpreted to be causative of the diagnosis.'}]",,,,,,,,GA4GH:interpretation_status,Interpretation Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA26406-1', 'label': 'Karyotyping'}, {'system': 'LOINC', 'code': 'LA26404-6', 'label': 'FISH'}, {'system': 'LOINC', 'code': 'LA26418-6', 'label': 'PCR'}, {'system': 'LOINC', 'code': 'LA26419-4', 'label': 'qPCR (real-time PCR)'}, {'system': 'LOINC', 'code': 'LA26400-4', 'label': 'SNP array'}, {'system': 'LOINC', 'code': 'LA26813-8', 'label': 'Restriction fragment length polymorphism (RFLP)'}, {'system': 'LOINC', 'code': 'LA26810-4', 'label': 'DNA hybridization'}, {'system': 'LOINC', 'code': 'LA26398-0', 'label': 'Sequencing'}, {'system': 'LOINC', 'code': 'LA26415-2', 'label': 'MLPA'}, {'system': 'LOINC', 'code': 'LA46-8', 'label': 'Other'}]",,,,,,,,LOINC:81304-8,Structural Variant Analysis Method Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA14032-9', 'label': 'NCBI Build 34 (hg16)'}, {'system': 'LOINC', 'code': 'LA14029-5', 'label': 'GRCh37 (hg19)'}, {'system': 'LOINC', 'code': 'LA14030-3', 'label': 'NCBI Build 36.1 (hg18)'}, {'system': 'LOINC', 'code': 'LA14031-1', 'label': 'NCBI Build 35 (hg17)'}, {'system': 'LOINC', 'code': 'LA26806-2', 'label': 'GRCh38 (hg38)'}]",,,,,,,,LOINC:62374-4,Reference Genome Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA6705-3', 'label': 'Homozygous'}, {'system': 'LOINC', 'code': 'LA6706-1', 'label': 'Heterozygous'}, {'system': 'LOINC', 'code': 'LA26217-2', 'label': 'Compound heterozygous'}, {'system': 'LOINC', 'code': 'LA26220-6', 'label': 'Double heterozygous'}, {'system': 'LOINC', 'code': 'LA6707-9', 'label': 'Hemizygous'}, {'system': 'LOINC', 'code': 'LA6703-8', 'label': 'Heteroplasmic'}, {'system': 'LOINC', 'code': 'LA6704-6', 'label': 'Homoplasmic'}, {'system': 'LOINC', 'code': 'LA46-8', 'label': 'Other'}]",,,,,,,,LOINC:53034-5,Zygosity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA6683-2', 'label': 'Germline'}, {'system': 'LOINC', 'code': 'LA6684-0', 'label': 'Somatic'}, {'system': 'LOINC', 'code': 'LA10429-1', 'label': 'Fetal'}, {'system': 'LOINC', 'code': 'LA18194-3', 'label': 'Likely germline'}, {'system': 'LOINC', 'code': 'LA18195-0', 'label': 'Likely somatic'}, {'system': 'LOINC', 'code': 'LA18196-8', 'label': 'Likely fetal'}, {'system': 'LOINC', 'code': 'LA18197-6', 'label': 'Unknown genomic origin'}, {'system': 'LOINC', 'code': 'LA26807-0', 'label': 'De novo'}]",,,,,,,,LOINC:48002-0,Genomic Source Class Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA9658-1', 'label': 'Wild Type'}, {'system': 'LOINC', 'code': 'LA6692-3', 'label': 'Deletion'}, {'system': 'LOINC', 'code': 'LA6686-5', 'label': 'Duplication'}, {'system': 'LOINC', 'code': 'LA6687-3', 'label': 'Insertion'}, {'system': 'LOINC', 'code': 'LA6688-1', 'label': 'Insertion/Deletion'}, {'system': 'LOINC', 'code': 'LA6689-9', 'label': 'Inversion'}, {'system': 'LOINC', 'code': 'LA6690-7', 'label': 'Substitution'}]",,,,,,,,LOINC:48019-4,DNA Change Type Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA6668-3', 'label': 'Pathogenic'}, {'system': 'LOINC', 'code': 'LA26332-9', 'label': 'Likely pathogenic'}, {'system': 'LOINC', 'code': 'LA26333-7', 'label': 'Uncertain significance'}, {'system': 'LOINC', 'code': 'LA26334-5', 'label': 'Likely benign'}, {'system': 'LOINC', 'code': 'LA6675-8', 'label': 'Benign'}, {'system': 'LOINC', 'code': 'LA4489-6', 'label': 'Unknown'}]",,,,,,,,LOINC:53037-8,Clinical Significance ACMG Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'GA4GH', 'code': 'UNKNOWN_ACTIONABILITY', 'label': 'There is not enough information at this time to support any therapeutic actionability for this variant.'}, {'system': 'GA4GH', 'code': 'NOT_ACTIONABLE', 'label': 'This variant has no therapeutic actionability.'}, {'system': 'GA4GH', 'code': 'ACTIONABLE', 'label': 'This variant is known to be therapeuticallyactionalbe.'}]",,,,,,,,GA4GH:therapeutic_actionability,Therapeutic Actionability Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'LOINC', 'code': 'LA30200-2', 'label': 'Very Strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30201-0', 'label': 'Strong evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30202-8', 'label': 'Moderate evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30203-6', 'label': 'Supporting evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30204-4', 'label': 'Supporting evidence benign'}, {'system': 'LOINC', 'code': 'LA30205-1', 'label': 'Strong evidence benign'}, {'system': 'LOINC', 'code': 'LA30206-9', 'label': 'Stand-alone evidence pathogenic'}, {'system': 'LOINC', 'code': 'LA30207-7', 'label': 'Stand-alone evidence benign'}, {'system': 'LOINC', 'code': 'LA26333-7', 'label': 'Uncertain significance'}]",,,,,,,,LOINC:93044-6,Clinical Annotation Level Of Evidence Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '410605003', 'label': 'Confirmed present'}, {'system': 'SNOMEDCT', 'code': '723511001', 'label': 'Refuted'}]",,,,,,,,CustomCode:phenotypicfeature.excluded,Phenotype Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HP', 'code': '0011460', 'label': 'Embryonal onset'}, {'system': 'HP', 'code': '0011461', 'label': 'Fetal onset'}, {'system': 'HP', 'code': '0003577', 'label': 'Congenital onset'}, {'system': 'HP', 'code': '0003623', 'label': 'Neonatal onset'}, {'system': 'HP', 'code': '0003593', 'label': 'Infantile onset'}, {'system': 'HP', 'code': '0011463', 'label': 'Childhood onset'}, {'system': 'HP', 'code': '0003621', 'label': 'Juvenile onset'}, {'system': 'HP', 'code': '0011462', 'label': 'Young adult onset'}, {'system': 'HP', 'code': '0003596', 'label': 'Middle age onset'}, {'system': 'HP', 'code': '0003584', 'label': 'Late onset'}]",,,,,,,,HP:0003674,Onset Category Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HP', 'code': '0011009', 'label': 'Acute'}, {'system': 'HP', 'code': '0011010', 'label': 'Chronic'}, {'system': 'HP', 'code': '0031914', 'label': 'Fluctuating'}, {'system': 'HP', 'code': '0025297', 'label': 'Prolonged'}, {'system': 'HP', 'code': '0031796', 'label': 'Recurrent'}, {'system': 'HP', 'code': '0031915', 'label': 'Stable'}, {'system': 'HP', 'code': '0011011', 'label': 'Subacute'}, {'system': 'HP', 'code': '0025153', 'label': 'Transient'}]",,,,,,,,HP:0011008,Temporal Pattern Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HP', 'code': '0012827', 'label': 'Borderline'}, {'system': 'HP', 'code': '0012825', 'label': 'Mild'}, {'system': 'HP', 'code': '0012826', 'label': 'Moderate'}, {'system': 'HP', 'code': '0012829', 'label': 'Profound'}, {'system': 'HP', 'code': '0012828', 'label': 'Severe'}]",,,,,,,,HP:0012824,Severity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:64245008,Propositus Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '65656005', 'label': 'Natural mother'}, {'system': 'SNOMEDCT', 'code': '9947008', 'label': 'Natural father'}, {'system': 'SNOMEDCT', 'code': '83420006', 'label': 'Natural daughter'}, {'system': 'SNOMEDCT', 'code': '113160008', 'label': 'Natural son'}, {'system': 'SNOMEDCT', 'code': '60614009', 'label': 'Natural brother'}, {'system': 'SNOMEDCT', 'code': '73678001', 'label': 'Natural sister'}, {'system': 'SNOMEDCT', 'code': '11286003', 'label': 'Twin sibling'}, {'system': 'SNOMEDCT', 'code': '45929001', 'label': 'Half-brother'}, {'system': 'SNOMEDCT', 'code': '2272004', 'label': 'Half-sister'}, {'system': 'SNOMEDCT', 'code': '62296006', 'label': 'Natural grandfather'}, {'system': 'SNOMEDCT', 'code': '17945006', 'label': 'Natural grandmother'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:408732007,Family Relationship To Index Case Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:842009,Consanguinity Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '65656005', 'label': 'Natural mother'}, {'system': 'SNOMEDCT', 'code': '9947008', 'label': 'Natural father'}, {'system': 'SNOMEDCT', 'code': '83420006', 'label': 'Natural daughter'}, {'system': 'SNOMEDCT', 'code': '113160008', 'label': 'Natural son'}, {'system': 'SNOMEDCT', 'code': '60614009', 'label': 'Natural brother'}, {'system': 'SNOMEDCT', 'code': '73678001', 'label': 'Natural sister'}, {'system': 'SNOMEDCT', 'code': '11286003', 'label': 'Twin sibling'}, {'system': 'SNOMEDCT', 'code': '45929001', 'label': 'Half-brother'}, {'system': 'SNOMEDCT', 'code': '2272004', 'label': 'Half-sister'}, {'system': 'SNOMEDCT', 'code': '62296006', 'label': 'Natural grandfather'}, {'system': 'SNOMEDCT', 'code': '17945006', 'label': 'Natural grandmother'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:444018008,FamilyMember Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'partial', 'label': 'Partial'}, {'system': 'HL7FHIR', 'code': 'completed', 'label': 'Completed'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}, {'system': 'HL7FHIR', 'code': 'health-unknown', 'label': 'Health Unknown'}]",,,,,,,,HL7FHIR:familymemberhistory.status,FamilyHistoryStatus Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '248152002', 'label': 'Female'}, {'system': 'SNOMEDCT', 'code': '248153007', 'label': 'Male'}, {'system': 'SNOMEDCT', 'code': '184115007', 'label': 'Patient sex unknown'}, {'system': 'SNOMEDCT', 'code': '32570691000036108', 'label': 'Intersex'}, {'system': 'SNOMEDCT', 'code': '1220561009', 'label': 'Not recorded'}]",,,,,,,,SNOMEDCT:54123-5,AdministrativeGender Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:740604001,Deceased Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'HL7FHIR', 'code': 'draft', 'label': 'Pending'}, {'system': 'HL7FHIR', 'code': 'proposed', 'label': 'Proposed'}, {'system': 'HL7FHIR', 'code': 'active', 'label': 'Active'}, {'system': 'HL7FHIR', 'code': 'rejected', 'label': 'Rejected'}, {'system': 'HL7FHIR', 'code': 'inactive', 'label': 'Inactive'}, {'system': 'HL7FHIR', 'code': 'entered-in-error', 'label': 'Entered in Error'}]",,,,,,,,HL7FHIR:309370004,Consent Status Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:consent_contact_research,Contact for Research Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:conset_data_reuse,Data Reuse Consent Value Set v2.0.0,,,,,,,,, -value_sets,"[{'system': 'SNOMEDCT', 'code': '373066001', 'label': 'Yes'}, {'system': 'SNOMEDCT', 'code': '373067005', 'label': 'No'}, {'system': 'SNOMEDCT', 'code': '261665006', 'label': 'Unknown'}]",,,,,,,,SNOMEDCT:123038009,Biological Sample Consent Value Set v2.0.0,,,,,,,,, diff --git a/src/rd_cdm/instances/v2_0_2/jsons/rd_cdm_v2_0_1.json b/src/rd_cdm/instances/v2_0_2/jsons/rd_cdm_v2_0_1.json deleted file mode 100644 index b45cb58..0000000 --- a/src/rd_cdm/instances/v2_0_2/jsons/rd_cdm_v2_0_1.json +++ /dev/null @@ -1,2184 +0,0 @@ -{ - "code_systems": { - "code_systems": [ - { - "id": "SNOMEDCT", - "namespace_iri": "http://purl.bioontology.org/ontology/SNOMEDCT/", - "version": "SNOMEDCT_US_2024_09_01", - "title": "Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT)" - }, - { - "id": "LOINC", - "namespace_iri": "http://loinc.org", - "version": "LNC278", - "title": "Logical Observation Identifiers Names and Codes (LOINC)" - }, - { - "id": "HP", - "namespace_iri": "http://purl.obolibrary.org/obo/HP", - "version": "2025-05-06", - "title": "Human Phenotype Ontology (HPO)" - }, - { - "id": "NCIT", - "namespace_iri": "http://purl.obolibrary.org/obo/NCIT/", - "version": "24.01e", - "title": "NCI Thesaurus (NCIT) OBO Edition" - }, - { - "id": "HL7FHIR", - "namespace_iri": "http://hl7.org/fhir/", - "version": "v4.0.1", - "title": "Health Level Seven Fast Healthcare Interoperability Resources, Release 4" - }, - { - "id": "GA4GH", - "namespace_iri": "https://ga4gh.github.io/phenopacket-v2/", - "version": "v2.0", - "title": "Global Alliance for Genomics and Health Phenopackets Schema" - }, - { - "id": "CustomCode", - "namespace_iri": "https://github.com/BIH-CEI/rd-cdm", - "version": "v2.0.0", - "title": "Custom Code System RD CDM v2.0.0" - }, - { - "id": "NCBITAXON", - "namespace_iri": "http://purl.obolibrary.org/obo/NCBITAXON/", - "version": "NCBI2024_04_02", - "title": "NCBI organismal classification" - }, - { - "id": "GENO", - "namespace_iri": "http://purl.obolibrary.org/obo/GENO/", - "version": "2023-10-08", - "title": "GENO – The Genotype Ontology" - }, - { - "id": "SO", - "namespace_iri": "http://purl.obolibrary.org/obo/SO/", - "version": "2.6", - "title": "Sequence Ontology" - }, - { - "id": "UO", - "namespace_iri": "http://purl.obolibrary.org/obo/UO/", - "version": "2023-05-25", - "title": "Units Ontology (UO)" - }, - { - "id": "ECO", - "namespace_iri": "http://purl.obolibrary.org/obo/ECO/", - "version": "2025-06-23", - "title": "Evidence & Conclusion Ontology (ECO)" - }, - { - "id": "ICD10CM", - "namespace_iri": "http://purl.bioontology.org/ontology/ICD10CM/", - "version": "CD10CM_2025", - "title": "International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)" - }, - { - "id": "MONDO", - "namespace_iri": "http://purl.obolibrary.org/obo/MONDO/", - "version": "2025-06-03", - "title": "Mondo Disease Ontology" - }, - { - "id": "ORDO", - "namespace_iri": "http://purl.obolibrary.org/obo/ORDO/", - "version": "4.7", - "title": "Orphanet Rare Disease Ontology (ORDO)" - }, - { - "id": "HGNC", - "namespace_iri": "http://identifiers.org/hgnc/", - "version": "2024-08-23", - "title": "HUGO Gene Nomenclature Committee (HGNC)" - }, - { - "id": "OMIM", - "namespace_iri": "http://purl.bioontology.org/ontology/OMIM/", - "version": "OMIM2024_08_09", - "title": "Online Mendelian Inheritance in Man (OMIM)" - }, - { - "id": "HGVS", - "namespace_iri": "https://varnomen.hgvs.org/", - "version": "21.0.0", - "title": "Human Genome Variation Society Nomenclature" - }, - { - "id": "ICD11", - "namespace_iri": "http://id.who.int/icd/release/11/mms/", - "version": "2024-09-01", - "title": "International Classification of Diseases, Eleventh Revision (ICD-11)" - }, - { - "id": "ISO3166", - "namespace_iri": "https://www.iso.org/iso-3166-country-codes.html", - "version": "2020(en)", - "title": "International Organization for Standardization – ISO 3166 Country Codes" - }, - { - "id": "ICF", - "namespace_iri": "https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health", - "version": "1.0.2", - "title": "International Classification of Functioning, Disability and Health (ICF)" - } - ], - "@type": "RdCdm" - }, - "data_elements": { - "data_elements": [ - { - "ordinal": "1.1", - "elementName": "Pseudonym", - "elementCode": { - "system": "SNOMEDCT", - "code": "422549004" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "1. Formal Criteria", - "dataType": "Identifier", - "dataSpecification": [ - "n/a" - ], - "fhirExpression_v4_0_1": "Patient.identifier.value", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Individual.id", - "recommendedDataSpec_phenopackets": "string", - "description": "The (local) patient-related identification code." - }, - { - "ordinal": "1.2", - "elementName": "Date of Admission", - "elementCode": { - "system": "SNOMEDCT", - "code": "399423000" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "1. Formal Criteria", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Encounter.period.start", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Individual.time_at_last_encounter", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The date of admission or data capture of the individual." - }, - { - "ordinal": "2.1", - "elementName": "Date of Birth", - "elementCode": { - "system": "SNOMEDCT", - "code": "184099003" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Date", - "dataSpecification": [ - "YYYY", - "YYYY-MM", - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Patient.birthDate", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Individual.date_of_birth", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The individual's date of birth." - }, - { - "ordinal": "2.2", - "elementName": "Sex at Birth", - "elementCode": { - "system": "SNOMEDCT", - "code": "281053000" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Sex at Birth Value Set v2.0.0", - "fhirExpression_v4_0_1": "Patient.extension:individual-recordedSexOrGender", - "recommendedDataSpec_fhir": "Recorded Sex Or Gender Type", - "phenopacketSchemaElement_v2_0": "Individual.sex", - "recommendedDataSpec_phenopackets": "Sex", - "description": "The individual's sex that was assigned at birth." - }, - { - "ordinal": "2.3", - "elementName": "Karyotypic Sex", - "elementCode": { - "system": "SNOMEDCT", - "code": "1296886006" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Code", - "dataSpecification": [ - "VSc" - ], - "valueSet": "Karyotypic Sex Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.value", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Individual.karyotypic_sex", - "recommendedDataSpec_phenopackets": "Karyotypic Sex", - "description": "The chromosomal sex of an individual." - }, - { - "ordinal": "2.4", - "elementName": "Gender Identity", - "elementCode": { - "system": "SNOMEDCT", - "code": "263495000" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Gender Identity Value Set v2.0.0", - "fhirExpression_v4_0_1": "Patient.extension:individual-genderIdentity", - "recommendedDataSpec_fhir": "Gender Identity", - "phenopacketSchemaElement_v2_0": "Individual.gender", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The self-assigned gender of the individual." - }, - { - "ordinal": "2.5", - "elementName": "Country of Birth", - "elementCode": { - "system": "SNOMEDCT", - "code": "370159000" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "fhirExpression_v4_0_1": "Patient.extension:patient-birthPlace", - "recommendedDataSpec_fhir": "DataType: Address", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The individual's country of birth." - }, - { - "ordinal": "3.1", - "elementName": "Vital Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "278844005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Vital Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Patient.deceased.deceasedBoolean|Observation.value", - "recommendedDataSpec_fhir": "Boolean|Code", - "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.status", - "recommendedDataSpec_phenopackets": "Value Set: VitalStatus.Status", - "description": "The individual’s general clinical status orvital status." - }, - { - "ordinal": "3.2", - "elementName": "Time of Death", - "elementCode": { - "system": "SNOMEDCT", - "code": "398299004" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Date", - "dataSpecification": [ - "YYYY", - "YYYY-MM", - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Patient.deceasedDateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.time_of_death", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "If deceased, the individual’s date of death." - }, - { - "ordinal": "3.3", - "elementName": "Cause of Death", - "elementCode": { - "system": "SNOMEDCT", - "code": "184305005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Code", - "dataSpecification": [ - "ICD-10CM" - ], - "fhirExpression_v4_0_1": "Observation.value.coding.code", - "recommendedDataSpec_fhir": "Code|CodeableConcept", - "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.cause_of_death", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "If deceased, the individual’s primary cause of death." - }, - { - "ordinal": "3.4", - "elementName": "Age Category", - "elementCode": { - "system": "SNOMEDCT", - "code": "105727008" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Age Category Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.value.coding.code", - "recommendedDataSpec_fhir": "CodableConcept", - "phenopacketSchemaElement_v2_0": "Individual.time_at_last_encounter", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The individual's age category at thetime of data capture." - }, - { - "ordinal": "3.5", - "elementName": "Length of Gestation at Birth [weeks+days]", - "elementCode": { - "system": "SNOMEDCT", - "code": "412726003" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "String", - "dataSpecification": [ - "XX+X" - ], - "fhirExpression_v4_0_1": "Observation.component:weeks.valueQuantity|Observation.component:days.valueQuantity", - "recommendedDataSpec_fhir": "Quantity", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The duration of the pregnancy in weeks and days,formatted as XX+X (weeks+days)." - }, - { - "ordinal": "3.6", - "elementName": "Undiagnosed RD Case", - "elementCode": { - "system": "SNOMEDCT", - "code": "723663001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Undiagnosed RD Case Value Set v2.0.0", - "fhirExpression_v4_0_1": "(Condition.code)", - "recommendedDataSpec_fhir": "Code(e.g. ORDO:616874 - Rare disorderwithout a determined diagnosis afterfull investigation)", - "phenopacketSchemaElement_v2_0": "(Disease.term)", - "recommendedDataSpec_phenopackets": "(OntologyClass (e.g. ORDO:616874 - Rare disorder without a determineddiagnosis after full investigation))", - "description": "Identifies cases where an RD diagnosis has notbeen established." - }, - { - "ordinal": "4.1", - "elementName": "Encounter Start", - "elementCode": { - "system": "HL7FHIR", - "code": "encounter.period.start" - }, - "elementCodeSystem": "HL7FHIR", - "section": "4. Care Pathway", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Encounter.period.start", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The beginning of an encounter of the individual." - }, - { - "ordinal": "4.2", - "elementName": "Encounter End", - "elementCode": { - "system": "HL7FHIR", - "code": "encounter.period.end" - }, - "elementCodeSystem": "HL7FHIR", - "section": "4. Care Pathway", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Encounter.period.end", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The end of an encounter of the individual." - }, - { - "ordinal": "4.3", - "elementName": "Encounter Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "305058001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "4. Care Pathway", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Encounter Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Encounter.status", - "recommendedDataSpec_fhir": "ValueSet: EncounterStatus", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The status of an encounter of the individual at thetime of data capture." - }, - { - "ordinal": "4.4", - "elementName": "Encounter Class", - "elementCode": { - "system": "HL7FHIR", - "code": "encounter.class" - }, - "elementCodeSystem": "HL7FHIR", - "section": "4. Care Pathway", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Encounter Class Value Set v2.0.0", - "fhirExpression_v4_0_1": "Encounter.class", - "recommendedDataSpec_fhir": "ValueSet: EncounterClass", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The class of an encounter of the individualat the time of data capture." - }, - { - "ordinal": "5.1", - "elementName": "Disease", - "elementCode": { - "system": "SNOMEDCT", - "code": "64572001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "Ontology Class (MONDO, ORDO, ICD-10, ICD-11, OMIM_g, OMIM_p)" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Condition.code", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "Disease.term", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "A disease that the individual was affected by. If agenetic diagnosis or subtypes were diagnosed, please also provide the respective OMIM_g and OMIM_p codes." - }, - { - "ordinal": "5.2", - "elementName": "Verification Status", - "elementCode": { - "system": "LOINC", - "code": "99498-8" - }, - "elementCodeSystem": "LOINC", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Verification Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.verificationStatus", - "recommendedDataSpec_fhir": "ValueSet: Condition Verficication Status", - "phenopacketSchemaElement_v2_0": "(Disease.excluded)", - "recommendedDataSpec_phenopackets": "boolean", - "description": "The verification status of the disease." - }, - { - "ordinal": "5.3", - "elementName": "Age at Onset", - "elementCode": { - "system": "SNOMEDCT", - "code": "424850005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Age at Onset Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.onsetString orObservation.valueCodeableConcept", - "recommendedDataSpec_fhir": "Disease.onset", - "phenopacketSchemaElement_v2_0": "Disease.onset", - "recommendedDataSpec_phenopackets": "Disease.onset", - "description": "The age at the onset of the first symptomsor signs of the disease." - }, - { - "ordinal": "5.4", - "elementName": "Date of Onset", - "elementCode": { - "system": "SNOMEDCT", - "code": "298059007" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Condition.onset", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "Disease.onset", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The date at onset of first symptoms orsigns of the disease." - }, - { - "ordinal": "5.5", - "elementName": "Age at Diagnosis", - "elementCode": { - "system": "SNOMEDCT", - "code": "423493009" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Age at Diagnosis Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.value", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "(Disease.onset)", - "recommendedDataSpec_phenopackets": "(TimeElement)", - "description": "The individual’s age when the diagnosis was made." - }, - { - "ordinal": "5.6", - "elementName": "Date of Diagnosis", - "elementCode": { - "system": "SNOMEDCT", - "code": "432213005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Condition.recordedDate", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "(Disease.onset)", - "recommendedDataSpec_phenopackets": "(TimeElement)", - "description": "The date on which the disease was determined." - }, - { - "ordinal": "5.7", - "elementName": "Body Site", - "elementCode": { - "system": "SNOMEDCT", - "code": "363698007" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Body Site Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.bodySite.coding:SNOMEDCT-ct", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "Disease.primary_site", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The specific body site affected by disease is encodedusing all descendants of SCT Body Structure (123037004)." - }, - { - "ordinal": "5.8", - "elementName": "Clinical Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "263493007" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Clinical Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.clinicalStatus", - "recommendedDataSpec_fhir": "ValueSet: ClinicalStatus", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The clinical status of the disease indicates whetherit is active, inactive, or resolved." - }, - { - "ordinal": "5.9", - "elementName": "Severity", - "elementCode": { - "system": "SNOMEDCT", - "code": "246112005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Severity Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.severity", - "recommendedDataSpec_fhir": "ValueSet: ConditionSeverity", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The severity of the disease is categorised byclinical evaluation." - }, - { - "ordinal": "6.1.1", - "elementName": "Genomic Diagnosis", - "elementCode": { - "system": "SNOMEDCT", - "code": "106221001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "OMIM_p", - "MONDO" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Condition.code", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "Interpretation.Diagnosis.disease", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The genomic diagnoses can correspond to the diagnoseddisease in (5.1) if the same OMIM codes are used." - }, - { - "ordinal": "6.1.2", - "elementName": "Progress Status of Interpretation", - "elementCode": { - "system": "GA4GH", - "code": "progress_status" - }, - "elementCodeSystem": "GA4GH", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Progress Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.extension", - "recommendedDataSpec_fhir": "VS: GA4GH ProgressStatus", - "phenopacketSchemaElement_v2_0": "Interpretation.progress_status", - "recommendedDataSpec_phenopackets": "ValueSet: ProgressStatus", - "description": "The interpretation has a ProgressStatus that refers tothe status of the attempted diagnosis." - }, - { - "ordinal": "6.1.3", - "elementName": "Interpretation Status", - "elementCode": { - "system": "GA4GH", - "code": "interpretation_status" - }, - "elementCodeSystem": "GA4GH", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Interpretation Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.extension", - "recommendedDataSpec_fhir": "VS: GA4GH InterpretationStatus", - "phenopacketSchemaElement_v2_0": "GenomicInterpretation.interpretation_status", - "recommendedDataSpec_phenopackets": "ValueSet: InterpretationStatus", - "description": "An enumeration that describes the conclusion made about the genomic interpretation." - }, - { - "ordinal": "6.1.4", - "elementName": "Structural Variant Analysis Method", - "elementCode": { - "system": "LOINC", - "code": "81304-8" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS", - "LOINC" - ], - "valueSet": "Structural Variant Analysis Method Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.method", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The method used to analyse structural variants in the genome." - }, - { - "ordinal": "6.1.5", - "elementName": "Reference Genome", - "elementCode": { - "system": "LOINC", - "code": "62374-4" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Reference Genome Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:reference-sequence-assembly", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The reference genome used for analysing the genetic variant." - }, - { - "ordinal": "6.1.6", - "elementName": "Genetic Mutation String", - "elementCode": { - "system": "LOINC", - "code": "LP7824-8" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "String", - "dataSpecification": [ - "n/a" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Variant.valueString", - "recommendedDataSpec_fhir": "string", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.Extension.value", - "recommendedDataSpec_phenopackets": "string", - "description": "An unvalidated (HGVS) string that describes the variant change" - }, - { - "ordinal": "6.1.7", - "elementName": "Genomic DNA Change", - "elementCode": { - "system": "LOINC", - "code": "81290-9" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "g.HGVS" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Variant.valueCode", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.Expression.value", - "recommendedDataSpec_phenopackets": "string", - "description": "The specific change in the genomic DNA sequence encoded with a validated g.HGVS expression." - }, - { - "ordinal": "6.1.8", - "elementName": "Sequence DNA Change", - "elementCode": { - "system": "LOINC", - "code": "48004-6" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "c.HGVS" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Variant.valueCode", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.Expression.value", - "recommendedDataSpec_phenopackets": "string", - "description": "The specific change in the DNA sequence at the nucleotide level with a validated c.HGVS expression." - }, - { - "ordinal": "6.1.9", - "elementName": "Amino Acid Change", - "elementCode": { - "system": "LOINC", - "code": "48005-3" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "p.HGVS" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Variant.valueCode", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.Expression.value", - "recommendedDataSpec_phenopackets": "string", - "description": "The specific change in the amino acid sequence resulting from agenetic variant as a validated p.HGVS expression." - }, - { - "ordinal": "6.1.10", - "elementName": "Gene", - "elementCode": { - "system": "LOINC", - "code": "48018-6" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "HGNC" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Gene", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "GeneDescriptor.value_id", - "recommendedDataSpec_phenopackets": "string", - "description": "The specific gene or genes that were analysed or identified in the study." - }, - { - "ordinal": "6.1.11", - "elementName": "Zygosity", - "elementCode": { - "system": "LOINC", - "code": "53034-5" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc", - "LOINC" - ], - "valueSet": "Zygosity Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:geneticsAllele.State", - "recommendedDataSpec_fhir": "VS: Allelic State", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.allelic_state", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The zygosity of the genetic variant." - }, - { - "ordinal": "6.1.12", - "elementName": "Genomic Source Class", - "elementCode": { - "system": "LOINC", - "code": "48002-0" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Genomic Source Class Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:GenomicSourceClass", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The classification of the genomic source, such as germline, somatic, or other origins." - }, - { - "ordinal": "6.1.13", - "elementName": "DNA Change Type", - "elementCode": { - "system": "LOINC", - "code": "48019-4" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "DNA Change Type Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:Variant.Type", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The variant’s type of DNA change, such as point mutation, deletion, insertion, or other types." - }, - { - "ordinal": "6.1.14", - "elementName": "Clinical Significance [ACMG]", - "elementCode": { - "system": "LOINC", - "code": "53037-8" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Clinical Significance ACMG Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:Variant.Interpretation", - "recommendedDataSpec_fhir": "", - "phenopacketSchemaElement_v2_0": "VariantInterpretation.acmg_pathogenicity_classification", - "recommendedDataSpec_phenopackets": "ValueSet: AcmgPathogenicityClassification", - "description": "The clinical significance of the genetic variant, indicating its impact on health and disease." - }, - { - "ordinal": "6.1.15", - "elementName": "Therapeutic Actionability", - "elementCode": { - "system": "GA4GH", - "code": "therapeutic_actionability" - }, - "elementCodeSystem": "GA4GH", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Therapeutic Actionability Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "VariantInterpretation.therapeutic_actionability", - "recommendedDataSpec_phenopackets": "ValueSet: TherapeuticActionability", - "description": "An enumeration flagging the variant as being a candidate for treatment or clinical intervention, which could improve the clinical outcome." - }, - { - "ordinal": "6.1.16", - "elementName": "Clinical Annotation Level Of Evidence", - "elementCode": { - "system": "LOINC", - "code": "93044-6" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Clinical Annotation Level Of Evidence Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.extension:Variant.Interpretation", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The level of evidence supporting the clinical annotation of the genetic variant." - }, - { - "ordinal": "6.2.1", - "elementName": "Phenotypic Feature", - "elementCode": { - "system": "SNOMEDCT", - "code": "8116006" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6. Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "HPO" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.code", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.type", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "An observed physical and clinical characteristicencoded with HPO." - }, - { - "ordinal": "6.2.2", - "elementName": "Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "363778006" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Phenotype Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.status", - "recommendedDataSpec_fhir": "ValueSet: ObservationStatus", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.excluded", - "recommendedDataSpec_phenopackets": "boolean", - "description": "The current status of the phenotypic feature, indicating whether it is confirmed or refuted." - }, - { - "ordinal": "6.2.3", - "elementName": "Determination Date", - "elementCode": { - "system": "SNOMEDCT", - "code": "439272007:704321009=363778006" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6. Phenotypic Feature", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.effectiveDateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.onset", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The date on which the phenotypic feature was observed or recorded. We recommend capturing the time acharacteristic was observed." - }, - { - "ordinal": "6.2.4", - "elementName": "Resolution Date", - "elementCode": { - "system": "HP", - "code": "0034382" - }, - "elementCodeSystem": "HP", - "section": "6.2 Phenotypic Feature", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.effectiveDateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.resolution", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "Time at which the feature resolved or abated." - }, - { - "ordinal": "6.2.5", - "elementName": "Onset Category", - "elementCode": { - "system": "HP", - "code": "0003674" - }, - "elementCodeSystem": "HP", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Onset Category Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.category", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.onset", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "Time at which the feature was first observed within HPO onset categories." - }, - { - "ordinal": "6.2.6", - "elementName": "Temporal Pattern", - "elementCode": { - "system": "HP", - "code": "0011008" - }, - "elementCodeSystem": "HP", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Temporal Pattern Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.interpretation", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.modifiers", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The speed at which disease manifestations appear and develop." - }, - { - "ordinal": "6.2.7", - "elementName": "Severity", - "elementCode": { - "system": "HP", - "code": "0012824" - }, - "elementCodeSystem": "HP", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Severity Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.interpretation", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.severity", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "A description of the severity of the feature." - }, - { - "ordinal": "6.2.8", - "elementName": "Modifiers", - "elementCode": { - "system": "GA4GH", - "code": "phenotypicfeature.modifier" - }, - "elementCodeSystem": "GA4GH", - "section": "6. Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "OntologyClass (HPO, NCBITAXON, SCT)" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Suggested: Observation.extension", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.modifiers", - "recommendedDataSpec_phenopackets": "list of OntologyClass", - "description": "Any number of additional modifiers describing a specific phenotypic feature further, such as severity (HP:0012824), clinical modifiers (HP:0012823), or linking causative infectious agents using the NCBITAXON Ontology." - }, - { - "ordinal": "6.2.9", - "elementName": "Evidence", - "elementCode": { - "system": "GA4GH", - "code": "phenotypicfeature.evidence" - }, - "elementCodeSystem": "GA4GH", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "ECO" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.method", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.evidence", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The evidence for an assertion of the observation of a type defined within the Evidence & Conclusion Ontology (ECO)." - }, - { - "ordinal": "6.3.1", - "elementName": "Assay", - "elementCode": { - "system": "NCIT", - "code": "C60819" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Code", - "dataSpecification": [ - "OntologyClass (e.g. LOINC)" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.code", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "Measurement.assay", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "A class that describes the assay used to producethe measurement." - }, - { - "ordinal": "6.3.2", - "elementName": "Value", - "elementCode": { - "system": "NCIT", - "code": "C25712" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Value", - "dataSpecification": [ - "float" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.value[x]", - "recommendedDataSpec_fhir": "Quantity|integer", - "phenopacketSchemaElement_v2_0": "Measurement.measurement_value", - "recommendedDataSpec_phenopackets": "Quantity[double/float]", - "description": "The result of the measurement." - }, - { - "ordinal": "6.3.3", - "elementName": "Value Unit", - "elementCode": { - "system": "NCIT", - "code": "C92571" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Code", - "dataSpecification": [ - "UO" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.value[x].unit", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "Measurement.measurement_value", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The unit of the result's measurement." - }, - { - "ordinal": "6.3.4", - "elementName": "Interpretation", - "elementCode": { - "system": "NCIT", - "code": "C41255" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Code", - "dataSpecification": [ - "NCIT" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.interpretation", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The interpretation of the measurement (e.g.: Below/Within/Above age-related reference range, Absent/Low/Normal, or Positive/Negative)." - }, - { - "ordinal": "6.3.5", - "elementName": "Time Observed", - "elementCode": { - "system": "NCIT", - "code": "C82577" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.effectiveDateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "Measurement.time_observed", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "Time at which the measurement was performed." - }, - { - "ordinal": "6.3.6", - "elementName": "Procedure", - "elementCode": { - "system": "SNOMEDCT", - "code": "122869004" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.3 Measurement", - "dataType": "Code", - "dataSpecification": [ - "OntologyClass (e.g. NCIT, SNOMEDCT)" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Procedure.code", - "recommendedDataSpec_fhir": "Measurement.procedure", - "phenopacketSchemaElement_v2_0": "Measurement.procedure", - "recommendedDataSpec_phenopackets": "Measurement.procedure", - "description": "Clinical procedure performed to acquire the sample used for the measurement." - }, - { - "ordinal": "6.4.1", - "elementName": "Family Member Pseudonym", - "elementCode": { - "system": "CustomCode", - "code": "family_member_id" - }, - "elementCodeSystem": "CustomCode", - "section": "6.4 Family History", - "dataType": "Identifier", - "dataSpecification": [ - "n/a" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.identifier", - "recommendedDataSpec_fhir": "Identifier", - "phenopacketSchemaElement_v2_0": "Family.Pedigree.Person.individual_id", - "recommendedDataSpec_phenopackets": "string", - "description": "A unique identifier or local pseudonym for the familymember." - }, - { - "ordinal": "6.4.2", - "elementName": "Propositus/-a", - "elementCode": { - "system": "SNOMEDCT", - "code": "64245008" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family History", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Propositus Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Is the individual the first affected family member who seeks medical attention for a genetic disorder, leading to the diagnosis of other family members. Disclaimer: The SCT code for propositus (64245008) refers to any gender." - }, - { - "ordinal": "6.4.3", - "elementName": "Relationship of the Individual to the Propositus", - "elementCode": { - "system": "SNOMEDCT", - "code": "408732007" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family History", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Family Relationship To Index Case Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Specifies the familial relationship of the individual being evaluated to the propositus. Disclaimer: The SNOMEDCT code for propositus (64245008) refers to any gender." - }, - { - "ordinal": "6.4.4", - "elementName": "Consanguinity", - "elementCode": { - "system": "SNOMEDCT", - "code": "842009" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family History", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Consanguinity Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Family.consanguinous_parents", - "recommendedDataSpec_phenopackets": "boolean", - "description": "The presence of a biological relationship between parents who are related by blood, typically as first or second cousins." - }, - { - "ordinal": "6.4.5", - "elementName": "Family Member Relationship", - "elementCode": { - "system": "SNOMEDCT", - "code": "444018008" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family History", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "FamilyMember Value Set v2.0.0", - "fhirExpression_v4_0_1": "FamilyMemberHistory.relationship.coding", - "recommendedDataSpec_fhir": "ValueSet: FamilyMember", - "phenopacketSchemaElement_v2_0": "Family.Pedigree.Person.individual_id", - "recommendedDataSpec_phenopackets": "string", - "description": "Specifies the relationship of the selected family member to the patient." - }, - { - "ordinal": "6.4.6", - "elementName": "Family Member Record Status", - "elementCode": { - "system": "HL7FHIR", - "code": "familymemberhistory.status" - }, - "elementCodeSystem": "HL7FHIR", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "FamilyHistoryStatus Value Set v2.0.0", - "fhirExpression_v4_0_1": "FamilyMemberHistory.status", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Specifies the record’s status of the family history of a specific family member." - }, - { - "ordinal": "6.4.7", - "elementName": "Family Member Sex", - "elementCode": { - "system": "LOINC", - "code": "54123-5" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "AdministrativeGender Value Set v2.0.0", - "fhirExpression_v4_0_1": "FamilyMemberHistory.sex", - "recommendedDataSpec_fhir": "ValueSet: AdministrativeGender", - "phenopacketSchemaElement_v2_0": "Family.Pedigree.Person.sex", - "recommendedDataSpec_phenopackets": "ValueSet: Sex", - "description": "Specifies the sex (or gender) of the specific family member. If possible, the sex assigned at birth should be selected." - }, - { - "ordinal": "6.4.8", - "elementName": "Family Member Age", - "elementCode": { - "system": "LOINC", - "code": "54141-7" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Integer", - "dataSpecification": [ - "Integer" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.ageAge", - "recommendedDataSpec_fhir": "Age", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Records the current age of the selected family member." - }, - { - "ordinal": "6.4.9", - "elementName": "Family Member Date of Birth", - "elementCode": { - "system": "LOINC", - "code": "54124-3" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.bornDate", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Records the date of birth of the selected family member." - }, - { - "ordinal": "6.4.10", - "elementName": "Family Member Deceased", - "elementCode": { - "system": "SNOMEDCT", - "code": "740604001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Deceased Value Set v2.0.0", - "fhirExpression_v4_0_1": "FamilyMemberHistory.deceased.deceasedBoolean", - "recommendedDataSpec_fhir": "boolean", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Indicates whether the selected family member is deceased." - }, - { - "ordinal": "6.4.11", - "elementName": "Family Member Cause of Death", - "elementCode": { - "system": "LOINC", - "code": "54112-8" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "ICD10CM" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.condition.code & FamilyMemberHistory.condition.contributedToDeath", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Records the cause of death of the selected deceasedfamily member." - }, - { - "ordinal": "6.4.12", - "elementName": "Family Member Deceased Age", - "elementCode": { - "system": "LOINC", - "code": "92662-6" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Integer", - "dataSpecification": [ - "Integer" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.deceasedAge", - "recommendedDataSpec_fhir": "Family.relatives", - "phenopacketSchemaElement_v2_0": "Family.relatives", - "recommendedDataSpec_phenopackets": "Family.relatives", - "description": "Records the age at which the selected family member died." - }, - { - "ordinal": "6.4.13", - "elementName": "Family Member Disease", - "elementCode": { - "system": "LOINC", - "code": "75315-2" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "Ontology Class", - "ORDO", - "ICD-10-CM", - "ICD-11", - "MONDO", - "OMIM_p" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.condition.code", - "recommendedDataSpec_fhir": "Family.relatives", - "phenopacketSchemaElement_v2_0": "Family.relatives", - "recommendedDataSpec_phenopackets": "Family.relatives", - "description": "Indicates whether the selected family member is affected by the same rare disease as the individual." - }, - { - "ordinal": "7.1", - "elementName": "Consent Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "309370004" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "7. Consent", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Consent Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Consent.status", - "recommendedDataSpec_fhir": "ValueSet: ConsentStatus", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Indicates the current status of the consent." - }, - { - "ordinal": "7.2", - "elementName": "Consent Date", - "elementCode": { - "system": "HL7FHIR", - "code": "consent.datetime" - }, - "elementCodeSystem": "HL7FHIR", - "section": "7. Consent", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Consent.dateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Records the date when the consent was given." - }, - { - "ordinal": "7.3", - "elementName": "Health Policy Monitoring", - "elementCode": { - "system": "SNOMEDCT", - "code": "386318002" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "7. Consent", - "dataType": "String", - "dataSpecification": [ - "n/a" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Consent.policy", - "recommendedDataSpec_fhir": "string", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "References to the policies that are included in thisconsent scope." - }, - { - "ordinal": "7.4", - "elementName": "Agreement to be Contacted for Research", - "elementCode": { - "system": "CustomCode", - "code": "consent_contact_research" - }, - "elementCodeSystem": "CustomCode", - "section": "7. Consent", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Contact for Research Value Set v2.0.0", - "fhirExpression_v4_0_1": "Consent.scope.coding", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Indicates whether the patient agrees to be contacted for research." - }, - { - "ordinal": "7.5", - "elementName": "Consent to the Reuse of Data", - "elementCode": { - "system": "CustomCode", - "code": "conset_data_reuse" - }, - "elementCodeSystem": "CustomCode", - "section": "7. Consent", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Data Reuse Consent Value Set v2.0.0", - "fhirExpression_v4_0_1": "Consent.scope.coding", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Indicates whether the patient consents to the reuse of their data." - }, - { - "ordinal": "7.6", - "elementName": "Biological Sample", - "elementCode": { - "system": "SNOMEDCT", - "code": "123038009" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "7. Consent", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Biological Sample Consent Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Indicates whether a patient's biological sample is available for research." - }, - { - "ordinal": "7.7", - "elementName": "Link to a Biobank", - "elementCode": { - "system": "CustomCode", - "code": "biobank_link" - }, - "elementCodeSystem": "CustomCode", - "section": "7. Consent", - "dataType": "String", - "dataSpecification": [ - "n/a" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "If there is a biological sample, this data element indicates the link to the biobank of the individual's biological sample." - }, - { - "ordinal": "8.1", - "elementName": "Classification of Functioning / Disability", - "elementCode": { - "system": "CustomCode", - "code": "icf_score" - }, - "elementCodeSystem": "CustomCode", - "section": "8. Disability", - "dataType": "Code", - "dataSpecification": [ - "ICF" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Specifies the classification of the individualss functioning or disability according to the International Classification of Functioning, Disability and Health (ICF)." - } - ], - "@type": "RdCdm" - }, - "value_sets": { - "value_sets": [ - { - "id": "SNOMEDCT:281053000", - "label": "Sex at Birth Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:1296886006", - "label": "Karyotypic Sex Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "74964007", - "label": "Other" - } - } - }, - { - "id": "SNOMEDCT:263495000", - "label": "Gender Identity Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:278844005", - "label": "Vital Status Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown - Other Reason" - } - } - }, - { - "id": "SNOMEDCT:105727008", - "label": "Age Category Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:278844005", - "label": "Vital Status Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown - Other Reason" - } - } - }, - { - "id": "SNOMEDCT:105727008", - "label": "Age Category Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:723663001", - "label": "Undiagnosed RD Case Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "373067005", - "label": "No" - } - } - }, - { - "id": "SNOMEDCT:305058001", - "label": "Encounter Status Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "unknown", - "label": "Unknown" - } - } - }, - { - "id": "HL7FHIR:encounter.class", - "label": "Encounter Class Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "HH", - "label": "Home Health" - }, - "CustomCode": { - "system": "CustomCode", - "code": "RDC", - "label": "RD Specialist Center" - }, - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "HL7FHIR:99498-8", - "label": "Verification Status Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "entered-in-error", - "label": "Entered in Error" - } - } - }, - { - "id": "SNOMEDCT:424850005", - "label": "Age at Onset Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:423493009", - "label": "Age at Diagnosis Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:363698007", - "label": "Body Site Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "442083009", - "label": "Anatomical or acquired body structure" - } - } - }, - { - "id": "SNOMEDCT:263493007", - "label": "Clinical Status Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "resolved", - "label": "Resolved" - } - } - }, - { - "id": "SNOMEDCT:246112005", - "label": "Severity Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "255604002", - "label": "Mild" - } - } - }, - { - "id": "GA4GH:progress_status", - "label": "Progress Status Value Set v2.0.0", - "codes": { - "GA4GH": { - "system": "GA4GH", - "code": "UNSOLVED", - "label": "The interpretation is complete but no definitive diagnosiswas found." - } - } - }, - { - "id": "GA4GH:interpretation_status", - "label": "Interpretation Status Value Set v2.0.0", - "codes": { - "GA4GH": { - "system": "GA4GH", - "code": "CAUSATIVE", - "label": "The variant or gene reported here is interpreted to be causative of the diagnosis." - } - } - }, - { - "id": "LOINC:81304-8", - "label": "Structural Variant Analysis Method Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA46-8", - "label": "Other" - } - } - }, - { - "id": "LOINC:62374-4", - "label": "Reference Genome Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA26806-2", - "label": "GRCh38 (hg38)" - } - } - }, - { - "id": "LOINC:53034-5", - "label": "Zygosity Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA46-8", - "label": "Other" - } - } - }, - { - "id": "LOINC:48002-0", - "label": "Genomic Source Class Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA26807-0", - "label": "De novo" - } - } - }, - { - "id": "LOINC:48019-4", - "label": "DNA Change Type Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA6690-7", - "label": "Substitution" - } - } - }, - { - "id": "LOINC:53037-8", - "label": "Clinical Significance ACMG Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA4489-6", - "label": "Unknown" - } - } - }, - { - "id": "GA4GH:therapeutic_actionability", - "label": "Therapeutic Actionability Value Set v2.0.0", - "codes": { - "GA4GH": { - "system": "GA4GH", - "code": "ACTIONABLE", - "label": "This variant is known to be therapeuticallyactionalbe." - } - } - }, - { - "id": "LOINC:93044-6", - "label": "Clinical Annotation Level Of Evidence Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA26333-7", - "label": "Uncertain significance" - } - } - }, - { - "id": "CustomCode:phenotypicfeature.excluded", - "label": "Phenotype Status Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "723511001", - "label": "Refuted" - } - } - }, - { - "id": "HP:0003674", - "label": "Onset Category Value Set v2.0.0", - "codes": { - "HP": { - "system": "HP", - "code": "0003584", - "label": "Late onset" - } - } - }, - { - "id": "HP:0011008", - "label": "Temporal Pattern Value Set v2.0.0", - "codes": { - "HP": { - "system": "HP", - "code": "0025153", - "label": "Transient" - } - } - }, - { - "id": "HP:0012824", - "label": "Severity Value Set v2.0.0", - "codes": { - "HP": { - "system": "HP", - "code": "0012828", - "label": "Severe" - } - } - }, - { - "id": "SNOMEDCT:64245008", - "label": "Propositus Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:408732007", - "label": "Family Relationship To Index Case Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:842009", - "label": "Consanguinity Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:444018008", - "label": "FamilyMember Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "HL7FHIR:familymemberhistory.status", - "label": "FamilyHistoryStatus Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "health-unknown", - "label": "Health Unknown" - } - } - }, - { - "id": "SNOMEDCT:54123-5", - "label": "AdministrativeGender Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:740604001", - "label": "Deceased Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "HL7FHIR:309370004", - "label": "Consent Status Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "entered-in-error", - "label": "Entered in Error" - } - } - }, - { - "id": "SNOMEDCT:consent_contact_research", - "label": "Contact for Research Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:conset_data_reuse", - "label": "Data Reuse Consent Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:123038009", - "label": "Biological Sample Consent Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - } - ], - "@type": "RdCdm" - } -} \ No newline at end of file diff --git a/src/rd_cdm/instances/v2_0_2/jsons/rd_cdm_v2_0_2.json b/src/rd_cdm/instances/v2_0_2/jsons/rd_cdm_v2_0_2.json deleted file mode 100644 index b45cb58..0000000 --- a/src/rd_cdm/instances/v2_0_2/jsons/rd_cdm_v2_0_2.json +++ /dev/null @@ -1,2184 +0,0 @@ -{ - "code_systems": { - "code_systems": [ - { - "id": "SNOMEDCT", - "namespace_iri": "http://purl.bioontology.org/ontology/SNOMEDCT/", - "version": "SNOMEDCT_US_2024_09_01", - "title": "Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT)" - }, - { - "id": "LOINC", - "namespace_iri": "http://loinc.org", - "version": "LNC278", - "title": "Logical Observation Identifiers Names and Codes (LOINC)" - }, - { - "id": "HP", - "namespace_iri": "http://purl.obolibrary.org/obo/HP", - "version": "2025-05-06", - "title": "Human Phenotype Ontology (HPO)" - }, - { - "id": "NCIT", - "namespace_iri": "http://purl.obolibrary.org/obo/NCIT/", - "version": "24.01e", - "title": "NCI Thesaurus (NCIT) OBO Edition" - }, - { - "id": "HL7FHIR", - "namespace_iri": "http://hl7.org/fhir/", - "version": "v4.0.1", - "title": "Health Level Seven Fast Healthcare Interoperability Resources, Release 4" - }, - { - "id": "GA4GH", - "namespace_iri": "https://ga4gh.github.io/phenopacket-v2/", - "version": "v2.0", - "title": "Global Alliance for Genomics and Health Phenopackets Schema" - }, - { - "id": "CustomCode", - "namespace_iri": "https://github.com/BIH-CEI/rd-cdm", - "version": "v2.0.0", - "title": "Custom Code System RD CDM v2.0.0" - }, - { - "id": "NCBITAXON", - "namespace_iri": "http://purl.obolibrary.org/obo/NCBITAXON/", - "version": "NCBI2024_04_02", - "title": "NCBI organismal classification" - }, - { - "id": "GENO", - "namespace_iri": "http://purl.obolibrary.org/obo/GENO/", - "version": "2023-10-08", - "title": "GENO – The Genotype Ontology" - }, - { - "id": "SO", - "namespace_iri": "http://purl.obolibrary.org/obo/SO/", - "version": "2.6", - "title": "Sequence Ontology" - }, - { - "id": "UO", - "namespace_iri": "http://purl.obolibrary.org/obo/UO/", - "version": "2023-05-25", - "title": "Units Ontology (UO)" - }, - { - "id": "ECO", - "namespace_iri": "http://purl.obolibrary.org/obo/ECO/", - "version": "2025-06-23", - "title": "Evidence & Conclusion Ontology (ECO)" - }, - { - "id": "ICD10CM", - "namespace_iri": "http://purl.bioontology.org/ontology/ICD10CM/", - "version": "CD10CM_2025", - "title": "International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM)" - }, - { - "id": "MONDO", - "namespace_iri": "http://purl.obolibrary.org/obo/MONDO/", - "version": "2025-06-03", - "title": "Mondo Disease Ontology" - }, - { - "id": "ORDO", - "namespace_iri": "http://purl.obolibrary.org/obo/ORDO/", - "version": "4.7", - "title": "Orphanet Rare Disease Ontology (ORDO)" - }, - { - "id": "HGNC", - "namespace_iri": "http://identifiers.org/hgnc/", - "version": "2024-08-23", - "title": "HUGO Gene Nomenclature Committee (HGNC)" - }, - { - "id": "OMIM", - "namespace_iri": "http://purl.bioontology.org/ontology/OMIM/", - "version": "OMIM2024_08_09", - "title": "Online Mendelian Inheritance in Man (OMIM)" - }, - { - "id": "HGVS", - "namespace_iri": "https://varnomen.hgvs.org/", - "version": "21.0.0", - "title": "Human Genome Variation Society Nomenclature" - }, - { - "id": "ICD11", - "namespace_iri": "http://id.who.int/icd/release/11/mms/", - "version": "2024-09-01", - "title": "International Classification of Diseases, Eleventh Revision (ICD-11)" - }, - { - "id": "ISO3166", - "namespace_iri": "https://www.iso.org/iso-3166-country-codes.html", - "version": "2020(en)", - "title": "International Organization for Standardization – ISO 3166 Country Codes" - }, - { - "id": "ICF", - "namespace_iri": "https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health", - "version": "1.0.2", - "title": "International Classification of Functioning, Disability and Health (ICF)" - } - ], - "@type": "RdCdm" - }, - "data_elements": { - "data_elements": [ - { - "ordinal": "1.1", - "elementName": "Pseudonym", - "elementCode": { - "system": "SNOMEDCT", - "code": "422549004" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "1. Formal Criteria", - "dataType": "Identifier", - "dataSpecification": [ - "n/a" - ], - "fhirExpression_v4_0_1": "Patient.identifier.value", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Individual.id", - "recommendedDataSpec_phenopackets": "string", - "description": "The (local) patient-related identification code." - }, - { - "ordinal": "1.2", - "elementName": "Date of Admission", - "elementCode": { - "system": "SNOMEDCT", - "code": "399423000" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "1. Formal Criteria", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Encounter.period.start", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Individual.time_at_last_encounter", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The date of admission or data capture of the individual." - }, - { - "ordinal": "2.1", - "elementName": "Date of Birth", - "elementCode": { - "system": "SNOMEDCT", - "code": "184099003" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Date", - "dataSpecification": [ - "YYYY", - "YYYY-MM", - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Patient.birthDate", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Individual.date_of_birth", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The individual's date of birth." - }, - { - "ordinal": "2.2", - "elementName": "Sex at Birth", - "elementCode": { - "system": "SNOMEDCT", - "code": "281053000" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Sex at Birth Value Set v2.0.0", - "fhirExpression_v4_0_1": "Patient.extension:individual-recordedSexOrGender", - "recommendedDataSpec_fhir": "Recorded Sex Or Gender Type", - "phenopacketSchemaElement_v2_0": "Individual.sex", - "recommendedDataSpec_phenopackets": "Sex", - "description": "The individual's sex that was assigned at birth." - }, - { - "ordinal": "2.3", - "elementName": "Karyotypic Sex", - "elementCode": { - "system": "SNOMEDCT", - "code": "1296886006" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Code", - "dataSpecification": [ - "VSc" - ], - "valueSet": "Karyotypic Sex Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.value", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Individual.karyotypic_sex", - "recommendedDataSpec_phenopackets": "Karyotypic Sex", - "description": "The chromosomal sex of an individual." - }, - { - "ordinal": "2.4", - "elementName": "Gender Identity", - "elementCode": { - "system": "SNOMEDCT", - "code": "263495000" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Gender Identity Value Set v2.0.0", - "fhirExpression_v4_0_1": "Patient.extension:individual-genderIdentity", - "recommendedDataSpec_fhir": "Gender Identity", - "phenopacketSchemaElement_v2_0": "Individual.gender", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The self-assigned gender of the individual." - }, - { - "ordinal": "2.5", - "elementName": "Country of Birth", - "elementCode": { - "system": "SNOMEDCT", - "code": "370159000" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "2. Personal Information", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "fhirExpression_v4_0_1": "Patient.extension:patient-birthPlace", - "recommendedDataSpec_fhir": "DataType: Address", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The individual's country of birth." - }, - { - "ordinal": "3.1", - "elementName": "Vital Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "278844005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Vital Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Patient.deceased.deceasedBoolean|Observation.value", - "recommendedDataSpec_fhir": "Boolean|Code", - "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.status", - "recommendedDataSpec_phenopackets": "Value Set: VitalStatus.Status", - "description": "The individual’s general clinical status orvital status." - }, - { - "ordinal": "3.2", - "elementName": "Time of Death", - "elementCode": { - "system": "SNOMEDCT", - "code": "398299004" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Date", - "dataSpecification": [ - "YYYY", - "YYYY-MM", - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Patient.deceasedDateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.time_of_death", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "If deceased, the individual’s date of death." - }, - { - "ordinal": "3.3", - "elementName": "Cause of Death", - "elementCode": { - "system": "SNOMEDCT", - "code": "184305005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Code", - "dataSpecification": [ - "ICD-10CM" - ], - "fhirExpression_v4_0_1": "Observation.value.coding.code", - "recommendedDataSpec_fhir": "Code|CodeableConcept", - "phenopacketSchemaElement_v2_0": "Individual.VitalStatus.cause_of_death", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "If deceased, the individual’s primary cause of death." - }, - { - "ordinal": "3.4", - "elementName": "Age Category", - "elementCode": { - "system": "SNOMEDCT", - "code": "105727008" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Age Category Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.value.coding.code", - "recommendedDataSpec_fhir": "CodableConcept", - "phenopacketSchemaElement_v2_0": "Individual.time_at_last_encounter", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The individual's age category at thetime of data capture." - }, - { - "ordinal": "3.5", - "elementName": "Length of Gestation at Birth [weeks+days]", - "elementCode": { - "system": "SNOMEDCT", - "code": "412726003" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "String", - "dataSpecification": [ - "XX+X" - ], - "fhirExpression_v4_0_1": "Observation.component:weeks.valueQuantity|Observation.component:days.valueQuantity", - "recommendedDataSpec_fhir": "Quantity", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The duration of the pregnancy in weeks and days,formatted as XX+X (weeks+days)." - }, - { - "ordinal": "3.6", - "elementName": "Undiagnosed RD Case", - "elementCode": { - "system": "SNOMEDCT", - "code": "723663001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "3. Patient Status", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Undiagnosed RD Case Value Set v2.0.0", - "fhirExpression_v4_0_1": "(Condition.code)", - "recommendedDataSpec_fhir": "Code(e.g. ORDO:616874 - Rare disorderwithout a determined diagnosis afterfull investigation)", - "phenopacketSchemaElement_v2_0": "(Disease.term)", - "recommendedDataSpec_phenopackets": "(OntologyClass (e.g. ORDO:616874 - Rare disorder without a determineddiagnosis after full investigation))", - "description": "Identifies cases where an RD diagnosis has notbeen established." - }, - { - "ordinal": "4.1", - "elementName": "Encounter Start", - "elementCode": { - "system": "HL7FHIR", - "code": "encounter.period.start" - }, - "elementCodeSystem": "HL7FHIR", - "section": "4. Care Pathway", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Encounter.period.start", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The beginning of an encounter of the individual." - }, - { - "ordinal": "4.2", - "elementName": "Encounter End", - "elementCode": { - "system": "HL7FHIR", - "code": "encounter.period.end" - }, - "elementCodeSystem": "HL7FHIR", - "section": "4. Care Pathway", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "fhirExpression_v4_0_1": "Encounter.period.end", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The end of an encounter of the individual." - }, - { - "ordinal": "4.3", - "elementName": "Encounter Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "305058001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "4. Care Pathway", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Encounter Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Encounter.status", - "recommendedDataSpec_fhir": "ValueSet: EncounterStatus", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The status of an encounter of the individual at thetime of data capture." - }, - { - "ordinal": "4.4", - "elementName": "Encounter Class", - "elementCode": { - "system": "HL7FHIR", - "code": "encounter.class" - }, - "elementCodeSystem": "HL7FHIR", - "section": "4. Care Pathway", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Encounter Class Value Set v2.0.0", - "fhirExpression_v4_0_1": "Encounter.class", - "recommendedDataSpec_fhir": "ValueSet: EncounterClass", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The class of an encounter of the individualat the time of data capture." - }, - { - "ordinal": "5.1", - "elementName": "Disease", - "elementCode": { - "system": "SNOMEDCT", - "code": "64572001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "Ontology Class (MONDO, ORDO, ICD-10, ICD-11, OMIM_g, OMIM_p)" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Condition.code", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "Disease.term", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "A disease that the individual was affected by. If agenetic diagnosis or subtypes were diagnosed, please also provide the respective OMIM_g and OMIM_p codes." - }, - { - "ordinal": "5.2", - "elementName": "Verification Status", - "elementCode": { - "system": "LOINC", - "code": "99498-8" - }, - "elementCodeSystem": "LOINC", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Verification Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.verificationStatus", - "recommendedDataSpec_fhir": "ValueSet: Condition Verficication Status", - "phenopacketSchemaElement_v2_0": "(Disease.excluded)", - "recommendedDataSpec_phenopackets": "boolean", - "description": "The verification status of the disease." - }, - { - "ordinal": "5.3", - "elementName": "Age at Onset", - "elementCode": { - "system": "SNOMEDCT", - "code": "424850005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Age at Onset Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.onsetString orObservation.valueCodeableConcept", - "recommendedDataSpec_fhir": "Disease.onset", - "phenopacketSchemaElement_v2_0": "Disease.onset", - "recommendedDataSpec_phenopackets": "Disease.onset", - "description": "The age at the onset of the first symptomsor signs of the disease." - }, - { - "ordinal": "5.4", - "elementName": "Date of Onset", - "elementCode": { - "system": "SNOMEDCT", - "code": "298059007" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Condition.onset", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "Disease.onset", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The date at onset of first symptoms orsigns of the disease." - }, - { - "ordinal": "5.5", - "elementName": "Age at Diagnosis", - "elementCode": { - "system": "SNOMEDCT", - "code": "423493009" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Age at Diagnosis Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.value", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "(Disease.onset)", - "recommendedDataSpec_phenopackets": "(TimeElement)", - "description": "The individual’s age when the diagnosis was made." - }, - { - "ordinal": "5.6", - "elementName": "Date of Diagnosis", - "elementCode": { - "system": "SNOMEDCT", - "code": "432213005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Condition.recordedDate", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "(Disease.onset)", - "recommendedDataSpec_phenopackets": "(TimeElement)", - "description": "The date on which the disease was determined." - }, - { - "ordinal": "5.7", - "elementName": "Body Site", - "elementCode": { - "system": "SNOMEDCT", - "code": "363698007" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Body Site Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.bodySite.coding:SNOMEDCT-ct", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "Disease.primary_site", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The specific body site affected by disease is encodedusing all descendants of SCT Body Structure (123037004)." - }, - { - "ordinal": "5.8", - "elementName": "Clinical Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "263493007" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Clinical Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.clinicalStatus", - "recommendedDataSpec_fhir": "ValueSet: ClinicalStatus", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The clinical status of the disease indicates whetherit is active, inactive, or resolved." - }, - { - "ordinal": "5.9", - "elementName": "Severity", - "elementCode": { - "system": "SNOMEDCT", - "code": "246112005" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "5. Disease", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Severity Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.severity", - "recommendedDataSpec_fhir": "ValueSet: ConditionSeverity", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The severity of the disease is categorised byclinical evaluation." - }, - { - "ordinal": "6.1.1", - "elementName": "Genomic Diagnosis", - "elementCode": { - "system": "SNOMEDCT", - "code": "106221001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "OMIM_p", - "MONDO" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Condition.code", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "Interpretation.Diagnosis.disease", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The genomic diagnoses can correspond to the diagnoseddisease in (5.1) if the same OMIM codes are used." - }, - { - "ordinal": "6.1.2", - "elementName": "Progress Status of Interpretation", - "elementCode": { - "system": "GA4GH", - "code": "progress_status" - }, - "elementCodeSystem": "GA4GH", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Progress Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.extension", - "recommendedDataSpec_fhir": "VS: GA4GH ProgressStatus", - "phenopacketSchemaElement_v2_0": "Interpretation.progress_status", - "recommendedDataSpec_phenopackets": "ValueSet: ProgressStatus", - "description": "The interpretation has a ProgressStatus that refers tothe status of the attempted diagnosis." - }, - { - "ordinal": "6.1.3", - "elementName": "Interpretation Status", - "elementCode": { - "system": "GA4GH", - "code": "interpretation_status" - }, - "elementCodeSystem": "GA4GH", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Interpretation Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Condition.extension", - "recommendedDataSpec_fhir": "VS: GA4GH InterpretationStatus", - "phenopacketSchemaElement_v2_0": "GenomicInterpretation.interpretation_status", - "recommendedDataSpec_phenopackets": "ValueSet: InterpretationStatus", - "description": "An enumeration that describes the conclusion made about the genomic interpretation." - }, - { - "ordinal": "6.1.4", - "elementName": "Structural Variant Analysis Method", - "elementCode": { - "system": "LOINC", - "code": "81304-8" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS", - "LOINC" - ], - "valueSet": "Structural Variant Analysis Method Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.method", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The method used to analyse structural variants in the genome." - }, - { - "ordinal": "6.1.5", - "elementName": "Reference Genome", - "elementCode": { - "system": "LOINC", - "code": "62374-4" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Reference Genome Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:reference-sequence-assembly", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The reference genome used for analysing the genetic variant." - }, - { - "ordinal": "6.1.6", - "elementName": "Genetic Mutation String", - "elementCode": { - "system": "LOINC", - "code": "LP7824-8" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "String", - "dataSpecification": [ - "n/a" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Variant.valueString", - "recommendedDataSpec_fhir": "string", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.Extension.value", - "recommendedDataSpec_phenopackets": "string", - "description": "An unvalidated (HGVS) string that describes the variant change" - }, - { - "ordinal": "6.1.7", - "elementName": "Genomic DNA Change", - "elementCode": { - "system": "LOINC", - "code": "81290-9" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "g.HGVS" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Variant.valueCode", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.Expression.value", - "recommendedDataSpec_phenopackets": "string", - "description": "The specific change in the genomic DNA sequence encoded with a validated g.HGVS expression." - }, - { - "ordinal": "6.1.8", - "elementName": "Sequence DNA Change", - "elementCode": { - "system": "LOINC", - "code": "48004-6" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "c.HGVS" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Variant.valueCode", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.Expression.value", - "recommendedDataSpec_phenopackets": "string", - "description": "The specific change in the DNA sequence at the nucleotide level with a validated c.HGVS expression." - }, - { - "ordinal": "6.1.9", - "elementName": "Amino Acid Change", - "elementCode": { - "system": "LOINC", - "code": "48005-3" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "p.HGVS" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Variant.valueCode", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.Expression.value", - "recommendedDataSpec_phenopackets": "string", - "description": "The specific change in the amino acid sequence resulting from agenetic variant as a validated p.HGVS expression." - }, - { - "ordinal": "6.1.10", - "elementName": "Gene", - "elementCode": { - "system": "LOINC", - "code": "48018-6" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "HGNC" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.component:Gene", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "GeneDescriptor.value_id", - "recommendedDataSpec_phenopackets": "string", - "description": "The specific gene or genes that were analysed or identified in the study." - }, - { - "ordinal": "6.1.11", - "elementName": "Zygosity", - "elementCode": { - "system": "LOINC", - "code": "53034-5" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc", - "LOINC" - ], - "valueSet": "Zygosity Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:geneticsAllele.State", - "recommendedDataSpec_fhir": "VS: Allelic State", - "phenopacketSchemaElement_v2_0": "VariationDescriptor.allelic_state", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The zygosity of the genetic variant." - }, - { - "ordinal": "6.1.12", - "elementName": "Genomic Source Class", - "elementCode": { - "system": "LOINC", - "code": "48002-0" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Genomic Source Class Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:GenomicSourceClass", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The classification of the genomic source, such as germline, somatic, or other origins." - }, - { - "ordinal": "6.1.13", - "elementName": "DNA Change Type", - "elementCode": { - "system": "LOINC", - "code": "48019-4" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "DNA Change Type Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:Variant.Type", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The variant’s type of DNA change, such as point mutation, deletion, insertion, or other types." - }, - { - "ordinal": "6.1.14", - "elementName": "Clinical Significance [ACMG]", - "elementCode": { - "system": "LOINC", - "code": "53037-8" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Clinical Significance ACMG Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.component:Variant.Interpretation", - "recommendedDataSpec_fhir": "", - "phenopacketSchemaElement_v2_0": "VariantInterpretation.acmg_pathogenicity_classification", - "recommendedDataSpec_phenopackets": "ValueSet: AcmgPathogenicityClassification", - "description": "The clinical significance of the genetic variant, indicating its impact on health and disease." - }, - { - "ordinal": "6.1.15", - "elementName": "Therapeutic Actionability", - "elementCode": { - "system": "GA4GH", - "code": "therapeutic_actionability" - }, - "elementCodeSystem": "GA4GH", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Therapeutic Actionability Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "VariantInterpretation.therapeutic_actionability", - "recommendedDataSpec_phenopackets": "ValueSet: TherapeuticActionability", - "description": "An enumeration flagging the variant as being a candidate for treatment or clinical intervention, which could improve the clinical outcome." - }, - { - "ordinal": "6.1.16", - "elementName": "Clinical Annotation Level Of Evidence", - "elementCode": { - "system": "LOINC", - "code": "93044-6" - }, - "elementCodeSystem": "LOINC", - "section": "6. Genetic Findings", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Clinical Annotation Level Of Evidence Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.extension:Variant.Interpretation", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The level of evidence supporting the clinical annotation of the genetic variant." - }, - { - "ordinal": "6.2.1", - "elementName": "Phenotypic Feature", - "elementCode": { - "system": "SNOMEDCT", - "code": "8116006" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6. Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "HPO" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.code", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.type", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "An observed physical and clinical characteristicencoded with HPO." - }, - { - "ordinal": "6.2.2", - "elementName": "Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "363778006" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Phenotype Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.status", - "recommendedDataSpec_fhir": "ValueSet: ObservationStatus", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.excluded", - "recommendedDataSpec_phenopackets": "boolean", - "description": "The current status of the phenotypic feature, indicating whether it is confirmed or refuted." - }, - { - "ordinal": "6.2.3", - "elementName": "Determination Date", - "elementCode": { - "system": "SNOMEDCT", - "code": "439272007:704321009=363778006" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6. Phenotypic Feature", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.effectiveDateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.onset", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "The date on which the phenotypic feature was observed or recorded. We recommend capturing the time acharacteristic was observed." - }, - { - "ordinal": "6.2.4", - "elementName": "Resolution Date", - "elementCode": { - "system": "HP", - "code": "0034382" - }, - "elementCodeSystem": "HP", - "section": "6.2 Phenotypic Feature", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.effectiveDateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.resolution", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "Time at which the feature resolved or abated." - }, - { - "ordinal": "6.2.5", - "elementName": "Onset Category", - "elementCode": { - "system": "HP", - "code": "0003674" - }, - "elementCodeSystem": "HP", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Onset Category Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.category", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.onset", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "Time at which the feature was first observed within HPO onset categories." - }, - { - "ordinal": "6.2.6", - "elementName": "Temporal Pattern", - "elementCode": { - "system": "HP", - "code": "0011008" - }, - "elementCodeSystem": "HP", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Temporal Pattern Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.interpretation", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.modifiers", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The speed at which disease manifestations appear and develop." - }, - { - "ordinal": "6.2.7", - "elementName": "Severity", - "elementCode": { - "system": "HP", - "code": "0012824" - }, - "elementCodeSystem": "HP", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Severity Value Set v2.0.0", - "fhirExpression_v4_0_1": "Observation.interpretation", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.severity", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "A description of the severity of the feature." - }, - { - "ordinal": "6.2.8", - "elementName": "Modifiers", - "elementCode": { - "system": "GA4GH", - "code": "phenotypicfeature.modifier" - }, - "elementCodeSystem": "GA4GH", - "section": "6. Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "OntologyClass (HPO, NCBITAXON, SCT)" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Suggested: Observation.extension", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.modifiers", - "recommendedDataSpec_phenopackets": "list of OntologyClass", - "description": "Any number of additional modifiers describing a specific phenotypic feature further, such as severity (HP:0012824), clinical modifiers (HP:0012823), or linking causative infectious agents using the NCBITAXON Ontology." - }, - { - "ordinal": "6.2.9", - "elementName": "Evidence", - "elementCode": { - "system": "GA4GH", - "code": "phenotypicfeature.evidence" - }, - "elementCodeSystem": "GA4GH", - "section": "6.2 Phenotypic Feature", - "dataType": "Code", - "dataSpecification": [ - "ECO" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.method", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "PhenotypicFeature.evidence", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The evidence for an assertion of the observation of a type defined within the Evidence & Conclusion Ontology (ECO)." - }, - { - "ordinal": "6.3.1", - "elementName": "Assay", - "elementCode": { - "system": "NCIT", - "code": "C60819" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Code", - "dataSpecification": [ - "OntologyClass (e.g. LOINC)" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.code", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "Measurement.assay", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "A class that describes the assay used to producethe measurement." - }, - { - "ordinal": "6.3.2", - "elementName": "Value", - "elementCode": { - "system": "NCIT", - "code": "C25712" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Value", - "dataSpecification": [ - "float" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.value[x]", - "recommendedDataSpec_fhir": "Quantity|integer", - "phenopacketSchemaElement_v2_0": "Measurement.measurement_value", - "recommendedDataSpec_phenopackets": "Quantity[double/float]", - "description": "The result of the measurement." - }, - { - "ordinal": "6.3.3", - "elementName": "Value Unit", - "elementCode": { - "system": "NCIT", - "code": "C92571" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Code", - "dataSpecification": [ - "UO" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.value[x].unit", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "Measurement.measurement_value", - "recommendedDataSpec_phenopackets": "OntologyClass", - "description": "The unit of the result's measurement." - }, - { - "ordinal": "6.3.4", - "elementName": "Interpretation", - "elementCode": { - "system": "NCIT", - "code": "C41255" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Code", - "dataSpecification": [ - "NCIT" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.interpretation", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "The interpretation of the measurement (e.g.: Below/Within/Above age-related reference range, Absent/Low/Normal, or Positive/Negative)." - }, - { - "ordinal": "6.3.5", - "elementName": "Time Observed", - "elementCode": { - "system": "NCIT", - "code": "C82577" - }, - "elementCodeSystem": "NCIT", - "section": "6.3 Measurement", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Observation.effectiveDateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "Measurement.time_observed", - "recommendedDataSpec_phenopackets": "TimeElement", - "description": "Time at which the measurement was performed." - }, - { - "ordinal": "6.3.6", - "elementName": "Procedure", - "elementCode": { - "system": "SNOMEDCT", - "code": "122869004" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.3 Measurement", - "dataType": "Code", - "dataSpecification": [ - "OntologyClass (e.g. NCIT, SNOMEDCT)" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Procedure.code", - "recommendedDataSpec_fhir": "Measurement.procedure", - "phenopacketSchemaElement_v2_0": "Measurement.procedure", - "recommendedDataSpec_phenopackets": "Measurement.procedure", - "description": "Clinical procedure performed to acquire the sample used for the measurement." - }, - { - "ordinal": "6.4.1", - "elementName": "Family Member Pseudonym", - "elementCode": { - "system": "CustomCode", - "code": "family_member_id" - }, - "elementCodeSystem": "CustomCode", - "section": "6.4 Family History", - "dataType": "Identifier", - "dataSpecification": [ - "n/a" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.identifier", - "recommendedDataSpec_fhir": "Identifier", - "phenopacketSchemaElement_v2_0": "Family.Pedigree.Person.individual_id", - "recommendedDataSpec_phenopackets": "string", - "description": "A unique identifier or local pseudonym for the familymember." - }, - { - "ordinal": "6.4.2", - "elementName": "Propositus/-a", - "elementCode": { - "system": "SNOMEDCT", - "code": "64245008" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family History", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Propositus Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Is the individual the first affected family member who seeks medical attention for a genetic disorder, leading to the diagnosis of other family members. Disclaimer: The SCT code for propositus (64245008) refers to any gender." - }, - { - "ordinal": "6.4.3", - "elementName": "Relationship of the Individual to the Propositus", - "elementCode": { - "system": "SNOMEDCT", - "code": "408732007" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family History", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "Family Relationship To Index Case Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Specifies the familial relationship of the individual being evaluated to the propositus. Disclaimer: The SNOMEDCT code for propositus (64245008) refers to any gender." - }, - { - "ordinal": "6.4.4", - "elementName": "Consanguinity", - "elementCode": { - "system": "SNOMEDCT", - "code": "842009" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family History", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Consanguinity Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "Family.consanguinous_parents", - "recommendedDataSpec_phenopackets": "boolean", - "description": "The presence of a biological relationship between parents who are related by blood, typically as first or second cousins." - }, - { - "ordinal": "6.4.5", - "elementName": "Family Member Relationship", - "elementCode": { - "system": "SNOMEDCT", - "code": "444018008" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family History", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "FamilyMember Value Set v2.0.0", - "fhirExpression_v4_0_1": "FamilyMemberHistory.relationship.coding", - "recommendedDataSpec_fhir": "ValueSet: FamilyMember", - "phenopacketSchemaElement_v2_0": "Family.Pedigree.Person.individual_id", - "recommendedDataSpec_phenopackets": "string", - "description": "Specifies the relationship of the selected family member to the patient." - }, - { - "ordinal": "6.4.6", - "elementName": "Family Member Record Status", - "elementCode": { - "system": "HL7FHIR", - "code": "familymemberhistory.status" - }, - "elementCodeSystem": "HL7FHIR", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "FamilyHistoryStatus Value Set v2.0.0", - "fhirExpression_v4_0_1": "FamilyMemberHistory.status", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Specifies the record’s status of the family history of a specific family member." - }, - { - "ordinal": "6.4.7", - "elementName": "Family Member Sex", - "elementCode": { - "system": "LOINC", - "code": "54123-5" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "VSe", - "VSc" - ], - "valueSet": "AdministrativeGender Value Set v2.0.0", - "fhirExpression_v4_0_1": "FamilyMemberHistory.sex", - "recommendedDataSpec_fhir": "ValueSet: AdministrativeGender", - "phenopacketSchemaElement_v2_0": "Family.Pedigree.Person.sex", - "recommendedDataSpec_phenopackets": "ValueSet: Sex", - "description": "Specifies the sex (or gender) of the specific family member. If possible, the sex assigned at birth should be selected." - }, - { - "ordinal": "6.4.8", - "elementName": "Family Member Age", - "elementCode": { - "system": "LOINC", - "code": "54141-7" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Integer", - "dataSpecification": [ - "Integer" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.ageAge", - "recommendedDataSpec_fhir": "Age", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Records the current age of the selected family member." - }, - { - "ordinal": "6.4.9", - "elementName": "Family Member Date of Birth", - "elementCode": { - "system": "LOINC", - "code": "54124-3" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.bornDate", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Records the date of birth of the selected family member." - }, - { - "ordinal": "6.4.10", - "elementName": "Family Member Deceased", - "elementCode": { - "system": "SNOMEDCT", - "code": "740604001" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Deceased Value Set v2.0.0", - "fhirExpression_v4_0_1": "FamilyMemberHistory.deceased.deceasedBoolean", - "recommendedDataSpec_fhir": "boolean", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Indicates whether the selected family member is deceased." - }, - { - "ordinal": "6.4.11", - "elementName": "Family Member Cause of Death", - "elementCode": { - "system": "LOINC", - "code": "54112-8" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "ICD10CM" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.condition.code & FamilyMemberHistory.condition.contributedToDeath", - "recommendedDataSpec_fhir": "Code", - "phenopacketSchemaElement_v2_0": "(Family.relatives → 1 Phenopacket per family member)", - "recommendedDataSpec_phenopackets": "(Family.relatives → 1 Phenopacket per family member)", - "description": "Records the cause of death of the selected deceasedfamily member." - }, - { - "ordinal": "6.4.12", - "elementName": "Family Member Deceased Age", - "elementCode": { - "system": "LOINC", - "code": "92662-6" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Integer", - "dataSpecification": [ - "Integer" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.deceasedAge", - "recommendedDataSpec_fhir": "Family.relatives", - "phenopacketSchemaElement_v2_0": "Family.relatives", - "recommendedDataSpec_phenopackets": "Family.relatives", - "description": "Records the age at which the selected family member died." - }, - { - "ordinal": "6.4.13", - "elementName": "Family Member Disease", - "elementCode": { - "system": "LOINC", - "code": "75315-2" - }, - "elementCodeSystem": "LOINC", - "section": "6.4 Family", - "dataType": "Code", - "dataSpecification": [ - "Ontology Class", - "ORDO", - "ICD-10-CM", - "ICD-11", - "MONDO", - "OMIM_p" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "FamilyMemberHistory.condition.code", - "recommendedDataSpec_fhir": "Family.relatives", - "phenopacketSchemaElement_v2_0": "Family.relatives", - "recommendedDataSpec_phenopackets": "Family.relatives", - "description": "Indicates whether the selected family member is affected by the same rare disease as the individual." - }, - { - "ordinal": "7.1", - "elementName": "Consent Status", - "elementCode": { - "system": "SNOMEDCT", - "code": "309370004" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "7. Consent", - "dataType": "Code", - "dataSpecification": [ - "VS" - ], - "valueSet": "Consent Status Value Set v2.0.0", - "fhirExpression_v4_0_1": "Consent.status", - "recommendedDataSpec_fhir": "ValueSet: ConsentStatus", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Indicates the current status of the consent." - }, - { - "ordinal": "7.2", - "elementName": "Consent Date", - "elementCode": { - "system": "HL7FHIR", - "code": "consent.datetime" - }, - "elementCodeSystem": "HL7FHIR", - "section": "7. Consent", - "dataType": "Date", - "dataSpecification": [ - "YYYY-MM-DD" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Consent.dateTime", - "recommendedDataSpec_fhir": "DateTime", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Records the date when the consent was given." - }, - { - "ordinal": "7.3", - "elementName": "Health Policy Monitoring", - "elementCode": { - "system": "SNOMEDCT", - "code": "386318002" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "7. Consent", - "dataType": "String", - "dataSpecification": [ - "n/a" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "Consent.policy", - "recommendedDataSpec_fhir": "string", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "References to the policies that are included in thisconsent scope." - }, - { - "ordinal": "7.4", - "elementName": "Agreement to be Contacted for Research", - "elementCode": { - "system": "CustomCode", - "code": "consent_contact_research" - }, - "elementCodeSystem": "CustomCode", - "section": "7. Consent", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Contact for Research Value Set v2.0.0", - "fhirExpression_v4_0_1": "Consent.scope.coding", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Indicates whether the patient agrees to be contacted for research." - }, - { - "ordinal": "7.5", - "elementName": "Consent to the Reuse of Data", - "elementCode": { - "system": "CustomCode", - "code": "conset_data_reuse" - }, - "elementCodeSystem": "CustomCode", - "section": "7. Consent", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Data Reuse Consent Value Set v2.0.0", - "fhirExpression_v4_0_1": "Consent.scope.coding", - "recommendedDataSpec_fhir": "CodeableConcept", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Indicates whether the patient consents to the reuse of their data." - }, - { - "ordinal": "7.6", - "elementName": "Biological Sample", - "elementCode": { - "system": "SNOMEDCT", - "code": "123038009" - }, - "elementCodeSystem": "SNOMEDCT", - "section": "7. Consent", - "dataType": "Code", - "dataSpecification": [ - "VSe" - ], - "valueSet": "Biological Sample Consent Value Set v2.0.0", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Indicates whether a patient's biological sample is available for research." - }, - { - "ordinal": "7.7", - "elementName": "Link to a Biobank", - "elementCode": { - "system": "CustomCode", - "code": "biobank_link" - }, - "elementCodeSystem": "CustomCode", - "section": "7. Consent", - "dataType": "String", - "dataSpecification": [ - "n/a" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "If there is a biological sample, this data element indicates the link to the biobank of the individual's biological sample." - }, - { - "ordinal": "8.1", - "elementName": "Classification of Functioning / Disability", - "elementCode": { - "system": "CustomCode", - "code": "icf_score" - }, - "elementCodeSystem": "CustomCode", - "section": "8. Disability", - "dataType": "Code", - "dataSpecification": [ - "ICF" - ], - "valueSet": "n/a", - "fhirExpression_v4_0_1": "n/a", - "recommendedDataSpec_fhir": "n/a", - "phenopacketSchemaElement_v2_0": "n/a", - "recommendedDataSpec_phenopackets": "n/a", - "description": "Specifies the classification of the individualss functioning or disability according to the International Classification of Functioning, Disability and Health (ICF)." - } - ], - "@type": "RdCdm" - }, - "value_sets": { - "value_sets": [ - { - "id": "SNOMEDCT:281053000", - "label": "Sex at Birth Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:1296886006", - "label": "Karyotypic Sex Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "74964007", - "label": "Other" - } - } - }, - { - "id": "SNOMEDCT:263495000", - "label": "Gender Identity Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:278844005", - "label": "Vital Status Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown - Other Reason" - } - } - }, - { - "id": "SNOMEDCT:105727008", - "label": "Age Category Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:278844005", - "label": "Vital Status Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown - Other Reason" - } - } - }, - { - "id": "SNOMEDCT:105727008", - "label": "Age Category Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:723663001", - "label": "Undiagnosed RD Case Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "373067005", - "label": "No" - } - } - }, - { - "id": "SNOMEDCT:305058001", - "label": "Encounter Status Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "unknown", - "label": "Unknown" - } - } - }, - { - "id": "HL7FHIR:encounter.class", - "label": "Encounter Class Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "HH", - "label": "Home Health" - }, - "CustomCode": { - "system": "CustomCode", - "code": "RDC", - "label": "RD Specialist Center" - }, - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "HL7FHIR:99498-8", - "label": "Verification Status Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "entered-in-error", - "label": "Entered in Error" - } - } - }, - { - "id": "SNOMEDCT:424850005", - "label": "Age at Onset Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:423493009", - "label": "Age at Diagnosis Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:363698007", - "label": "Body Site Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "442083009", - "label": "Anatomical or acquired body structure" - } - } - }, - { - "id": "SNOMEDCT:263493007", - "label": "Clinical Status Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "resolved", - "label": "Resolved" - } - } - }, - { - "id": "SNOMEDCT:246112005", - "label": "Severity Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "255604002", - "label": "Mild" - } - } - }, - { - "id": "GA4GH:progress_status", - "label": "Progress Status Value Set v2.0.0", - "codes": { - "GA4GH": { - "system": "GA4GH", - "code": "UNSOLVED", - "label": "The interpretation is complete but no definitive diagnosiswas found." - } - } - }, - { - "id": "GA4GH:interpretation_status", - "label": "Interpretation Status Value Set v2.0.0", - "codes": { - "GA4GH": { - "system": "GA4GH", - "code": "CAUSATIVE", - "label": "The variant or gene reported here is interpreted to be causative of the diagnosis." - } - } - }, - { - "id": "LOINC:81304-8", - "label": "Structural Variant Analysis Method Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA46-8", - "label": "Other" - } - } - }, - { - "id": "LOINC:62374-4", - "label": "Reference Genome Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA26806-2", - "label": "GRCh38 (hg38)" - } - } - }, - { - "id": "LOINC:53034-5", - "label": "Zygosity Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA46-8", - "label": "Other" - } - } - }, - { - "id": "LOINC:48002-0", - "label": "Genomic Source Class Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA26807-0", - "label": "De novo" - } - } - }, - { - "id": "LOINC:48019-4", - "label": "DNA Change Type Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA6690-7", - "label": "Substitution" - } - } - }, - { - "id": "LOINC:53037-8", - "label": "Clinical Significance ACMG Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA4489-6", - "label": "Unknown" - } - } - }, - { - "id": "GA4GH:therapeutic_actionability", - "label": "Therapeutic Actionability Value Set v2.0.0", - "codes": { - "GA4GH": { - "system": "GA4GH", - "code": "ACTIONABLE", - "label": "This variant is known to be therapeuticallyactionalbe." - } - } - }, - { - "id": "LOINC:93044-6", - "label": "Clinical Annotation Level Of Evidence Value Set v2.0.0", - "codes": { - "LOINC": { - "system": "LOINC", - "code": "LA26333-7", - "label": "Uncertain significance" - } - } - }, - { - "id": "CustomCode:phenotypicfeature.excluded", - "label": "Phenotype Status Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "723511001", - "label": "Refuted" - } - } - }, - { - "id": "HP:0003674", - "label": "Onset Category Value Set v2.0.0", - "codes": { - "HP": { - "system": "HP", - "code": "0003584", - "label": "Late onset" - } - } - }, - { - "id": "HP:0011008", - "label": "Temporal Pattern Value Set v2.0.0", - "codes": { - "HP": { - "system": "HP", - "code": "0025153", - "label": "Transient" - } - } - }, - { - "id": "HP:0012824", - "label": "Severity Value Set v2.0.0", - "codes": { - "HP": { - "system": "HP", - "code": "0012828", - "label": "Severe" - } - } - }, - { - "id": "SNOMEDCT:64245008", - "label": "Propositus Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:408732007", - "label": "Family Relationship To Index Case Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:842009", - "label": "Consanguinity Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:444018008", - "label": "FamilyMember Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "HL7FHIR:familymemberhistory.status", - "label": "FamilyHistoryStatus Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "health-unknown", - "label": "Health Unknown" - } - } - }, - { - "id": "SNOMEDCT:54123-5", - "label": "AdministrativeGender Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "1220561009", - "label": "Not recorded" - } - } - }, - { - "id": "SNOMEDCT:740604001", - "label": "Deceased Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "HL7FHIR:309370004", - "label": "Consent Status Value Set v2.0.0", - "codes": { - "HL7FHIR": { - "system": "HL7FHIR", - "code": "entered-in-error", - "label": "Entered in Error" - } - } - }, - { - "id": "SNOMEDCT:consent_contact_research", - "label": "Contact for Research Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:conset_data_reuse", - "label": "Data Reuse Consent Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - }, - { - "id": "SNOMEDCT:123038009", - "label": "Biological Sample Consent Value Set v2.0.0", - "codes": { - "SNOMEDCT": { - "system": "SNOMEDCT", - "code": "261665006", - "label": "Unknown" - } - } - } - ], - "@type": "RdCdm" - } -} \ No newline at end of file diff --git a/src/rd_cdm/instances/v2_0_2/rd_cdm_v2_0_2.yaml b/src/rd_cdm/instances/v2_0_2/rd_cdm_v2_0_2.yaml deleted file mode 100644 index 0b85150..0000000 --- a/src/rd_cdm/instances/v2_0_2/rd_cdm_v2_0_2.yaml +++ /dev/null @@ -1,2292 +0,0 @@ -code_systems: -# Codesystems that encode elements and value set items -- id: SNOMEDCT - namespace_iri: http://purl.bioontology.org/ontology/SNOMEDCT/ - version: "SNOMEDCT_US_2024_09_01" - title: "Systematized Nomenclature of Medicine – Clinical Terms (SNOMED CT)" - -- id: LOINC - namespace_iri: http://loinc.org - version: "LNC278" - title: "Logical Observation Identifiers Names and Codes (LOINC)" - -- id: HP - namespace_iri: http://purl.obolibrary.org/obo/HP - version: "2025-05-06" - title: "Human Phenotype Ontology (HPO)" - -- id: NCIT - namespace_iri: http://purl.obolibrary.org/obo/NCIT/ - version: "24.01e" - title: "NCI Thesaurus (NCIT) OBO Edition" - -- id: HL7FHIR - namespace_iri: http://hl7.org/fhir/ - version: "v4.0.1" - title: "Health Level Seven Fast Healthcare Interoperability Resources, Release 4" - -- id: GA4GH - namespace_iri: https://ga4gh.github.io/phenopacket-v2/ - version: "v2.0" - title: "Global Alliance for Genomics and Health Phenopackets Schema" - -- id: CustomCode - namespace_iri: https://github.com/BIH-CEI/rd-cdm - version: "v2.0.0" - title: "Custom Code System RD CDM v2.0.0" - -# Codesystems that can encode values of data elements -- id: NCBITAXON - namespace_iri: http://purl.obolibrary.org/obo/NCBITAXON/ - version: "NCBI2024_04_02" - title: "NCBI organismal classification" - -- id: GENO - namespace_iri: http://purl.obolibrary.org/obo/GENO/ - version: "2023-10-08" - title: "GENO – The Genotype Ontology" - -- id: SO - namespace_iri: http://purl.obolibrary.org/obo/SO/ - version: "2.6" - title: "Sequence Ontology" - -- id: UO - namespace_iri: http://purl.obolibrary.org/obo/UO/ - version: "2023-05-25" - title: "Units Ontology (UO)" - -- id: ECO - namespace_iri: http://purl.obolibrary.org/obo/ECO/ - version: "2025-06-23" - title: "Evidence & Conclusion Ontology (ECO)" -- id: ICD10CM - namespace_iri: http://purl.bioontology.org/ontology/ICD10CM/ - version: "CD10CM_2025" - title: "International Classification of Diseases, Tenth Revision, Clinical Modification - (ICD-10-CM)" - -- id: MONDO - namespace_iri: http://purl.obolibrary.org/obo/MONDO/ - version: "2025-06-03" - title: "Mondo Disease Ontology" - -- id: ORDO - namespace_iri: http://purl.obolibrary.org/obo/ORDO/ - version: "4.7" - title: "Orphanet Rare Disease Ontology (ORDO)" - -- id: HGNC - namespace_iri: http://identifiers.org/hgnc/ - version: "2024-08-23" - title: "HUGO Gene Nomenclature Committee (HGNC)" - -- id: OMIM - namespace_iri: http://purl.bioontology.org/ontology/OMIM/ - version: "OMIM2024_08_09" - title: "Online Mendelian Inheritance in Man (OMIM)" - -- id: HGVS - namespace_iri: https://varnomen.hgvs.org/ - version: "21.0.0" - title: "Human Genome Variation Society Nomenclature" - -- id: ICD11 - namespace_iri: http://id.who.int/icd/release/11/mms/ - version: "2024-09-01" - title: "International Classification of Diseases, Eleventh Revision (ICD-11)" - -- id: ISO3166 - namespace_iri: https://www.iso.org/iso-3166-country-codes.html - version: "2020(en)" - title: "International Organization for Standardization – ISO 3166 Country Codes" - -- id: ICF - namespace_iri: - https://www.who.int/standards/classifications/international-classification-of-functioning-disability-and-health - version: "1.0.2" - title: "International Classification of Functioning, Disability and Health (ICF)" -data_elements: -- ordinal: '1.1' - section: 1. Formal Criteria - elementName: Pseudonym - elementCode: - system: SNOMEDCT - code: '422549004' - elementCodeSystem: SNOMEDCT - dataType: Identifier - dataSpecification: - - n/a - valueSet: - fhirExpression_v4_0_1: Patient.identifier.value - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: Individual.id - recommendedDataSpec_phenopackets: string - description: The (local) patient-related identification code. -- ordinal: '1.2' - section: 1. Formal Criteria - elementName: Date of Admission - elementCode: - system: SNOMEDCT - code: '399423000' - elementCodeSystem: SNOMEDCT - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: - fhirExpression_v4_0_1: Encounter.period.start - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: Individual.time_at_last_encounter - recommendedDataSpec_phenopackets: TimeElement - description: The date of admission or data capture of the individual. -- ordinal: '2.1' - section: 2. Personal Information - elementName: Date of Birth - elementCode: - system: SNOMEDCT - code: '184099003' - elementCodeSystem: SNOMEDCT - dataType: Date - dataSpecification: - - YYYY - - YYYY-MM - - YYYY-MM-DD - valueSet: - fhirExpression_v4_0_1: Patient.birthDate - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: Individual.date_of_birth - recommendedDataSpec_phenopackets: TimeElement - description: The individual's date of birth. -- ordinal: '2.2' - section: 2. Personal Information - elementName: Sex at Birth - elementCode: - system: SNOMEDCT - code: '281053000' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Sex at Birth Value Set v2.0.0 - fhirExpression_v4_0_1: Patient.extension:individual-recordedSexOrGender - recommendedDataSpec_fhir: Recorded Sex Or Gender Type - phenopacketSchemaElement_v2_0: Individual.sex - recommendedDataSpec_phenopackets: Sex - description: The individual's sex that was assigned at birth. -- ordinal: '2.3' - section: 2. Personal Information - elementName: Karyotypic Sex - elementCode: - system: SNOMEDCT - code: '1296886006' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSc - valueSet: Karyotypic Sex Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.value - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: Individual.karyotypic_sex - recommendedDataSpec_phenopackets: Karyotypic Sex - description: The chromosomal sex of an individual. -- ordinal: '2.4' - section: 2. Personal Information - elementName: Gender Identity - elementCode: - system: SNOMEDCT - code: '263495000' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Gender Identity Value Set v2.0.0 - fhirExpression_v4_0_1: Patient.extension:individual-genderIdentity - recommendedDataSpec_fhir: Gender Identity - phenopacketSchemaElement_v2_0: Individual.gender - recommendedDataSpec_phenopackets: OntologyClass - description: The self-assigned gender of the individual. -- ordinal: '2.5' - section: 2. Personal Information - elementName: Country of Birth - elementCode: - system: SNOMEDCT - code: '370159000' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VS - valueSet: - fhirExpression_v4_0_1: Patient.extension:patient-birthPlace - recommendedDataSpec_fhir: 'DataType: Address' - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The individual's country of birth. -- ordinal: '3.1' - section: 3. Patient Status - elementName: Vital Status - elementCode: - system: SNOMEDCT - code: '278844005' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Vital Status Value Set v2.0.0 - fhirExpression_v4_0_1: Patient.deceased.deceasedBoolean|Observation.value - recommendedDataSpec_fhir: Boolean|Code - phenopacketSchemaElement_v2_0: Individual.VitalStatus.status - recommendedDataSpec_phenopackets: 'Value Set: VitalStatus.Status' - description: "The individual’s general clinical status orvital status." -- ordinal: '3.2' - section: 3. Patient Status - elementName: Time of Death - elementCode: - system: SNOMEDCT - code: '398299004' - elementCodeSystem: SNOMEDCT - dataType: Date - dataSpecification: - - YYYY - - YYYY-MM - - YYYY-MM-DD - valueSet: - fhirExpression_v4_0_1: Patient.deceasedDateTime - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: Individual.VitalStatus.time_of_death - recommendedDataSpec_phenopackets: TimeElement - description: "If deceased, the individual’s date of death." -- ordinal: '3.3' - section: 3. Patient Status - elementName: Cause of Death - elementCode: - system: SNOMEDCT - code: '184305005' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - ICD-10CM - valueSet: - fhirExpression_v4_0_1: Observation.value.coding.code - recommendedDataSpec_fhir: Code|CodeableConcept - phenopacketSchemaElement_v2_0: Individual.VitalStatus.cause_of_death - recommendedDataSpec_phenopackets: OntologyClass - description: "If deceased, the individual’s primary cause of death." -- ordinal: '3.4' - section: 3. Patient Status - elementName: Age Category - elementCode: - system: SNOMEDCT - code: '105727008' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - valueSet: Age Category Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.value.coding.code - recommendedDataSpec_fhir: CodableConcept - phenopacketSchemaElement_v2_0: Individual.time_at_last_encounter - recommendedDataSpec_phenopackets: TimeElement - description: The individual's age category at thetime of data capture. -- ordinal: '3.5' - section: 3. Patient Status - elementName: Length of Gestation at Birth [weeks+days] - elementCode: - system: SNOMEDCT - code: '412726003' - elementCodeSystem: SNOMEDCT - dataType: String - dataSpecification: - - XX+X - valueSet: - fhirExpression_v4_0_1: - Observation.component:weeks.valueQuantity|Observation.component:days.valueQuantity - recommendedDataSpec_fhir: Quantity - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The duration of the pregnancy in weeks and days,formatted as XX+X - (weeks+days). -- ordinal: '3.6' - section: 3. Patient Status - elementName: Undiagnosed RD Case - elementCode: - system: SNOMEDCT - code: '723663001' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - valueSet: Undiagnosed RD Case Value Set v2.0.0 - fhirExpression_v4_0_1: (Condition.code) - recommendedDataSpec_fhir: Code(e.g. ORDO:616874 - Rare disorderwithout a - determined diagnosis afterfull investigation) - phenopacketSchemaElement_v2_0: (Disease.term) - recommendedDataSpec_phenopackets: (OntologyClass (e.g. ORDO:616874 - Rare - disorder without a determineddiagnosis after full investigation)) - description: Identifies cases where an RD diagnosis has notbeen established. -- ordinal: '4.1' - section: 4. Care Pathway - elementName: Encounter Start - elementCode: - system: HL7FHIR - code: 'encounter.period.start' - elementCodeSystem: HL7FHIR - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: - fhirExpression_v4_0_1: Encounter.period.start - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The beginning of an encounter of the individual. -- ordinal: '4.2' - section: 4. Care Pathway - elementName: Encounter End - elementCode: - system: HL7FHIR - code: 'encounter.period.end' - elementCodeSystem: HL7FHIR - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: - fhirExpression_v4_0_1: Encounter.period.end - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The end of an encounter of the individual. -- ordinal: '4.3' - section: 4. Care Pathway - elementName: Encounter Status - elementCode: - system: SNOMEDCT - code: '305058001' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Encounter Status Value Set v2.0.0 - fhirExpression_v4_0_1: Encounter.status - recommendedDataSpec_fhir: 'ValueSet: EncounterStatus' - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The status of an encounter of the individual at thetime of data - capture. -- ordinal: '4.4' - section: 4. Care Pathway - elementName: Encounter Class - elementCode: - system: HL7FHIR - code: encounter.class - elementCodeSystem: HL7FHIR - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Encounter Class Value Set v2.0.0 - fhirExpression_v4_0_1: Encounter.class - recommendedDataSpec_fhir: 'ValueSet: EncounterClass' - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The class of an encounter of the individualat the time of data - capture. -- ordinal: '5.1' - section: 5. Disease - elementName: Disease - elementCode: - system: SNOMEDCT - code: '64572001' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - Ontology Class (MONDO, ORDO, ICD-10, ICD-11, OMIM_g, OMIM_p) - valueSet: n/a - fhirExpression_v4_0_1: Condition.code - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: Disease.term - recommendedDataSpec_phenopackets: OntologyClass - description: A disease that the individual was affected by. If agenetic - diagnosis or subtypes were diagnosed, please also provide the respective - OMIM_g and OMIM_p codes. -- ordinal: '5.2' - section: 5. Disease - elementName: Verification Status - elementCode: - system: LOINC - code: '99498-8' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - VS - valueSet: Verification Status Value Set v2.0.0 - fhirExpression_v4_0_1: Condition.verificationStatus - recommendedDataSpec_fhir: 'ValueSet: Condition Verficication Status' - phenopacketSchemaElement_v2_0: (Disease.excluded) - recommendedDataSpec_phenopackets: boolean - description: The verification status of the disease. -- ordinal: '5.3' - section: 5. Disease - elementName: Age at Onset - elementCode: - system: SNOMEDCT - code: '424850005' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Age at Onset Value Set v2.0.0 - fhirExpression_v4_0_1: Condition.onsetString - orObservation.valueCodeableConcept - recommendedDataSpec_fhir: Disease.onset - phenopacketSchemaElement_v2_0: Disease.onset - recommendedDataSpec_phenopackets: Disease.onset - description: The age at the onset of the first symptomsor signs of the - disease. -- ordinal: '5.4' - section: 5. Disease - elementName: Date of Onset - elementCode: - system: SNOMEDCT - code: '298059007' - elementCodeSystem: SNOMEDCT - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: n/a - fhirExpression_v4_0_1: Condition.onset - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: Disease.onset - recommendedDataSpec_phenopackets: TimeElement - description: The date at onset of first symptoms orsigns of the disease. -- ordinal: '5.5' - section: 5. Disease - elementName: Age at Diagnosis - elementCode: - system: SNOMEDCT - code: '423493009' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Age at Diagnosis Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.value - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: (Disease.onset) - recommendedDataSpec_phenopackets: (TimeElement) - description: "The individual’s age when the diagnosis was made." -- ordinal: '5.6' - section: 5. Disease - elementName: Date of Diagnosis - elementCode: - system: SNOMEDCT - code: '432213005' - elementCodeSystem: SNOMEDCT - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: n/a - fhirExpression_v4_0_1: Condition.recordedDate - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: (Disease.onset) - recommendedDataSpec_phenopackets: (TimeElement) - description: The date on which the disease was determined. -- ordinal: '5.7' - section: 5. Disease - elementName: Body Site - elementCode: - system: SNOMEDCT - code: '363698007' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VS - valueSet: Body Site Value Set v2.0.0 - fhirExpression_v4_0_1: Condition.bodySite.coding:SNOMEDCT-ct - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: Disease.primary_site - recommendedDataSpec_phenopackets: OntologyClass - description: The specific body site affected by disease is encodedusing all - descendants of SCT Body Structure (123037004). -- ordinal: '5.8' - section: 5. Disease - elementName: Clinical Status - elementCode: - system: SNOMEDCT - code: '263493007' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VS - valueSet: Clinical Status Value Set v2.0.0 - fhirExpression_v4_0_1: Condition.clinicalStatus - recommendedDataSpec_fhir: 'ValueSet: ClinicalStatus' - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The clinical status of the disease indicates whetherit is active, - inactive, or resolved. -- ordinal: '5.9' - section: 5. Disease - elementName: Severity - elementCode: - system: SNOMEDCT - code: '246112005' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VS - valueSet: Severity Value Set v2.0.0 - fhirExpression_v4_0_1: Condition.severity - recommendedDataSpec_fhir: 'ValueSet: ConditionSeverity' - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The severity of the disease is categorised byclinical evaluation. -- ordinal: 6.1.1 - section: 6. Genetic Findings - elementName: Genomic Diagnosis - elementCode: - system: SNOMEDCT - code: '106221001' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - OMIM_p - - MONDO - valueSet: n/a - fhirExpression_v4_0_1: Condition.code - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: Interpretation.Diagnosis.disease - recommendedDataSpec_phenopackets: OntologyClass - description: The genomic diagnoses can correspond to the diagnoseddisease in - (5.1) if the same OMIM codes are used. -- ordinal: 6.1.2 - section: 6. Genetic Findings - elementName: Progress Status of Interpretation - elementCode: - system: GA4GH - code: progress_status - elementCodeSystem: GA4GH - dataType: Code - dataSpecification: - - VS - valueSet: Progress Status Value Set v2.0.0 - fhirExpression_v4_0_1: Condition.extension - recommendedDataSpec_fhir: 'VS: GA4GH ProgressStatus' - phenopacketSchemaElement_v2_0: Interpretation.progress_status - recommendedDataSpec_phenopackets: 'ValueSet: ProgressStatus' - description: The interpretation has a ProgressStatus that refers tothe status - of the attempted diagnosis. -- ordinal: 6.1.3 - section: 6. Genetic Findings - elementName: Interpretation Status - elementCode: - system: GA4GH - code: interpretation_status - elementCodeSystem: GA4GH - dataType: Code - dataSpecification: - - VS - valueSet: Interpretation Status Value Set v2.0.0 - fhirExpression_v4_0_1: Condition.extension - recommendedDataSpec_fhir: 'VS: GA4GH InterpretationStatus' - phenopacketSchemaElement_v2_0: GenomicInterpretation.interpretation_status - recommendedDataSpec_phenopackets: 'ValueSet: InterpretationStatus' - description: An enumeration that describes the conclusion made about the - genomic interpretation. -- ordinal: 6.1.4 - section: 6. Genetic Findings - elementName: Structural Variant Analysis Method - elementCode: - system: LOINC - code: '81304-8' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - VS - - LOINC - valueSet: Structural Variant Analysis Method Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.method - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The method used to analyse structural variants in the genome. -- ordinal: 6.1.5 - section: 6. Genetic Findings - elementName: Reference Genome - elementCode: - system: LOINC - code: '62374-4' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - VS - valueSet: Reference Genome Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.component:reference-sequence-assembly - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The reference genome used for analysing the genetic variant. -- ordinal: 6.1.6 - section: 6. Genetic Findings - elementName: Genetic Mutation String - elementCode: - system: LOINC - code: 'LP7824-8' - elementCodeSystem: LOINC - dataType: String - dataSpecification: - - n/a - valueSet: n/a - fhirExpression_v4_0_1: Observation.component:Variant.valueString - recommendedDataSpec_fhir: string - phenopacketSchemaElement_v2_0: VariationDescriptor.Extension.value - recommendedDataSpec_phenopackets: string - description: An unvalidated (HGVS) string that describes the variant change -- ordinal: 6.1.7 - section: 6. Genetic Findings - elementName: Genomic DNA Change - elementCode: - system: LOINC - code: '81290-9' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - g.HGVS - valueSet: n/a - fhirExpression_v4_0_1: Observation.component:Variant.valueCode - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: VariationDescriptor.Expression.value - recommendedDataSpec_phenopackets: string - description: The specific change in the genomic DNA sequence encoded with a - validated g.HGVS expression. -- ordinal: 6.1.8 - section: 6. Genetic Findings - elementName: Sequence DNA Change - elementCode: - system: LOINC - code: '48004-6' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - c.HGVS - valueSet: n/a - fhirExpression_v4_0_1: Observation.component:Variant.valueCode - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: VariationDescriptor.Expression.value - recommendedDataSpec_phenopackets: string - description: The specific change in the DNA sequence at the nucleotide level - with a validated c.HGVS expression. -- ordinal: 6.1.9 - section: 6. Genetic Findings - elementName: Amino Acid Change - elementCode: - system: LOINC - code: '48005-3' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - p.HGVS - valueSet: n/a - fhirExpression_v4_0_1: Observation.component:Variant.valueCode - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: VariationDescriptor.Expression.value - recommendedDataSpec_phenopackets: string - description: The specific change in the amino acid sequence resulting from - agenetic variant as a validated p.HGVS expression. -- ordinal: 6.1.10 - section: 6. Genetic Findings - elementName: Gene - elementCode: - system: LOINC - code: '48018-6' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - HGNC - valueSet: n/a - fhirExpression_v4_0_1: Observation.component:Gene - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: GeneDescriptor.value_id - recommendedDataSpec_phenopackets: string - description: The specific gene or genes that were analysed or identified in - the study. -- ordinal: 6.1.11 - section: 6. Genetic Findings - elementName: Zygosity - elementCode: - system: LOINC - code: '53034-5' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - VSe - - VSc - - LOINC - valueSet: Zygosity Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.component:geneticsAllele.State - recommendedDataSpec_fhir: 'VS: Allelic State' - phenopacketSchemaElement_v2_0: VariationDescriptor.allelic_state - recommendedDataSpec_phenopackets: OntologyClass - description: The zygosity of the genetic variant. -- ordinal: 6.1.12 - section: 6. Genetic Findings - elementName: Genomic Source Class - elementCode: - system: LOINC - code: '48002-0' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - VS - valueSet: Genomic Source Class Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.component:GenomicSourceClass - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The classification of the genomic source, such as germline, - somatic, or other origins. -- ordinal: 6.1.13 - section: 6. Genetic Findings - elementName: DNA Change Type - elementCode: - system: LOINC - code: '48019-4' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - VS - valueSet: DNA Change Type Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.component:Variant.Type - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: "The variant’s type of DNA change, such as point mutation, deletion, - insertion, or other types." -- ordinal: 6.1.14 - section: 6. Genetic Findings - elementName: Clinical Significance [ACMG] - elementCode: - system: LOINC - code: '53037-8' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Clinical Significance ACMG Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.component:Variant.Interpretation - recommendedDataSpec_fhir: '' - phenopacketSchemaElement_v2_0: - VariantInterpretation.acmg_pathogenicity_classification - recommendedDataSpec_phenopackets: 'ValueSet: AcmgPathogenicityClassification' - description: The clinical significance of the genetic variant, indicating its - impact on health and disease. -- ordinal: 6.1.15 - section: 6. Genetic Findings - elementName: Therapeutic Actionability - elementCode: - system: GA4GH - code: therapeutic_actionability - elementCodeSystem: GA4GH - dataType: Code - dataSpecification: - - VS - valueSet: Therapeutic Actionability Value Set v2.0.0 - fhirExpression_v4_0_1: n/a - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: VariantInterpretation.therapeutic_actionability - recommendedDataSpec_phenopackets: 'ValueSet: TherapeuticActionability' - description: An enumeration flagging the variant as being a candidate for - treatment or clinical intervention, which could improve the clinical - outcome. -- ordinal: 6.1.16 - section: 6. Genetic Findings - elementName: Clinical Annotation Level Of Evidence - elementCode: - system: LOINC - code: '93044-6' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Clinical Annotation Level Of Evidence Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.extension:Variant.Interpretation - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: The level of evidence supporting the clinical annotation of the - genetic variant. -- ordinal: 6.2.1 - section: 6. Phenotypic Feature - elementName: Phenotypic Feature - elementCode: - system: SNOMEDCT - code: '8116006' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - HPO - valueSet: n/a - fhirExpression_v4_0_1: Observation.code - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: PhenotypicFeature.type - recommendedDataSpec_phenopackets: OntologyClass - description: An observed physical and clinical characteristicencoded with HPO. -- ordinal: 6.2.2 - section: 6.2 Phenotypic Feature - elementName: Status - elementCode: - system: SNOMEDCT - code: '363778006' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Phenotype Status Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.status - recommendedDataSpec_fhir: 'ValueSet: ObservationStatus' - phenopacketSchemaElement_v2_0: PhenotypicFeature.excluded - recommendedDataSpec_phenopackets: boolean - description: The current status of the phenotypic feature, indicating whether - it is confirmed or refuted. -- ordinal: 6.2.3 - section: 6. Phenotypic Feature - elementName: Determination Date - elementCode: - system: SNOMEDCT - code: '439272007:704321009=363778006' - elementCodeSystem: SNOMEDCT - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: n/a - fhirExpression_v4_0_1: Observation.effectiveDateTime - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: PhenotypicFeature.onset - recommendedDataSpec_phenopackets: TimeElement - description: The date on which the phenotypic feature was observed or - recorded. We recommend capturing the time acharacteristic was observed. -- ordinal: 6.2.4 - section: 6.2 Phenotypic Feature - elementName: Resolution Date - elementCode: - system: HP - code: '0034382' - elementCodeSystem: HP - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: n/a - fhirExpression_v4_0_1: Observation.effectiveDateTime - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: PhenotypicFeature.resolution - recommendedDataSpec_phenopackets: TimeElement - description: Time at which the feature resolved or abated. -- ordinal: 6.2.5 - section: 6.2 Phenotypic Feature - elementName: Onset Category - elementCode: - system: HP - code: '0003674' - elementCodeSystem: HP - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Onset Category Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.category - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: PhenotypicFeature.onset - recommendedDataSpec_phenopackets: OntologyClass - description: Time at which the feature was first observed within HPO onset - categories. -- ordinal: 6.2.6 - section: 6.2 Phenotypic Feature - elementName: Temporal Pattern - elementCode: - system: HP - code: '0011008' - elementCodeSystem: HP - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Temporal Pattern Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.interpretation - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: PhenotypicFeature.modifiers - recommendedDataSpec_phenopackets: OntologyClass - description: The speed at which disease manifestations appear and develop. -- ordinal: 6.2.7 - section: 6.2 Phenotypic Feature - elementName: Severity - elementCode: - system: HP - code: '0012824' - elementCodeSystem: HP - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Severity Value Set v2.0.0 - fhirExpression_v4_0_1: Observation.interpretation - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: PhenotypicFeature.severity - recommendedDataSpec_phenopackets: OntologyClass - description: A description of the severity of the feature. -- ordinal: 6.2.8 - section: 6. Phenotypic Feature - elementName: Modifiers - elementCode: - system: GA4GH - code: 'phenotypicfeature.modifier' - elementCodeSystem: GA4GH - dataType: Code - dataSpecification: - - OntologyClass (HPO, NCBITAXON, SCT) - valueSet: n/a - fhirExpression_v4_0_1: 'Suggested: Observation.extension' - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: PhenotypicFeature.modifiers - recommendedDataSpec_phenopackets: list of OntologyClass - description: Any number of additional modifiers describing a specific - phenotypic feature further, such as severity (HP:0012824), clinical - modifiers (HP:0012823), or linking causative infectious agents using the - NCBITAXON Ontology. -- ordinal: 6.2.9 - section: 6.2 Phenotypic Feature - elementName: Evidence - elementCode: - system: GA4GH - code: 'phenotypicfeature.evidence' - elementCodeSystem: GA4GH - dataType: Code - dataSpecification: - - ECO - valueSet: n/a - fhirExpression_v4_0_1: Observation.method - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: PhenotypicFeature.evidence - recommendedDataSpec_phenopackets: OntologyClass - description: The evidence for an assertion of the observation of a type - defined within the Evidence & Conclusion Ontology (ECO). -- ordinal: 6.3.1 - section: 6.3 Measurement - elementName: Assay - elementCode: - system: NCIT - code: 'C60819' - elementCodeSystem: NCIT - dataType: Code - dataSpecification: - - OntologyClass (e.g. LOINC) - valueSet: n/a - fhirExpression_v4_0_1: Observation.code - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: Measurement.assay - recommendedDataSpec_phenopackets: OntologyClass - description: A class that describes the assay used to producethe measurement. -- ordinal: 6.3.2 - section: 6.3 Measurement - elementName: Value - elementCode: - system: NCIT - code: 'C25712' - elementCodeSystem: NCIT - dataType: Value - dataSpecification: - - float - valueSet: n/a - fhirExpression_v4_0_1: Observation.value[x] - recommendedDataSpec_fhir: Quantity|integer - phenopacketSchemaElement_v2_0: Measurement.measurement_value - recommendedDataSpec_phenopackets: Quantity[double/float] - description: The result of the measurement. -- ordinal: 6.3.3 - section: 6.3 Measurement - elementName: Value Unit - elementCode: - system: NCIT - code: 'C92571' - elementCodeSystem: NCIT - dataType: Code - dataSpecification: - - UO - valueSet: n/a - fhirExpression_v4_0_1: Observation.value[x].unit - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: Measurement.measurement_value - recommendedDataSpec_phenopackets: OntologyClass - description: The unit of the result's measurement. -- ordinal: 6.3.4 - section: 6.3 Measurement - elementName: Interpretation - elementCode: - system: NCIT - code: 'C41255' - elementCodeSystem: NCIT - dataType: Code - dataSpecification: - - NCIT - valueSet: n/a - fhirExpression_v4_0_1: Observation.interpretation - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: 'The interpretation of the measurement (e.g.: Below/Within/Above age-related - reference range, Absent/Low/Normal, or Positive/Negative).' -- ordinal: 6.3.5 - section: 6.3 Measurement - elementName: Time Observed - elementCode: - system: NCIT - code: 'C82577' - elementCodeSystem: NCIT - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: n/a - fhirExpression_v4_0_1: Observation.effectiveDateTime - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: Measurement.time_observed - recommendedDataSpec_phenopackets: TimeElement - description: Time at which the measurement was performed. -- ordinal: 6.3.6 - section: 6.3 Measurement - elementName: Procedure - elementCode: - system: SNOMEDCT - code: '122869004' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - OntologyClass (e.g. NCIT, SNOMEDCT) - valueSet: n/a - fhirExpression_v4_0_1: Procedure.code - recommendedDataSpec_fhir: Measurement.procedure - phenopacketSchemaElement_v2_0: Measurement.procedure - recommendedDataSpec_phenopackets: Measurement.procedure - description: Clinical procedure performed to acquire the sample used for the - measurement. -- ordinal: 6.4.1 - section: 6.4 Family History - elementName: Family Member Pseudonym - elementCode: - system: CustomCode - code: 'family_member_id' - elementCodeSystem: CustomCode - dataType: Identifier - dataSpecification: - - n/a - valueSet: n/a - fhirExpression_v4_0_1: FamilyMemberHistory.identifier - recommendedDataSpec_fhir: Identifier - phenopacketSchemaElement_v2_0: Family.Pedigree.Person.individual_id - recommendedDataSpec_phenopackets: string - description: A unique identifier or local pseudonym for the familymember. -- ordinal: 6.4.2 - section: 6.4 Family History - elementName: Propositus/-a - elementCode: - system: SNOMEDCT - code: '64245008' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Propositus Value Set v2.0.0 - fhirExpression_v4_0_1: n/a - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: "(Family.relatives → 1 Phenopacket per family member)" - recommendedDataSpec_phenopackets: "(Family.relatives → 1 Phenopacket per family - member)" - description: 'Is the individual the first affected family member who seeks medical - attention for a genetic disorder, leading to the diagnosis of other family members. - Disclaimer: The SCT code for propositus (64245008) refers to any gender.' -- ordinal: 6.4.3 - section: 6.4 Family History - elementName: Relationship of the Individual to the Propositus - elementCode: - system: SNOMEDCT - code: '408732007' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: Family Relationship To Index Case Value Set v2.0.0 - fhirExpression_v4_0_1: n/a - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: "(Family.relatives → 1 Phenopacket per family member)" - recommendedDataSpec_phenopackets: "(Family.relatives → 1 Phenopacket per family - member)" - description: 'Specifies the familial relationship of the individual being evaluated - to the propositus. Disclaimer: The SNOMEDCT code for propositus (64245008) refers - to any gender.' -- ordinal: 6.4.4 - section: 6.4 Family History - elementName: Consanguinity - elementCode: - system: SNOMEDCT - code: '842009' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - valueSet: Consanguinity Value Set v2.0.0 - fhirExpression_v4_0_1: n/a - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: Family.consanguinous_parents - recommendedDataSpec_phenopackets: boolean - description: The presence of a biological relationship between parents who are - related by blood, typically as first or second cousins. -- ordinal: 6.4.5 - section: 6.4 Family History - elementName: Family Member Relationship - elementCode: - system: SNOMEDCT - code: '444018008' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: FamilyMember Value Set v2.0.0 - fhirExpression_v4_0_1: FamilyMemberHistory.relationship.coding - recommendedDataSpec_fhir: 'ValueSet: FamilyMember' - phenopacketSchemaElement_v2_0: Family.Pedigree.Person.individual_id - recommendedDataSpec_phenopackets: string - description: Specifies the relationship of the selected family member to the - patient. -- ordinal: 6.4.6 - section: 6.4 Family - elementName: Family Member Record Status - elementCode: - system: HL7FHIR - code: 'familymemberhistory.status' - elementCodeSystem: HL7FHIR - dataType: Code - dataSpecification: - - VS - valueSet: FamilyHistoryStatus Value Set v2.0.0 - fhirExpression_v4_0_1: FamilyMemberHistory.status - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: "Specifies the record’s status of the family history of a specific - family member." -- ordinal: 6.4.7 - section: 6.4 Family - elementName: Family Member Sex - elementCode: - system: LOINC - code: '54123-5' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - VSe - - VSc - valueSet: AdministrativeGender Value Set v2.0.0 - fhirExpression_v4_0_1: FamilyMemberHistory.sex - recommendedDataSpec_fhir: 'ValueSet: AdministrativeGender' - phenopacketSchemaElement_v2_0: Family.Pedigree.Person.sex - recommendedDataSpec_phenopackets: 'ValueSet: Sex' - description: Specifies the sex (or gender) of the specific family member. If - possible, the sex assigned at birth should be selected. -- ordinal: 6.4.8 - section: 6.4 Family - elementName: Family Member Age - elementCode: - system: LOINC - code: '54141-7' - elementCodeSystem: LOINC - dataType: Integer - dataSpecification: - - Integer - valueSet: n/a - fhirExpression_v4_0_1: FamilyMemberHistory.ageAge - recommendedDataSpec_fhir: Age - phenopacketSchemaElement_v2_0: "(Family.relatives → 1 Phenopacket per family member)" - recommendedDataSpec_phenopackets: "(Family.relatives → 1 Phenopacket per family - member)" - description: Records the current age of the selected family member. -- ordinal: 6.4.9 - section: 6.4 Family - elementName: Family Member Date of Birth - elementCode: - system: LOINC - code: '54124-3' - elementCodeSystem: LOINC - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: n/a - fhirExpression_v4_0_1: FamilyMemberHistory.bornDate - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: "(Family.relatives → 1 Phenopacket per family member)" - recommendedDataSpec_phenopackets: "(Family.relatives → 1 Phenopacket per family - member)" - description: Records the date of birth of the selected family member. -- ordinal: 6.4.10 - section: 6.4 Family - elementName: Family Member Deceased - elementCode: - system: SNOMEDCT - code: '740604001' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - valueSet: Deceased Value Set v2.0.0 - fhirExpression_v4_0_1: FamilyMemberHistory.deceased.deceasedBoolean - recommendedDataSpec_fhir: boolean - phenopacketSchemaElement_v2_0: "(Family.relatives → 1 Phenopacket per family member)" - recommendedDataSpec_phenopackets: "(Family.relatives → 1 Phenopacket per family - member)" - description: Indicates whether the selected family member is deceased. -- ordinal: 6.4.11 - section: 6.4 Family - elementName: Family Member Cause of Death - elementCode: - system: LOINC - code: '54112-8' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - ICD10CM - valueSet: n/a - fhirExpression_v4_0_1: FamilyMemberHistory.condition.code & - FamilyMemberHistory.condition.contributedToDeath - recommendedDataSpec_fhir: Code - phenopacketSchemaElement_v2_0: "(Family.relatives → 1 Phenopacket per family member)" - recommendedDataSpec_phenopackets: "(Family.relatives → 1 Phenopacket per family - member)" - description: Records the cause of death of the selected deceasedfamily member. -- ordinal: 6.4.12 - section: 6.4 Family - elementName: Family Member Deceased Age - elementCode: - system: LOINC - code: '92662-6' - elementCodeSystem: LOINC - dataType: Integer - dataSpecification: - - Integer - valueSet: n/a - fhirExpression_v4_0_1: FamilyMemberHistory.deceasedAge - recommendedDataSpec_fhir: Family.relatives - phenopacketSchemaElement_v2_0: Family.relatives - recommendedDataSpec_phenopackets: Family.relatives - description: Records the age at which the selected family member died. -- ordinal: 6.4.13 - section: 6.4 Family - elementName: Family Member Disease - elementCode: - system: LOINC - code: '75315-2' - elementCodeSystem: LOINC - dataType: Code - dataSpecification: - - Ontology Class - - ORDO - - ICD-10-CM - - ICD-11 - - MONDO - - OMIM_p - valueSet: n/a - fhirExpression_v4_0_1: FamilyMemberHistory.condition.code - recommendedDataSpec_fhir: Family.relatives - phenopacketSchemaElement_v2_0: Family.relatives - recommendedDataSpec_phenopackets: Family.relatives - description: Indicates whether the selected family member is affected by the - same rare disease as the individual. -- ordinal: '7.1' - section: 7. Consent - elementName: Consent Status - elementCode: - system: SNOMEDCT - code: '309370004' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VS - valueSet: Consent Status Value Set v2.0.0 - fhirExpression_v4_0_1: Consent.status - recommendedDataSpec_fhir: 'ValueSet: ConsentStatus' - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: Indicates the current status of the consent. -- ordinal: '7.2' - section: 7. Consent - elementName: Consent Date - elementCode: - system: HL7FHIR - code: 'consent.datetime' - elementCodeSystem: HL7FHIR - dataType: Date - dataSpecification: - - YYYY-MM-DD - valueSet: n/a - fhirExpression_v4_0_1: Consent.dateTime - recommendedDataSpec_fhir: DateTime - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: Records the date when the consent was given. -- ordinal: '7.3' - section: 7. Consent - elementName: Health Policy Monitoring - elementCode: - system: SNOMEDCT - code: '386318002' - elementCodeSystem: SNOMEDCT - dataType: String - dataSpecification: - - n/a - valueSet: n/a - fhirExpression_v4_0_1: Consent.policy - recommendedDataSpec_fhir: string - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: References to the policies that are included in thisconsent - scope. -- ordinal: '7.4' - section: 7. Consent - elementName: Agreement to be Contacted for Research - elementCode: - system: CustomCode - code: 'consent_contact_research' - elementCodeSystem: CustomCode - dataType: Code - dataSpecification: - - VSe - valueSet: Contact for Research Value Set v2.0.0 - fhirExpression_v4_0_1: Consent.scope.coding - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: Indicates whether the patient agrees to be contacted for - research. -- ordinal: '7.5' - section: 7. Consent - elementName: Consent to the Reuse of Data - elementCode: - system: CustomCode - code: 'conset_data_reuse' - elementCodeSystem: CustomCode - dataType: Code - dataSpecification: - - VSe - valueSet: Data Reuse Consent Value Set v2.0.0 - fhirExpression_v4_0_1: Consent.scope.coding - recommendedDataSpec_fhir: CodeableConcept - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: Indicates whether the patient consents to the reuse of their - data. -- ordinal: '7.6' - section: 7. Consent - elementName: Biological Sample - elementCode: - system: SNOMEDCT - code: '123038009' - elementCodeSystem: SNOMEDCT - dataType: Code - dataSpecification: - - VSe - valueSet: Biological Sample Consent Value Set v2.0.0 - fhirExpression_v4_0_1: n/a - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: Indicates whether a patient's biological sample is available for - research. -- ordinal: '7.7' - section: 7. Consent - elementName: Link to a Biobank - elementCode: - system: CustomCode - code: 'biobank_link' - elementCodeSystem: CustomCode - dataType: String - dataSpecification: - - n/a - valueSet: n/a - fhirExpression_v4_0_1: n/a - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: If there is a biological sample, this data element indicates the - link to the biobank of the individual's biological sample. -- ordinal: '8.1' - section: 8. Disability - elementName: Classification of Functioning / Disability - elementCode: - system: CustomCode - code: 'icf_score' - elementCodeSystem: CustomCode - dataType: Code - dataSpecification: - - ICF - valueSet: n/a - fhirExpression_v4_0_1: n/a - recommendedDataSpec_fhir: n/a - phenopacketSchemaElement_v2_0: n/a - recommendedDataSpec_phenopackets: n/a - description: Specifies the classification of the individualss functioning or - disability according to the International Classification of Functioning, - Disability and Health (ICF). -value_sets: -- id: SNOMEDCT:281053000 - label: Sex at Birth Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '248152002' - label: Female - - system: SNOMEDCT - code: '248153007' - label: Male - - system: SNOMEDCT - code: '184115007' - label: Patient sex unknown - - system: SNOMEDCT - code: '32570691000036108' - label: Intersex - - system: SNOMEDCT - code: '1220561009' - label: Not recorded -- id: SNOMEDCT:1296886006 - label: Karyotypic Sex Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '734875008' - label: XX - - system: SNOMEDCT - code: '734876009' - label: XY - - system: SNOMEDCT - code: '80427008' - label: X0 - - system: SNOMEDCT - code: '65162001' - label: XXY - - system: SNOMEDCT - code: '35111009' - label: XXX - - system: SNOMEDCT - code: '403760006' - label: XXYY - - system: SNOMEDCT - code: '78317008' - label: XXXY - - system: SNOMEDCT - code: '10567003' - label: XXXX - - system: SNOMEDCT - code: '48930007' - label: XYY - - system: SNOMEDCT - code: '74964007' - label: Other -- id: SNOMEDCT:263495000 - label: Gender Identity Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '446141000124107' - label: Female gender identity - - system: SNOMEDCT - code: '446151000124109' - label: Male gender identity - - system: SNOMEDCT - code: '394743007' - label: Gender unknown - - system: SNOMEDCT - code: '33791000087105' - label: Identifies as nonbinary gender - - system: SNOMEDCT - code: '1220561009' - label: Not recorded -- id: SNOMEDCT:278844005 - label: Vital Status Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '438949009' - label: Alive - - system: SNOMEDCT - code: '419099009' - label: Dead - - system: SNOMEDCT - code: '399307001' - label: Unknown - Lost in follow-up - - system: SNOMEDCT - code: '185924006' - label: Unknown - Opted-out - - system: SNOMEDCT - code: '261665006' - label: Unknown - Other Reason -- id: SNOMEDCT:105727008 - label: Age Category Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '3658006' - label: Infancy - - system: SNOMEDCT - code: '713153009' - label: Toddler - - system: SNOMEDCT - code: '255398004' - label: Childhood - - system: SNOMEDCT - code: '263659003' - label: Adolescence - - system: SNOMEDCT - code: '41847000' - label: Adulthood - - system: SNOMEDCT - code: '303112003' - label: Fetal period - - system: SNOMEDCT - code: '419099009' - label: Dead - - system: SNOMEDCT - code: '261665006' - label: Unknown -- id: SNOMEDCT:278844005 - label: Vital Status Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '438949009' - label: Alive - - system: SNOMEDCT - code: '419099009' - label: Dead - - system: SNOMEDCT - code: '399307001' - label: Unknown - Lost in follow-up - - system: SNOMEDCT - code: '185924006' - label: Unknown - Opted-out - - system: SNOMEDCT - code: '261665006' - label: Unknown - Other Reason -- id: SNOMEDCT:105727008 - label: Age Category Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '3658006' - label: Infancy - - system: SNOMEDCT - code: '713153009' - label: Toddler - - system: SNOMEDCT - code: '255398004' - label: Childhood - - system: SNOMEDCT - code: '263659003' - label: Adolescence - - system: SNOMEDCT - code: '41847000' - label: Adulthood - - system: SNOMEDCT - code: '303112003' - label: Fetal period - - system: SNOMEDCT - code: '419099009' - label: Dead - - system: SNOMEDCT - code: '261665006' - label: Unknown -- id: SNOMEDCT:723663001 - label: Undiagnosed RD Case Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '373066001' - label: 'Yes' - - system: SNOMEDCT - code: '373067005' - label: 'No' -- id: SNOMEDCT:305058001 - label: Encounter Status Value Set v2.0.0 - codes: - - system: HL7FHIR - code: 'planned' - label: Planned - - system: HL7FHIR - code: 'arrived' - label: Arrived - - system: HL7FHIR - code: 'triaged' - label: Triaged - - system: HL7FHIR - code: 'in-progress' - label: In Progress - - system: HL7FHIR - code: 'onleave' - label: On Leave - - system: HL7FHIR - code: 'finished' - label: Finished - - system: HL7FHIR - code: 'cancelled' - label: Cancelled - - system: HL7FHIR - code: 'entered-in-error' - label: Entered in Error - - system: HL7FHIR - code: 'unknown' - label: Unknown -- id: HL7FHIR:encounter.class - label: Encounter Class Value Set v2.0.0 - codes: - - system: HL7FHIR - code: 'AMB' - label: Ambulatory - - system: HL7FHIR - code: 'IMP' - label: Inpatient - - system: HL7FHIR - code: 'OBSENC' - label: Observation - - system: HL7FHIR - code: 'EMER' - label: Emergency - - system: HL7FHIR - code: 'VR' - label: Virtual - - system: HL7FHIR - code: 'HH' - label: Home Health - - system: CustomCode - code: 'RDC' - label: RD Specialist Center - - system: SNOMEDCT - code: '261665006' - label: Unknown -- id: HL7FHIR:99498-8 - label: Verification Status Value Set v2.0.0 - codes: - - system: HL7FHIR - code: 'unconfirmed' - label: Unconfirmed - - system: HL7FHIR - code: 'provisional' - label: Provisional - - system: HL7FHIR - code: 'differential' - label: Differential - - system: HL7FHIR - code: 'confirmed' - label: Confirmed - - system: HL7FHIR - code: 'refuted' - label: Refuted - - system: HL7FHIR - code: 'entered-in-error' - label: Entered in Error -- id: SNOMEDCT:424850005 - label: Age at Onset Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '118189007' - label: Prenatal - - system: SNOMEDCT - code: '3950001' - label: Birth - - system: SNOMEDCT - code: '410672004' - label: Date - - system: SNOMEDCT - code: '261665006' - label: Unknown -- id: SNOMEDCT:423493009 - label: Age at Diagnosis Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '118189007' - label: Prenatal - - system: SNOMEDCT - code: '3950001' - label: Birth - - system: SNOMEDCT - code: '410672004' - label: Date - - system: SNOMEDCT - code: '261665006' - label: Unknown -- id: SNOMEDCT:363698007 - label: Body Site Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '442083009' - label: Anatomical or acquired body structure -- id: SNOMEDCT:263493007 - label: Clinical Status Value Set v2.0.0 - codes: - - system: HL7FHIR - code: 'active' - label: Active - - system: HL7FHIR - code: 'recurrence' - label: Recurrence - - system: HL7FHIR - code: 'relapse' - label: Relapse - - system: HL7FHIR - code: 'inactive' - label: Inactive - - system: HL7FHIR - code: 'remission' - label: Remission - - system: HL7FHIR - code: 'resolved' - label: Resolved -- id: SNOMEDCT:246112005 - label: Severity Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '24484000' - label: Severe - - system: SNOMEDCT - code: '6736007' - label: Moderate severity - - system: SNOMEDCT - code: '255604002' - label: Mild -- id: GA4GH:progress_status - label: Progress Status Value Set v2.0.0 - codes: - - system: GA4GH - code: 'UNKNOWN_PROGRESS' - label: No information is available aboutthe diagnosis - - system: GA4GH - code: 'IN_PROGRESS' - label: No diagnosis has been found to date but additional differential - diagnostic work is in progress. - - system: GA4GH - code: 'COMPLETED' - label: The work on the interpretation is complete. - - system: GA4GH - code: 'SOLVED' - label: The interpretation is complete and also considered to be a definitive - diagnosis. - - system: GA4GH - code: 'UNSOLVED' - label: The interpretation is complete but no definitive diagnosiswas found. -- id: GA4GH:interpretation_status - label: Interpretation Status Value Set v2.0.0 - codes: - - system: GA4GH - code: 'UNKNOWN_STATUS' - label: No information is available about the status - - system: GA4GH - code: 'REJECTED' - label: The variant or gene reported here is interpreted not to be related - to the diagnosis. - - system: GA4GH - code: 'CANDIDATE' - label: The variant or gene reported here is interpreted to possibly be - related to the diagnosis. - - system: GA4GH - code: 'CONTRIBUTORY' - label: The variant or gene reported here is interpreted to be related to - the diagnosis. - - system: GA4GH - code: 'CAUSATIVE' - label: The variant or gene reported here is interpreted to be causative of - the diagnosis. -- id: LOINC:81304-8 - label: Structural Variant Analysis Method Value Set v2.0.0 - codes: - - system: LOINC - code: 'LA26406-1' - label: Karyotyping - - system: LOINC - code: 'LA26404-6' - label: FISH - - system: LOINC - code: 'LA26418-6' - label: PCR - - system: LOINC - code: 'LA26419-4' - label: qPCR (real-time PCR) - - system: LOINC - code: 'LA26400-4' - label: SNP array - - system: LOINC - code: 'LA26813-8' - label: Restriction fragment length polymorphism (RFLP) - - system: LOINC - code: 'LA26810-4' - label: DNA hybridization - - system: LOINC - code: 'LA26398-0' - label: Sequencing - - system: LOINC - code: 'LA26415-2' - label: MLPA - - system: LOINC - code: 'LA46-8' - label: Other -- id: LOINC:62374-4 - label: Reference Genome Value Set v2.0.0 - codes: - - system: LOINC - code: 'LA14032-9' - label: NCBI Build 34 (hg16) - - system: LOINC - code: 'LA14029-5' - label: GRCh37 (hg19) - - system: LOINC - code: 'LA14030-3' - label: NCBI Build 36.1 (hg18) - - system: LOINC - code: 'LA14031-1' - label: NCBI Build 35 (hg17) - - system: LOINC - code: 'LA26806-2' - label: GRCh38 (hg38) -- id: LOINC:53034-5 - label: Zygosity Value Set v2.0.0 - codes: - - system: LOINC - code: 'LA6705-3' - label: Homozygous - - system: LOINC - code: 'LA6706-1' - label: Heterozygous - - system: LOINC - code: 'LA26217-2' - label: Compound heterozygous - - system: LOINC - code: 'LA26220-6' - label: Double heterozygous - - system: LOINC - code: 'LA6707-9' - label: Hemizygous - - system: LOINC - code: 'LA6703-8' - label: Heteroplasmic - - system: LOINC - code: 'LA6704-6' - label: Homoplasmic - - system: LOINC - code: 'LA46-8' - label: Other -- id: LOINC:48002-0 - label: Genomic Source Class Value Set v2.0.0 - codes: - - system: LOINC - code: 'LA6683-2' - label: Germline - - system: LOINC - code: 'LA6684-0' - label: Somatic - - system: LOINC - code: 'LA10429-1' - label: Fetal - - system: LOINC - code: 'LA18194-3' - label: Likely germline - - system: LOINC - code: 'LA18195-0' - label: Likely somatic - - system: LOINC - code: 'LA18196-8' - label: Likely fetal - - system: LOINC - code: 'LA18197-6' - label: Unknown genomic origin - - system: LOINC - code: 'LA26807-0' - label: De novo -- id: LOINC:48019-4 - label: DNA Change Type Value Set v2.0.0 - codes: - - system: LOINC - code: 'LA9658-1' - label: Wild Type - - system: LOINC - code: 'LA6692-3' - label: Deletion - - system: LOINC - code: 'LA6686-5' - label: Duplication - - system: LOINC - code: 'LA6687-3' - label: Insertion - - system: LOINC - code: 'LA6688-1' - label: Insertion/Deletion - - system: LOINC - code: 'LA6689-9' - label: Inversion - - system: LOINC - code: 'LA6690-7' - label: Substitution -- id: LOINC:53037-8 - label: Clinical Significance ACMG Value Set v2.0.0 - codes: - - system: LOINC - code: 'LA6668-3' - label: Pathogenic - - system: LOINC - code: 'LA26332-9' - label: Likely pathogenic - - system: LOINC - code: 'LA26333-7' - label: Uncertain significance - - system: LOINC - code: 'LA26334-5' - label: Likely benign - - system: LOINC - code: 'LA6675-8' - label: Benign - - system: LOINC - code: 'LA4489-6' - label: Unknown -- id: GA4GH:therapeutic_actionability - label: Therapeutic Actionability Value Set v2.0.0 - codes: - - system: GA4GH - code: 'UNKNOWN_ACTIONABILITY' - label: There is not enough information at this time to support any - therapeutic actionability for this variant. - - system: GA4GH - code: 'NOT_ACTIONABLE' - label: This variant has no therapeutic actionability. - - system: GA4GH - code: 'ACTIONABLE' - label: This variant is known to be therapeuticallyactionalbe. -- id: LOINC:93044-6 - label: Clinical Annotation Level Of Evidence Value Set v2.0.0 - codes: - - system: LOINC - code: 'LA30200-2' - label: Very Strong evidence pathogenic - - system: LOINC - code: 'LA30201-0' - label: Strong evidence pathogenic - - system: LOINC - code: 'LA30202-8' - label: Moderate evidence pathogenic - - system: LOINC - code: 'LA30203-6' - label: Supporting evidence pathogenic - - system: LOINC - code: 'LA30204-4' - label: Supporting evidence benign - - system: LOINC - code: 'LA30205-1' - label: Strong evidence benign - - system: LOINC - code: 'LA30206-9' - label: Stand-alone evidence pathogenic - - system: LOINC - code: 'LA30207-7' - label: Stand-alone evidence benign - - system: LOINC - code: 'LA26333-7' - label: Uncertain significance -- id: CustomCode:phenotypicfeature.excluded - label: Phenotype Status Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '410605003' - label: Confirmed present - - system: SNOMEDCT - code: '723511001' - label: Refuted -- id: HP:0003674 - label: Onset Category Value Set v2.0.0 - codes: - - system: HP - code: '0011460' - label: Embryonal onset - - system: HP - code: '0011461' - label: Fetal onset - - system: HP - code: '0003577' - label: Congenital onset - - system: HP - code: '0003623' - label: Neonatal onset - - system: HP - code: '0003593' - label: Infantile onset - - system: HP - code: '0011463' - label: Childhood onset - - system: HP - code: '0003621' - label: Juvenile onset - - system: HP - code: '0011462' - label: Young adult onset - - system: HP - code: '0003596' - label: Middle age onset - - system: HP - code: '0003584' - label: Late onset -- id: HP:0011008 - label: Temporal Pattern Value Set v2.0.0 - codes: - - system: HP - code: '0011009' - label: Acute - - system: HP - code: '0011010' - label: Chronic - - system: HP - code: '0031914' - label: Fluctuating - - system: HP - code: '0025297' - label: Prolonged - - system: HP - code: '0031796' - label: Recurrent - - system: HP - code: '0031915' - label: Stable - - system: HP - code: '0011011' - label: Subacute - - system: HP - code: '0025153' - label: Transient -- id: HP:0012824 - label: Severity Value Set v2.0.0 - codes: - - system: HP - code: '0012827' - label: Borderline - - system: HP - code: '0012825' - label: Mild - - system: HP - code: '0012826' - label: Moderate - - system: HP - code: '0012829' - label: Profound - - system: HP - code: '0012828' - label: Severe -- id: SNOMEDCT:64245008 - label: Propositus Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '373066001' - label: 'Yes' - - system: SNOMEDCT - code: '373067005' - label: 'No' - - system: SNOMEDCT - code: '261665006' - label: Unknown - - system: SNOMEDCT - code: '1220561009' - label: Not recorded -- id: SNOMEDCT:408732007 - label: Family Relationship To Index Case Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '65656005' - label: Natural mother - - system: SNOMEDCT - code: '9947008' - label: Natural father - - system: SNOMEDCT - code: '83420006' - label: Natural daughter - - system: SNOMEDCT - code: '113160008' - label: Natural son - - system: SNOMEDCT - code: '60614009' - label: Natural brother - - system: SNOMEDCT - code: '73678001' - label: Natural sister - - system: SNOMEDCT - code: '11286003' - label: Twin sibling - - system: SNOMEDCT - code: '45929001' - label: Half-brother - - system: SNOMEDCT - code: '2272004' - label: Half-sister - - system: SNOMEDCT - code: '62296006' - label: Natural grandfather - - system: SNOMEDCT - code: '17945006' - label: Natural grandmother - - system: SNOMEDCT - code: '1220561009' - label: Not recorded -- id: SNOMEDCT:842009 - label: Consanguinity Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '373066001' - label: 'Yes' - - system: SNOMEDCT - code: '373067005' - label: 'No' - - system: SNOMEDCT - code: '261665006' - label: Unknown - - system: SNOMEDCT - code: '1220561009' - label: Not recorded -- id: SNOMEDCT:444018008 - label: FamilyMember Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '65656005' - label: Natural mother - - system: SNOMEDCT - code: '9947008' - label: Natural father - - system: SNOMEDCT - code: '83420006' - label: Natural daughter - - system: SNOMEDCT - code: '113160008' - label: Natural son - - system: SNOMEDCT - code: '60614009' - label: Natural brother - - system: SNOMEDCT - code: '73678001' - label: Natural sister - - system: SNOMEDCT - code: '11286003' - label: Twin sibling - - system: SNOMEDCT - code: '45929001' - label: Half-brother - - system: SNOMEDCT - code: '2272004' - label: Half-sister - - system: SNOMEDCT - code: '62296006' - label: Natural grandfather - - system: SNOMEDCT - code: '17945006' - label: Natural grandmother - - system: SNOMEDCT - code: '1220561009' - label: Not recorded -- id: HL7FHIR:familymemberhistory.status - label: FamilyHistoryStatus Value Set v2.0.0 - codes: - - system: HL7FHIR - code: partial - label: Partial - - system: HL7FHIR - code: completed - label: Completed - - system: HL7FHIR - code: entered-in-error - label: Entered in Error - - system: HL7FHIR - code: health-unknown - label: Health Unknown -- id: SNOMEDCT:54123-5 - label: AdministrativeGender Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '248152002' - label: Female - - system: SNOMEDCT - code: '248153007' - label: Male - - system: SNOMEDCT - code: '184115007' - label: Patient sex unknown - - system: SNOMEDCT - code: '32570691000036108' - label: Intersex - - system: SNOMEDCT - code: '1220561009' - label: Not recorded -- id: SNOMEDCT:740604001 - label: Deceased Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '373066001' - label: 'Yes' - - system: SNOMEDCT - code: '373067005' - label: 'No' - - system: SNOMEDCT - code: '261665006' - label: Unknown -- id: HL7FHIR:309370004 - label: Consent Status Value Set v2.0.0 - codes: - - system: HL7FHIR - code: 'draft' - label: Pending - - system: HL7FHIR - code: 'proposed' - label: Proposed - - system: HL7FHIR - code: 'active' - label: Active - - system: HL7FHIR - code: 'rejected' - label: Rejected - - system: HL7FHIR - code: 'inactive' - label: Inactive - - system: HL7FHIR - code: 'entered-in-error' - label: Entered in Error -- id: SNOMEDCT:consent_contact_research - label: Contact for Research Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '373066001' - label: 'Yes' - - system: SNOMEDCT - code: '373067005' - label: 'No' - - system: SNOMEDCT - code: '261665006' - label: Unknown -- id: SNOMEDCT:conset_data_reuse - label: Data Reuse Consent Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '373066001' - label: 'Yes' - - system: SNOMEDCT - code: '373067005' - label: 'No' - - system: SNOMEDCT - code: '261665006' - label: Unknown -- id: SNOMEDCT:123038009 - label: Biological Sample Consent Value Set v2.0.0 - codes: - - system: SNOMEDCT - code: '373066001' - label: 'Yes' - - system: SNOMEDCT - code: '373067005' - label: 'No' - - system: SNOMEDCT - code: '261665006' - label: Unknown diff --git a/src/rd_cdm/instances/v2_0_2/value_sets.yaml b/src/rd_cdm/instances/value_sets.yaml similarity index 100% rename from src/rd_cdm/instances/v2_0_2/value_sets.yaml rename to src/rd_cdm/instances/value_sets.yaml diff --git a/src/rd_cdm/python_classes/rd_cdm.py b/src/rd_cdm/python_classes/rd_cdm.py index fa14db7..a2bbf66 100644 --- a/src/rd_cdm/python_classes/rd_cdm.py +++ b/src/rd_cdm/python_classes/rd_cdm.py @@ -1,42 +1,70 @@ -# Auto generated from rd_cdm.yaml by pythongen.py version: 0.0.1 -# Generation date: 2025-08-07T14:59:42 -# Schema: rd_cdm.schema.yaml +# AUTO-GENERATED by src/rd_cdm/utils/gen_pydantic.py (PythonGenerator) +# Schema: /Users/adamgraefe/Documents/git/rd-cdm/src/rd_cdm/schema/rd_cdm.yaml +# Do not edit manually — re-run gen_pydantic.py to regenerate. + +# Auto generated from tmpe_1_xxje.yaml by pythongen.py version: 0.0.1 +# Generation date: 2026-03-24T17:00:59 +# Schema: rd-cdm # # id: https://github.com/BIH-CEI/rd-cdm/linkml/rd_cdm.schema.yaml # description: # license: CC0 - +import dataclasses +import re from dataclasses import dataclass +from datetime import ( + date, + datetime, + time +) from typing import ( Any, ClassVar, + Dict, + List, Optional, Union ) from jsonasobj2 import ( + JsonObj, as_dict ) +from linkml_runtime.linkml_model.meta import ( + EnumDefinition, + PermissibleValue, + PvFormulaOptions +) from linkml_runtime.utils.curienamespace import CurieNamespace +from linkml_runtime.utils.enumerations import EnumDefinitionImpl +from linkml_runtime.utils.formatutils import ( + camelcase, + sfx, + underscore +) from linkml_runtime.utils.metamodelcore import ( + bnode, empty_dict, empty_list ) from linkml_runtime.utils.slot import Slot from linkml_runtime.utils.yamlutils import ( YAMLRoot, + extended_float, + extended_int, extended_str ) from rdflib import ( + Namespace, URIRef ) -from linkml_runtime.linkml_model.types import Curie -from linkml_runtime.utils.metamodelcore import URI +from linkml_runtime.linkml_model.types import Curie, Date, String, Uri +from linkml_runtime.utils.metamodelcore import Curie, URI, XSDDate metamodel_version = "1.7.0" -version = None +version = "2.0.3" # Namespaces LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') @@ -64,20 +92,28 @@ class RdCdm(YAMLRoot): class_name: ClassVar[str] = "RdCdm" class_model_uri: ClassVar[URIRef] = URIRef("https://github.com/BIH-CEI/rd-cdm/linkml/rd_cdm.schema.yaml/RdCdm") + rd_cdm_version: str = None + rd_cdm_date: Union[str, XSDDate] = None code_systems: Optional[Union[dict[Union[str, CodeSystemId], Union[dict, "CodeSystem"]], list[Union[dict, "CodeSystem"]]]] = empty_dict() data_elements: Optional[Union[Union[dict, "DataElement"], list[Union[dict, "DataElement"]]]] = empty_list() value_sets: Optional[Union[Union[dict, "ValueSet"], list[Union[dict, "ValueSet"]]]] = empty_list() def __post_init__(self, *_: str, **kwargs: Any): + if self._is_empty(self.rd_cdm_version): + self.MissingRequiredField("rd_cdm_version") + if not isinstance(self.rd_cdm_version, str): + self.rd_cdm_version = str(self.rd_cdm_version) + + if self._is_empty(self.rd_cdm_date): + self.MissingRequiredField("rd_cdm_date") + if not isinstance(self.rd_cdm_date, XSDDate): + self.rd_cdm_date = XSDDate(self.rd_cdm_date) + self._normalize_inlined_as_list(slot_name="code_systems", slot_type=CodeSystem, key_name="id", keyed=True) - if not isinstance(self.data_elements, list): - self.data_elements = [self.data_elements] if self.data_elements is not None else [] - self.data_elements = [v if isinstance(v, DataElement) else DataElement(**as_dict(v)) for v in self.data_elements] + self._normalize_inlined_as_list(slot_name="data_elements", slot_type=DataElement, key_name="ordinal", keyed=False) - if not isinstance(self.value_sets, list): - self.value_sets = [self.value_sets] if self.value_sets is not None else [] - self.value_sets = [v if isinstance(v, ValueSet) else ValueSet(**as_dict(v)) for v in self.value_sets] + self._normalize_inlined_as_list(slot_name="value_sets", slot_type=ValueSet, key_name="id", keyed=False) super().__post_init__(**kwargs) @@ -185,7 +221,7 @@ def __post_init__(self, *_: str, **kwargs: Any): if not isinstance(self.label, str): self.label = str(self.label) - self._normalize_inlined_as_dict(slot_name="codes", slot_type=Coding, key_name="system", keyed=False) + self._normalize_inlined_as_list(slot_name="codes", slot_type=Coding, key_name="system", keyed=False) super().__post_init__(**kwargs) @@ -275,6 +311,12 @@ def __post_init__(self, *_: str, **kwargs: Any): class slots: pass +slots.rdCdm__rd_cdm_version = Slot(uri=DEFAULT_.rd_cdm_version, name="rdCdm__rd_cdm_version", curie=DEFAULT_.curie('rd_cdm_version'), + model_uri=DEFAULT_.rdCdm__rd_cdm_version, domain=None, range=str) + +slots.rdCdm__rd_cdm_date = Slot(uri=DEFAULT_.rd_cdm_date, name="rdCdm__rd_cdm_date", curie=DEFAULT_.curie('rd_cdm_date'), + model_uri=DEFAULT_.rdCdm__rd_cdm_date, domain=None, range=Union[str, XSDDate]) + slots.rdCdm__code_systems = Slot(uri=DEFAULT_.code_systems, name="rdCdm__code_systems", curie=DEFAULT_.curie('code_systems'), model_uri=DEFAULT_.rdCdm__code_systems, domain=None, range=Optional[Union[dict[Union[str, CodeSystemId], Union[dict, CodeSystem]], list[Union[dict, CodeSystem]]]]) @@ -355,4 +397,3 @@ class slots: slots.dataElement__description = Slot(uri=DEFAULT_.description, name="dataElement__description", curie=DEFAULT_.curie('description'), model_uri=DEFAULT_.dataElement__description, domain=None, range=Optional[str]) - diff --git a/src/rd_cdm/python_classes/rd_cdm_pydantic.py b/src/rd_cdm/python_classes/rd_cdm_pydantic.py index 51450b4..abefb4f 100644 --- a/src/rd_cdm/python_classes/rd_cdm_pydantic.py +++ b/src/rd_cdm/python_classes/rd_cdm_pydantic.py @@ -1,7 +1,8 @@ -# AUTO-GENERATED by src/rd_cdm/utils/gen_pydantic.py -# Schema: /Users/adam/Documents/git/rd-cdm/src/rd_cdm/schema/rd_cdm.yaml +# AUTO-GENERATED by src/rd_cdm/utils/gen_pydantic.py (PydanticGenerator) +# Schema: /Users/adamgraefe/Documents/git/rd-cdm/src/rd_cdm/schema/rd_cdm.yaml +# Do not edit manually — re-run gen_pydantic.py to regenerate. -from __future__ import annotations +from __future__ import annotations import re import sys @@ -10,8 +11,8 @@ datetime, time ) -from decimal import Decimal -from enum import Enum +from decimal import Decimal +from enum import Enum from typing import ( Any, ClassVar, @@ -25,16 +26,21 @@ ConfigDict, Field, RootModel, - field_validator + SerializationInfo, + SerializerFunctionWrapHandler, + field_validator, + model_serializer ) -metamodel_version = "None" -version = "None" +metamodel_version = "1.7.0" +version = "2.0.3" class ConfiguredBaseModel(BaseModel): model_config = ConfigDict( + serialize_by_alias = True, + validate_by_name = True, validate_assignment = True, validate_default = True, extra = "forbid", @@ -42,7 +48,7 @@ class ConfiguredBaseModel(BaseModel): use_enum_values = True, strict = False, ) - pass + @@ -68,14 +74,16 @@ def __contains__(self, key:str) -> bool: 'id': 'https://github.com/BIH-CEI/rd-cdm/linkml/rd_cdm.schema.yaml', 'imports': ['linkml:types'], 'license': 'CC0', - 'name': 'rd_cdm.schema.yaml', + 'name': 'rd-cdm', 'prefixes': {'linkml': {'prefix_prefix': 'linkml', 'prefix_reference': 'https://w3id.org/linkml/'}, 'rdcdm': {'prefix_prefix': 'rdcdm', 'prefix_reference': 'https://github.com/BIH-CEI/rd-cdm/'}, 'xsd': {'prefix_prefix': 'xsd', 'prefix_reference': 'http://www.w3.org/2001/XMLSchema#'}}, - 'source_file': '/Users/adam/Documents/git/rd-cdm/src/rd_cdm/schema/rd_cdm.yaml'} ) + 'source_file': '/var/folders/yj/9p08lt_93y3gvmv0pp1dg7kr0000gn/T/tmpe_1_xxje.yaml', + 'title': 'ontology-based rare disease common data model (RD-CDM) harmonising ' + 'international registries, FHIR, and Phenopackets'} ) class RdCdm(ConfiguredBaseModel): @@ -85,9 +93,11 @@ class RdCdm(ConfiguredBaseModel): linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://github.com/BIH-CEI/rd-cdm/linkml/rd_cdm.schema.yaml', 'tree_root': True}) - code_systems: Optional[list[CodeSystem]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'code_systems', 'domain_of': ['RdCdm']} }) - data_elements: Optional[list[DataElement]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'data_elements', 'domain_of': ['RdCdm']} }) - value_sets: Optional[list[ValueSet]] = Field(default=None, json_schema_extra = { "linkml_meta": {'alias': 'value_sets', 'domain_of': ['RdCdm']} }) + rd_cdm_version: str = Field(default=..., description="""Version of the RD-CDM schema""", json_schema_extra = { "linkml_meta": {'domain_of': ['RdCdm']} }) + rd_cdm_date: date = Field(default=..., description="""Date of the RD-CDM release""", json_schema_extra = { "linkml_meta": {'domain_of': ['RdCdm']} }) + code_systems: Optional[list[CodeSystem]] = Field(default=None, json_schema_extra = { "linkml_meta": {'domain_of': ['RdCdm']} }) + data_elements: Optional[list[DataElement]] = Field(default=None, json_schema_extra = { "linkml_meta": {'domain_of': ['RdCdm']} }) + value_sets: Optional[list[ValueSet]] = Field(default=None, json_schema_extra = { "linkml_meta": {'domain_of': ['RdCdm']} }) class CodeSystem(ConfiguredBaseModel): @@ -97,12 +107,12 @@ class CodeSystem(ConfiguredBaseModel): linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://github.com/BIH-CEI/rd-cdm/linkml/rd_cdm.schema.yaml'}) id: str = Field(default=..., description="""The CURIE prefix used for terms in this code system (e.g. “ncbitaxon”, “snomedct”, “icd10cm”). -""", json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['CodeSystem', 'ValueSet']} }) +""", json_schema_extra = { "linkml_meta": {'domain_of': ['CodeSystem', 'ValueSet']} }) namespace_iri: str = Field(default=..., description="""The base namespace IRI for this ontology, used by OAKlib to expand CURIEs and load the adapter. -""", json_schema_extra = { "linkml_meta": {'alias': 'namespace_iri', 'domain_of': ['CodeSystem']} }) - version: str = Field(default=..., description="""The release version or publication date of the ontology""", json_schema_extra = { "linkml_meta": {'alias': 'version', 'domain_of': ['CodeSystem']} }) - title: Optional[str] = Field(default=None, description="""A human-readable title for this code system""", json_schema_extra = { "linkml_meta": {'alias': 'title', 'domain_of': ['CodeSystem']} }) - homepage: Optional[str] = Field(default=None, description="""A URL for human browsing or documentation""", json_schema_extra = { "linkml_meta": {'alias': 'homepage', 'domain_of': ['CodeSystem']} }) +""", json_schema_extra = { "linkml_meta": {'domain_of': ['CodeSystem']} }) + version: str = Field(default=..., description="""The release version or publication date of the ontology""", json_schema_extra = { "linkml_meta": {'domain_of': ['CodeSystem']} }) + title: Optional[str] = Field(default=None, description="""A human-readable title for this code system""", json_schema_extra = { "linkml_meta": {'domain_of': ['CodeSystem']} }) + homepage: Optional[str] = Field(default=None, description="""A URL for human browsing or documentation""", json_schema_extra = { "linkml_meta": {'domain_of': ['CodeSystem']} }) class Coding(ConfiguredBaseModel): @@ -111,9 +121,9 @@ class Coding(ConfiguredBaseModel): """ linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://github.com/BIH-CEI/rd-cdm/linkml/rd_cdm.schema.yaml'}) - system: str = Field(default=..., description="""CURIE for the code system""", json_schema_extra = { "linkml_meta": {'alias': 'system', 'domain_of': ['Coding']} }) - code: str = Field(default=..., description="""The code within the system""", json_schema_extra = { "linkml_meta": {'alias': 'code', 'domain_of': ['Coding']} }) - label: Optional[str] = Field(default=None, description="""Preferred label for the code""", json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Coding', 'ValueSet']} }) + system: str = Field(default=..., description="""CURIE for the code system""", json_schema_extra = { "linkml_meta": {'domain_of': ['Coding']} }) + code: str = Field(default=..., description="""The code within the system""", json_schema_extra = { "linkml_meta": {'domain_of': ['Coding']} }) + label: Optional[str] = Field(default=None, description="""Preferred label for the code""", json_schema_extra = { "linkml_meta": {'domain_of': ['Coding', 'ValueSet']} }) class ValueSet(ConfiguredBaseModel): @@ -122,9 +132,9 @@ class ValueSet(ConfiguredBaseModel): """ linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://github.com/BIH-CEI/rd-cdm/linkml/rd_cdm.schema.yaml'}) - id: str = Field(default=..., description="""Unique identifier for the value set""", json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['CodeSystem', 'ValueSet']} }) - label: str = Field(default=..., description="""Human-readable name""", json_schema_extra = { "linkml_meta": {'alias': 'label', 'domain_of': ['Coding', 'ValueSet']} }) - codes: Optional[list[Coding]] = Field(default=None, description="""List of allowed codes""", json_schema_extra = { "linkml_meta": {'alias': 'codes', 'domain_of': ['ValueSet']} }) + id: str = Field(default=..., description="""Unique identifier for the value set""", json_schema_extra = { "linkml_meta": {'domain_of': ['CodeSystem', 'ValueSet']} }) + label: str = Field(default=..., description="""Human-readable name""", json_schema_extra = { "linkml_meta": {'domain_of': ['Coding', 'ValueSet']} }) + codes: Optional[list[Coding]] = Field(default=None, description="""List of allowed codes""", json_schema_extra = { "linkml_meta": {'domain_of': ['ValueSet']} }) class DataElement(ConfiguredBaseModel): @@ -133,19 +143,19 @@ class DataElement(ConfiguredBaseModel): """ linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://github.com/BIH-CEI/rd-cdm/linkml/rd_cdm.schema.yaml'}) - ordinal: str = Field(default=..., description="""Position within the form or section""", json_schema_extra = { "linkml_meta": {'alias': 'ordinal', 'domain_of': ['DataElement']} }) - section: Optional[str] = Field(default=None, description="""Logical grouping or heading""", json_schema_extra = { "linkml_meta": {'alias': 'section', 'domain_of': ['DataElement']} }) - elementName: str = Field(default=..., description="""Human-readable name of the element""", json_schema_extra = { "linkml_meta": {'alias': 'elementName', 'domain_of': ['DataElement']} }) - elementCode: Coding = Field(default=..., description="""Primary code describing the element""", json_schema_extra = { "linkml_meta": {'alias': 'elementCode', 'domain_of': ['DataElement']} }) - elementCodeSystem: str = Field(default=..., description="""Identifier of the code system (matches one of the `CodeSystem.id` values, e.g. “SNOMEDCT”, “LOINC”, “CustomCode”).""", json_schema_extra = { "linkml_meta": {'alias': 'elementCodeSystem', 'domain_of': ['DataElement']} }) - dataType: Optional[str] = Field(default=None, description="""Data type (e.g., string, integer, identifier)""", json_schema_extra = { "linkml_meta": {'alias': 'dataType', 'domain_of': ['DataElement']} }) - dataSpecification: Optional[list[str]] = Field(default=None, description="""Reference or link to specification""", json_schema_extra = { "linkml_meta": {'alias': 'dataSpecification', 'domain_of': ['DataElement']} }) - valueSet: Optional[str] = Field(default=None, description="""Value set CURIE if applicable""", json_schema_extra = { "linkml_meta": {'alias': 'valueSet', 'domain_of': ['DataElement']} }) - fhirExpression_v4_0_1: Optional[str] = Field(default=None, description="""FHIRPath expression for FHIR mapping""", json_schema_extra = { "linkml_meta": {'alias': 'fhirExpression_v4_0_1', 'domain_of': ['DataElement']} }) - recommendedDataSpec_fhir: Optional[str] = Field(default=None, description="""Recommendations for FHIR profiling""", json_schema_extra = { "linkml_meta": {'alias': 'recommendedDataSpec_fhir', 'domain_of': ['DataElement']} }) - phenopacketSchemaElement_v2_0: Optional[str] = Field(default=None, description="""Phenopacket schema path""", json_schema_extra = { "linkml_meta": {'alias': 'phenopacketSchemaElement_v2_0', 'domain_of': ['DataElement']} }) - recommendedDataSpec_phenopackets: Optional[str] = Field(default=None, description="""Recommended Phenopacket datatype or format""", json_schema_extra = { "linkml_meta": {'alias': 'recommendedDataSpec_phenopackets', 'domain_of': ['DataElement']} }) - description: Optional[str] = Field(default=None, description="""Full textual description of the element""", json_schema_extra = { "linkml_meta": {'alias': 'description', 'domain_of': ['DataElement']} }) + ordinal: str = Field(default=..., description="""Position within the form or section""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + section: Optional[str] = Field(default=None, description="""Logical grouping or heading""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + elementName: str = Field(default=..., description="""Human-readable name of the element""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + elementCode: Coding = Field(default=..., description="""Primary code describing the element""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + elementCodeSystem: str = Field(default=..., description="""Identifier of the code system (matches one of the `CodeSystem.id` values, e.g. “SNOMEDCT”, “LOINC”, “CustomCode”).""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + dataType: Optional[str] = Field(default=None, description="""Data type (e.g., string, integer, identifier)""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + dataSpecification: Optional[list[str]] = Field(default=None, description="""Reference or link to specification""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + valueSet: Optional[str] = Field(default=None, description="""Value set CURIE if applicable""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + fhirExpression_v4_0_1: Optional[str] = Field(default=None, description="""FHIRPath expression for FHIR mapping""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + recommendedDataSpec_fhir: Optional[str] = Field(default=None, description="""Recommendations for FHIR profiling""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + phenopacketSchemaElement_v2_0: Optional[str] = Field(default=None, description="""Phenopacket schema path""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + recommendedDataSpec_phenopackets: Optional[str] = Field(default=None, description="""Recommended Phenopacket datatype or format""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) + description: Optional[str] = Field(default=None, description="""Full textual description of the element""", json_schema_extra = { "linkml_meta": {'domain_of': ['DataElement']} }) # Model rebuild diff --git a/src/rd_cdm/schema/rd_cdm.yaml b/src/rd_cdm/schema/rd_cdm.yaml index 2f0e7b1..13dedc0 100644 --- a/src/rd_cdm/schema/rd_cdm.yaml +++ b/src/rd_cdm/schema/rd_cdm.yaml @@ -1,4 +1,9 @@ id: https://github.com/BIH-CEI/rd-cdm/linkml/rd_cdm.schema.yaml +name: rd-cdm +title: ontology-based rare disease common data model (RD-CDM) harmonising + international registries, FHIR, and Phenopackets +version: 2.0.3 +date: 2026-03-24 license: CC0 prefixes: rdcdm: https://github.com/BIH-CEI/rd-cdm/ @@ -14,6 +19,14 @@ classes: description: "Root class for the Rare Disease Common Data Model (RD-CDM)" tree_root: true attributes: + rd_cdm_version: + description: "Version of the RD-CDM schema" + range: string + required: true + rd_cdm_date: + description: "Date of the RD-CDM release" + range: date + required: true code_systems: range: CodeSystem multivalued: true diff --git a/src/rd_cdm/utils/config.py b/src/rd_cdm/utils/config.py index 3ad91a3..1a03f12 100644 --- a/src/rd_cdm/utils/config.py +++ b/src/rd_cdm/utils/config.py @@ -4,26 +4,13 @@ from pydantic_settings import BaseSettings from rd_cdm.utils.versioning import ( - resolve_instances_dir, - normalize_dir_to_version, - version_to_tag, + resolve_instances_dir ) -class VersioningConfig(BaseSettings): - """Controls which RD-CDM version/tag is used when resolving instance paths.""" - model_config = ConfigDict(env_prefix="RDCDM_", extra="ignore") - version: str | None = Field( - default=None, - description='e.g. "2.0.1", "v2.0.1", or "v2_0_1" (None=latest)', - ) - class PathsConfig(BaseModel): - """Resolved paths for the current run. Usually computed, not provided directly.""" model_config = ConfigDict(arbitrary_types_allowed=True) src_root: Path instances_dir: Path - version_tag: str # e.g. "v2_0_1" - version_norm: str # e.g. "2.0.1" class ExportConfig(BaseSettings): """Controls which exports are produced and where.""" @@ -31,14 +18,7 @@ class ExportConfig(BaseSettings): write_json: bool = True write_csv: bool = True -def resolve_paths(cfg: VersioningConfig) -> PathsConfig: - instances_dir = resolve_instances_dir(cfg.version) - src_root = instances_dir.parents[2] - v_norm = normalize_dir_to_version(instances_dir.name) or instances_dir.name - v_tag = version_to_tag(v_norm) - return PathsConfig( - src_root=src_root, - instances_dir=instances_dir, - version_tag=v_tag, - version_norm=v_norm, - ) +def resolve_paths() -> PathsConfig: + instances_dir = resolve_instances_dir() + src_root = instances_dir.parents[1] # src/rd_cdm/instances -> src/ + return PathsConfig(src_root=src_root, instances_dir=instances_dir) \ No newline at end of file diff --git a/src/rd_cdm/utils/csv_parsing.py b/src/rd_cdm/utils/csv_parsing.py index a3cdc8d..ecd519b 100644 --- a/src/rd_cdm/utils/csv_parsing.py +++ b/src/rd_cdm/utils/csv_parsing.py @@ -1,102 +1,112 @@ #!/usr/bin/env python3 from __future__ import annotations import csv -import argparse import sys +import argparse import ruamel.yaml from pathlib import Path -from rd_cdm.utils.config import VersioningConfig, PathsConfig -from rd_cdm.utils.versioning import resolve_instances_dir, normalize_dir_to_version, version_to_tag +from rd_cdm.utils.config import resolve_paths -def _resolve_paths(vc: VersioningConfig) -> PathsConfig: - base = resolve_instances_dir(vc.version) - v_norm = normalize_dir_to_version(base.name) or base.name - v_tag = version_to_tag(v_norm) - src_root = base.parents[2] - return PathsConfig(src_root=src_root, instances_dir=base, version_tag=v_tag, version_norm=v_norm) -def write_csvs_from_instances(version: str | None = None) -> int: +def _write_csv(rows: list[dict], out_path: Path) -> None: + header_keys = sorted( + {k for r in rows for k in (r.keys() if isinstance(r, dict) else [])} + ) or ["id"] + with out_path.open("w", encoding="utf-8", newline="") as f: + w = csv.DictWriter(f, fieldnames=header_keys, extrasaction="ignore") + w.writeheader() + for r in rows: + flat = { + k: (repr(v) if isinstance((v := r.get(k, "")), (list, dict)) else v) + for k in header_keys + } + w.writerow(flat) + + +def main() -> int: """ - Export versioned RD-CDM instance YAMLs to CSV. + Export the merged rd_cdm.yaml to CSV files. - Outputs in: src/rd_cdm/instances/{vTAG}/csvs/ + Reads from: src/rd_cdm/instances/rd_cdm.yaml + Writes to: src/rd_cdm/instances/csvs/ - code_systems.csv - data_elements.csv - value_sets.csv - - rd_cdm_{version}.csv (stacked view with a `_section` column) + - rd_cdm.csv (combined, with _section column and _metadata row for version) + + The version (rd_cdm_version, rd_cdm_date) appears as the first row in the + combined rd_cdm.csv under section '_metadata'. """ - paths = _resolve_paths(VersioningConfig(version=version)) - out_dir = paths.src_root / "rd_cdm" / "instances" / paths.version_tag / "csvs" + paths = resolve_paths() + merged_path = paths.instances_dir / "rd_cdm.yaml" + if not merged_path.exists(): + print(f"ERROR: merged instance not found at {merged_path}. Run rd-cdm-merge first.") + return 1 + + out_dir = paths.instances_dir / "csvs" out_dir.mkdir(parents=True, exist_ok=True) yaml = ruamel.yaml.YAML() - yaml.preserve_quotes = True - - def _load_toplist(filename: str, top_key: str) -> list[dict]: - p = paths.instances_dir / filename - if not p.exists(): - print(f"ERROR: missing required file: {p}", file=sys.stderr) - sys.exit(1) - with p.open("r", encoding="utf-8") as fh: - data = yaml.load(fh) or {} - lst = data.get(top_key, []) or [] - if not isinstance(lst, list): - print(f"ERROR: `{top_key}` in {filename} is not a list", file=sys.stderr) - sys.exit(1) - norm: list[dict] = [] - for row in lst: + with merged_path.open("r", encoding="utf-8") as fh: + data = yaml.load(fh) or {} + + rd_cdm_version = data.get("rd_cdm_version", "unknown") + rd_cdm_date = data.get("rd_cdm_date", "unknown") + + def _to_rows(raw) -> list[dict]: + rows = [] + for row in (raw or []): if row is None: - norm.append({}) + rows.append({}) elif isinstance(row, dict): - norm.append(row) + rows.append(row) else: - norm.append({"value": row}) - return norm - - code_systems = _load_toplist("code_systems.yaml", "code_systems") - data_elements = _load_toplist("data_elements.yaml", "data_elements") - value_sets = _load_toplist("value_sets.yaml", "value_sets") - - def _write_csv(rows: list[dict], out_path: Path) -> None: - header_keys = sorted({k for r in rows for k in (r.keys() if isinstance(r, dict) else [])}) or ["id"] - with out_path.open("w", encoding="utf-8", newline="") as f: - w = csv.DictWriter(f, fieldnames=header_keys, extrasaction="ignore") - w.writeheader() - for r in rows: - flat = {k: (repr(v) if isinstance((v := r.get(k, "")), (list, dict)) else v) for k in header_keys} - w.writerow(flat) + rows.append({"value": row}) + return rows + + code_systems = _to_rows(data.get("code_systems", [])) + data_elements = _to_rows(data.get("data_elements", [])) + value_sets = _to_rows(data.get("value_sets", [])) _write_csv(code_systems, out_dir / "code_systems.csv") _write_csv(data_elements, out_dir / "data_elements.csv") _write_csv(value_sets, out_dir / "value_sets.csv") - # combined + # Combined CSV — version as first metadata row all_rows = ( - [("_section", "code_systems", r) for r in code_systems] + - [("_section", "data_elements", r) for r in data_elements] + - [("_section", "value_sets", r) for r in value_sets] + [("_metadata", {"rd_cdm_version": rd_cdm_version, "rd_cdm_date": str(rd_cdm_date)})] + + [("code_systems", r) for r in code_systems] + + [("data_elements", r) for r in data_elements] + + [("value_sets", r) for r in value_sets] ) - key_union = set() - for _, _, r in all_rows: + key_union: set[str] = set() + for _, r in all_rows: if isinstance(r, dict): key_union.update(r.keys()) header = ["_section"] + sorted(key_union) if key_union else ["_section", "id"] - combined_path = out_dir / f"rd_cdm_{paths.version_tag}.csv" + + combined_path = out_dir / "rd_cdm.csv" with combined_path.open("w", encoding="utf-8", newline="") as f: w = csv.DictWriter(f, fieldnames=header, extrasaction="ignore") w.writeheader() - for _, section, r in all_rows: + for section, r in all_rows: row = {"_section": section} for k in header[1:]: v = r.get(k, "") row[k] = repr(v) if isinstance(v, (list, dict)) else v w.writerow(row) - print(f"✅ Wrote CSVs to {out_dir}: code_systems.csv, data_elements.csv, value_sets.csv, {combined_path.name}") + print( + f"✅ Wrote CSVs to {out_dir}: " + f"code_systems.csv, data_elements.csv, value_sets.csv, rd_cdm.csv " + f"(rd_cdm_version={rd_cdm_version})" + ) return 0 + if __name__ == "__main__": - ap = argparse.ArgumentParser() - ap.add_argument("-v","--version", help='Version like "2.0.1" / "v2.0.1" / "v2_0_1".') - args = ap.parse_args() - raise SystemExit(write_csvs_from_instances(args.version)) + ap = argparse.ArgumentParser( + description="Export merged RD-CDM YAML to CSV files." + ) + ap.parse_args() + raise SystemExit(main()) \ No newline at end of file diff --git a/src/rd_cdm/utils/gen_pydantic.py b/src/rd_cdm/utils/gen_pydantic.py index 9eb0ceb..e4f0434 100644 --- a/src/rd_cdm/utils/gen_pydantic.py +++ b/src/rd_cdm/utils/gen_pydantic.py @@ -1,29 +1,27 @@ #!/usr/bin/env python3 """ -Generate Pydantic models from the LinkML schema into: - src/rd_cdm/python_classes/rd_cdm_pydantic.py - -This uses the LinkML Python API only (no CLI flags), so it’s stable across -LinkML versions. It does NOT generate any versioned models. +Generate Python classes from the LinkML schema into: + src/rd_cdm/python_classes/rd_cdm.py (LinkML runtime dataclasses) + src/rd_cdm/python_classes/rd_cdm_pydantic.py (Pydantic v2 models) """ from __future__ import annotations from pathlib import Path import sys import re +import tempfile +import ruamel.yaml + +# Top-level fields we added to the schema that are not valid LinkML SchemaDefinition fields +_STRIP_FROM_SCHEMA = {"date"} def _rewrite_pydantic_config_to_v2(src: str) -> str: - """ - Replace Pydantic v1 `class Config:` blocks with v2 `model_config = ConfigDict(...)`. - """ - # Ensure ConfigDict is imported + """Replace Pydantic v1 `class Config:` blocks with v2 `model_config = ConfigDict(...)`.""" if "ConfigDict" not in src: src = src.replace( "from pydantic import BaseModel", "from pydantic import BaseModel, ConfigDict" ) - - # Match a Config class definition with indented attributes pattern = re.compile(r"(?ms)^class\s+Config:\n((?:\s+.+\n)+)") def repl(m: re.Match) -> str: @@ -41,47 +39,94 @@ def repl(m: re.Match) -> str: return re.sub(pattern, repl, src) +def _write_generated(code_str: str, out_file: Path, schema: Path, generator_name: str) -> bool: + """Write generated code with a header comment. Returns True on success.""" + header = ( + f"# AUTO-GENERATED by src/rd_cdm/utils/gen_pydantic.py ({generator_name})\n" + f"# Schema: {schema}\n" + f"# Do not edit manually — re-run gen_pydantic.py to regenerate.\n\n" + ) + try: + out_file.parent.mkdir(parents=True, exist_ok=True) + out_file.write_text(header + code_str, encoding="utf-8") + return True + except Exception as e: + print(f"ERROR: Failed to write {out_file}: {e}", file=sys.stderr) + return False + + def main() -> int: - # utils/ -> repo root repo_root = Path(__file__).resolve().parents[3] schema = repo_root / "src" / "rd_cdm" / "schema" / "rd_cdm.yaml" - out_file = repo_root / "src" / "rd_cdm" / "python_classes" / "rd_cdm_pydantic.py" + out_dataclasses = repo_root / "src" / "rd_cdm" / "python_classes" / "rd_cdm.py" + out_pydantic = repo_root / "src" / "rd_cdm" / "python_classes" / "rd_cdm_pydantic.py" if not schema.exists(): print(f"ERROR: schema not found at {schema}", file=sys.stderr) return 2 try: + from linkml.generators.pythongen import PythonGenerator from linkml.generators.pydanticgen import PydanticGenerator except Exception as e: - print("ERROR: Could not import PydanticGenerator (is 'linkml' installed?)", file=sys.stderr) + print( + "ERROR: Could not import LinkML generators. " + "Is 'linkml' installed? (dev dependency)", + file=sys.stderr, + ) print(f"Details: {e}", file=sys.stderr) return 1 - try: - gen = PydanticGenerator(str(schema)) - code_str = gen.serialize() # Python source as a string - code_str = _rewrite_pydantic_config_to_v2(code_str) # Patch for Pydantic v2 - except Exception as e: - print("ERROR: Failed to generate Pydantic code from schema.", file=sys.stderr) - print(f"Details: {e}", file=sys.stderr) - return 1 + # Strip custom top-level fields that LinkML SchemaDefinition doesn't accept + yaml = ruamel.yaml.YAML() + with schema.open("r", encoding="utf-8") as fh: + schema_data = yaml.load(fh) or {} + for field in _STRIP_FROM_SCHEMA: + schema_data.pop(field, None) - header = ( - "# AUTO-GENERATED by src/rd_cdm/utils/gen_pydantic.py\n" - f"# Schema: {schema}\n\n" - ) + tmp_path = None try: - out_file.parent.mkdir(parents=True, exist_ok=True) - out_file.write_text(header + code_str, encoding="utf-8") - except Exception as e: - print(f"ERROR: Failed to write {out_file}", file=sys.stderr) - print(f"Details: {e}", file=sys.stderr) - return 1 + with tempfile.NamedTemporaryFile( + mode="w", suffix=".yaml", delete=False, encoding="utf-8" + ) as tmp: + yaml.dump(schema_data, tmp) + tmp_path = tmp.name + + # 1) LinkML runtime dataclasses (rd_cdm.py) + print("Generating LinkML runtime dataclasses...") + try: + python_gen = PythonGenerator(tmp_path) + dataclass_code = python_gen.serialize() + except Exception as e: + print("ERROR: Failed to generate LinkML dataclasses.", file=sys.stderr) + print(f"Details: {e}", file=sys.stderr) + return 1 + + if not _write_generated(dataclass_code, out_dataclasses, schema, "PythonGenerator"): + return 1 + print(f"✅ LinkML dataclasses written to {out_dataclasses}") + + # 2) Pydantic v2 models (rd_cdm_pydantic.py) + print("Generating Pydantic v2 models...") + try: + pydantic_gen = PydanticGenerator(tmp_path) + pydantic_code = pydantic_gen.serialize() + pydantic_code = _rewrite_pydantic_config_to_v2(pydantic_code) + except Exception as e: + print("ERROR: Failed to generate Pydantic models.", file=sys.stderr) + print(f"Details: {e}", file=sys.stderr) + return 1 + + if not _write_generated(pydantic_code, out_pydantic, schema, "PydanticGenerator"): + return 1 + print(f"✅ Pydantic models written to {out_pydantic}") + + finally: + if tmp_path: + Path(tmp_path).unlink(missing_ok=True) - print(f"✅ Pydantic models written to {out_file}") return 0 if __name__ == "__main__": - raise SystemExit(main()) + raise SystemExit(main()) \ No newline at end of file diff --git a/src/rd_cdm/utils/json_parsing.py b/src/rd_cdm/utils/json_parsing.py index 33357dd..64b0082 100644 --- a/src/rd_cdm/utils/json_parsing.py +++ b/src/rd_cdm/utils/json_parsing.py @@ -2,68 +2,51 @@ from __future__ import annotations import json import argparse -from linkml_runtime.loaders import yaml_loader -from linkml_runtime.dumpers import json_dumper -from rd_cdm.python_classes.rd_cdm import RdCdm -from rd_cdm.utils.config import VersioningConfig, PathsConfig -from rd_cdm.utils.versioning import resolve_instances_dir, normalize_dir_to_version, version_to_tag +import ruamel.yaml +from rd_cdm.utils.config import resolve_paths +import datetime -def _resolve_paths(vc: VersioningConfig) -> PathsConfig: - base = resolve_instances_dir(vc.version) - v_norm = normalize_dir_to_version(base.name) or base.name - v_tag = version_to_tag(v_norm) - src_root = base.parents[2] - return PathsConfig(src_root=src_root, instances_dir=base, version_tag=v_tag, version_norm=v_norm) +def _default(obj): + if isinstance(obj, datetime.date): + return str(obj) + raise TypeError(f"Object of type {type(obj).__name__} is not JSON serializable") -def main(version: str | None = None) -> int: + +def main() -> int: """ - Convert LinkML instance YAMLs in the resolved versioned instances dir to JSON, - writing them under: src/rd_cdm/instances/{vTAG}/jsons/ - Also creates a combined `rd_cdm_vX_Y_Z.json`. + Convert the merged rd_cdm.yaml to rd_cdm.json. + + Reads from: src/rd_cdm/instances/rd_cdm.yaml + Writes to: src/rd_cdm/instances/jsons/rd_cdm.json - Notes - ----- - • Skips already-merged YAMLs (rd_cdm_full.yaml and rd_cdm_v*.yaml) during per-file conversion. - • The combined file name matches the merged YAML naming (rd_cdm_vX_Y_Z.json). + The version (rd_cdm_version, rd_cdm_date) is already embedded in the + merged YAML by the merge step and will appear at the top of the JSON. """ - paths = _resolve_paths(VersioningConfig(version=version)) - out_dir = paths.src_root / "rd_cdm" / "instances" / paths.version_tag / "jsons" + paths = resolve_paths() + merged_path = paths.instances_dir / "rd_cdm.yaml" + if not merged_path.exists(): + print(f"ERROR: merged instance not found at {merged_path}. Run rd-cdm-merge first.") + return 1 + + out_dir = paths.instances_dir / "jsons" out_dir.mkdir(parents=True, exist_ok=True) - yamls = list(paths.instances_dir.glob("*.yaml")) + list(paths.instances_dir.glob("*.yml")) - if not yamls: - print(f"⚠️ No YAML files found in {paths.instances_dir}") - return 0 + yaml = ruamel.yaml.YAML() + with merged_path.open("r", encoding="utf-8") as fh: + data = yaml.load(fh) or {} - ok, fail = 0, 0 - combined_data: dict[str, dict] = {} - for yf in sorted(yamls): - stem = yf.stem - if stem.startswith("rd_cdm_full") or stem.startswith("rd_cdm_v"): - continue - try: - obj = yaml_loader.load(str(yf), target_class=RdCdm) - out_path = out_dir / (stem + ".json") - json_str = json_dumper.dumps(obj) - json_obj = json.loads(json_str) - with out_path.open("w", encoding="utf-8") as f: - json.dump(json_obj, f, indent=2, ensure_ascii=False) - combined_data[stem] = json_obj - print(f"✅ {yf.name} -> rd_cdm/instances/{paths.version_tag}/jsons/{out_path.name}") - ok += 1 - except Exception as e: - print(f"❌ {yf.name}: {e}") - fail += 1 + out_path = out_dir / "rd_cdm.json" + with out_path.open("w", encoding="utf-8") as f: + json.dump(data, f, indent=2, ensure_ascii=False, default=_default) - combined_path = out_dir / f"rd_cdm_{paths.version_tag}.json" - with combined_path.open("w", encoding="utf-8") as f: - json.dump(combined_data, f, indent=2, ensure_ascii=False) + version = data.get("rd_cdm_version", "unknown") + print(f"✅ Wrote {out_path} (rd_cdm_version={version})") + return 0 - print(f"\nDone. Wrote {ok} JSON(s); {fail} file(s) failed. Combined JSON at {combined_path}") - return 0 if fail == 0 else 1 if __name__ == "__main__": - ap = argparse.ArgumentParser() - ap.add_argument("-v","--version", help='Version like "2.0.1" / "v2.0.1" / "v2_0_1".') - args = ap.parse_args() - raise SystemExit(main(args.version)) + ap = argparse.ArgumentParser( + description="Export merged RD-CDM YAML to JSON." + ) + ap.parse_args() + raise SystemExit(main()) \ No newline at end of file diff --git a/src/rd_cdm/utils/merge_instances.py b/src/rd_cdm/utils/merge_instances.py index b9ff059..8f6cdee 100644 --- a/src/rd_cdm/utils/merge_instances.py +++ b/src/rd_cdm/utils/merge_instances.py @@ -4,67 +4,74 @@ import sys import argparse import ruamel.yaml -from rd_cdm.utils.config import VersioningConfig, PathsConfig -from rd_cdm.utils.versioning import resolve_instances_dir, normalize_dir_to_version, version_to_tag +from rd_cdm.utils.config import resolve_paths -def _resolve_paths(vc: VersioningConfig) -> PathsConfig: - base = resolve_instances_dir(vc.version) - v_norm = normalize_dir_to_version(base.name) or base.name - v_tag = version_to_tag(v_norm) - src_root = base.parents[2] - return PathsConfig(src_root=src_root, instances_dir=base, version_tag=v_tag, version_norm=v_norm) +def _read_schema_meta(schema_path) -> dict: + """Read version and date from the LinkML schema (single source of truth).""" + yaml = ruamel.yaml.YAML() + with schema_path.open("r", encoding="utf-8") as fh: + schema = yaml.load(fh) or {} + return { + "rd_cdm_version": schema.get("version", "unknown"), + "rd_cdm_date": schema.get("date", "unknown"), + } -def main(version: str | None = None) -> int: - """ - Merge versioned instance YAML parts into a single `rd_cdm_vX_Y_Z.yaml`. - Version resolution order: - 1) Explicit `--version` argument (accepts "2.0.1", "v2.0.1", or "v2_0_1") - 2) Environment variable RDCDM_VERSION - 3) Version from `pyproject.toml` ([tool.poetry].version or [project].version) - 4) Latest directory under `src/rd_cdm/instances/` (by semantic version) +def main() -> int: + """ + Merge RD-CDM instance YAML parts into a single `rd_cdm.yaml`. What this script does: - • Resolves the correct `src/rd_cdm/instances/{vTAG}/` directory. - • Loads `code_systems.yaml`, `data_elements.yaml`, and `value_sets.yaml` - using ruamel.yaml (preserving quotes/comments where possible). - • Merges them into a structured mapping: + • Resolves `src/rd_cdm/instances/` (no versioned subdirs). + • Reads `rd_cdm_version` and `rd_cdm_date` from `schema/rd_cdm.yaml` + (the single source of truth for the data model version). + • Loads `code_systems.yaml`, `data_elements.yaml`, and `value_sets.yaml`. + • Merges everything into a single structured `rd_cdm.yaml`: { + "rd_cdm_version": "2.0.3", + "rd_cdm_date": "2025-03-24", "code_systems": [...], "data_elements": [...], "value_sets": [...] } - • Writes the merged result to `rd_cdm_vX_Y_Z.yaml` in the same versioned folder. + • Writes the result to `src/rd_cdm/instances/rd_cdm.yaml`. """ try: - paths = _resolve_paths(VersioningConfig(version=version)) + paths = resolve_paths() except Exception as e: print(f"ERROR: could not resolve instances directory: {e}", file=sys.stderr) return 2 + schema_path = paths.src_root / "rd_cdm" / "schema" / "rd_cdm.yaml" + if not schema_path.exists(): + print(f"ERROR: schema not found at {schema_path}", file=sys.stderr) + return 2 + yaml = ruamel.yaml.YAML() yaml.preserve_quotes = True - def load_file(name: str): + def load_file(name: str) -> dict: p = paths.instances_dir / name if not p.exists(): print(f"ERROR: missing required file: {p}", file=sys.stderr) sys.exit(1) with p.open("r", encoding="utf-8") as fh: - return yaml.load(fh) + return yaml.load(fh) or {} - cs = load_file("code_systems.yaml") or {} - de = load_file("data_elements.yaml") or {} - vs = load_file("value_sets.yaml") or {} + meta = _read_schema_meta(schema_path) + cs = load_file("code_systems.yaml") + de = load_file("data_elements.yaml") + vs = load_file("value_sets.yaml") merged = { + **meta, "code_systems": cs.get("code_systems", []), "data_elements": de.get("data_elements", []), "value_sets": vs.get("value_sets", []), } - out = paths.instances_dir / f"rd_cdm_{paths.version_tag}.yaml" + out = paths.instances_dir / "rd_cdm.yaml" try: with out.open("w", encoding="utf-8") as f: yaml.dump(merged, f) @@ -72,11 +79,17 @@ def load_file(name: str): print(f"ERROR: failed to write {out}: {e}", file=sys.stderr) return 3 - print(f"Wrote {out}") + print( + f"✅ Wrote {out} " + f"(rd_cdm_version={meta['rd_cdm_version']}, " + f"rd_cdm_date={meta['rd_cdm_date']})" + ) return 0 + if __name__ == "__main__": - p = argparse.ArgumentParser(description="Merge RD-CDM instance YAMLs into rd_cdm_vX_Y_Z.yaml for a specific version.") - p.add_argument("-v","--version", help='Version like "2.0.1", "v2.0.1", or "v2_0_1".') - args = p.parse_args() - raise SystemExit(main(args.version)) \ No newline at end of file + ap = argparse.ArgumentParser( + description="Merge RD-CDM instance YAMLs into rd_cdm.yaml." + ) + ap.parse_args() + raise SystemExit(main()) \ No newline at end of file diff --git a/src/rd_cdm/utils/settings.py b/src/rd_cdm/utils/settings.py index 125251f..cf43450 100644 --- a/src/rd_cdm/utils/settings.py +++ b/src/rd_cdm/utils/settings.py @@ -1,12 +1,12 @@ from __future__ import annotations +from pydantic import ConfigDict from pydantic_settings import BaseSettings + class ValidationSettings(BaseSettings): """ Environment-driven settings for validation steps. """ - bioportal_api_key: str = "" # set in CI/locally; validation step will check emptiness + model_config = ConfigDict(env_prefix="", extra="ignore") - class Config: - env_prefix = "" # BIOPORTAL_API_KEY - env_file = ".env" + bioportal_api_key: str = "" # set via BIOPORTAL_API_KEY env var or .env file \ No newline at end of file diff --git a/src/rd_cdm/utils/validation.py b/src/rd_cdm/utils/validation.py index 6c39474..9b2035f 100644 --- a/src/rd_cdm/utils/validation.py +++ b/src/rd_cdm/utils/validation.py @@ -1,128 +1,128 @@ #!/usr/bin/env python3 +from __future__ import annotations import sys import argparse import requests import ruamel.yaml -from linkml_runtime.loaders import yaml_loader -from rd_cdm.python_classes.rd_cdm import RdCdm -from rd_cdm.utils.versioning import resolve_instances_dir, normalize_dir_to_version, version_to_tag +from tqdm import tqdm +from rd_cdm.utils.config import resolve_paths from rd_cdm.utils.validation_utils import clean_code, get_remote_version, get_remote_label from rd_cdm.utils.settings import ValidationSettings -# ——— CONFIG —————————————————————————————————————————————— VALIDATION_SYSTEMS = {"SNOMEDCT", "LOINC", "HP", "NCIT"} SKIP_VERSION_CHECK = {"CustomCode", "GA4GH", "HL7FHIR", "HGVS", "ICD11", "ISO3166"} -BP_BASE = "https://data.bioontology.org" -# ——— MAIN ————————————————————————————————————————————————— -#!/usr/bin/env python3 def main(): - """ - Entry point for RD-CDM validation against BioPortal. - - What it does - ------------ - 1) Resolves the instances directory (from --version, pyproject version, or latest). - 2) Loads the merged LinkML instance (rd_cdm_vX_Y_Z.yaml) as RdCdm. - 3) Builds a map of CodeSystems and checks live version drift for each ontology - (except those explicitly skipped). - 4) Validates every DataElement.elementCode (system+code): - - Skips composite codes (contain '='). - - Uses get_remote_label to verify existence and optionally detect label drift. - 5) Validates every ValueSet member (only items under 'codes', not the ValueSet id): - - Accepts both dict entries (with system/code/label) and strings 'PREFIX:ID'. - - Skips composite codes. - - Uses get_remote_label as above. - 6) Prints a summary: counts of DataElements checked, ValueSet members checked, - valid/missing/skipped terms, and number of warnings. - 7) Prints detailed Errors and Warnings sections. - 8) Exits with status 1 if any errors were found; otherwise exits 0. - - Inputs & configuration - ---------------------- - - BIOPORTAL_API_KEY must be set in the environment for API calls to succeed. - - VALIDATION_SYSTEMS controls which ontologies are validated for code existence. - - SKIP_VERSION_CHECK lists ontologies for which version drift is ignored. - - Side effects - ------------ - - Prints to stdout/stderr. - - Terminates the process via sys.exit with 0 (success) or 1 (errors). - - Returns - ------- - None - (Terminates the process.) - """ - ap = argparse.ArgumentParser() - ap.add_argument("--version", help="Instances version (e.g., 2.0.1 or v2_0_1).") - args = ap.parse_args() + ap = argparse.ArgumentParser( + description="Validate RD-CDM ontology codes against BioPortal." + ) + ap.parse_args() settings = ValidationSettings() if not settings.bioportal_api_key: print("ERROR: BIOPORTAL_API_KEY not set", file=sys.stderr) sys.exit(2) - instances_dir = resolve_instances_dir(args.version) - - v_norm = normalize_dir_to_version(instances_dir.name) or instances_dir.name - v_tag = version_to_tag(v_norm) - full_path = instances_dir / f"rd_cdm_{v_tag}.yaml" + paths = resolve_paths() + full_path = paths.instances_dir / "rd_cdm.yaml" if not full_path.exists(): - print(f"ERROR: merged instance not found: {full_path}", file=sys.stderr) + print( + f"ERROR: merged instance not found at {full_path}. " + "Run rd-cdm-merge first.", + file=sys.stderr, + ) sys.exit(1) - model: RdCdm = yaml_loader.load(str(full_path), RdCdm) - cs_map = {cs.id: cs for cs in model.code_systems} + yaml_s = ruamel.yaml.YAML(typ="safe") + with open(full_path, "r", encoding="utf-8") as fh: + merged = yaml_s.load(fh) or {} + + cs_map = { + cs["id"]: type("CS", (), { + "id": cs["id"], + "version": cs.get("version", ""), + "namespace_iri": cs.get("namespace_iri", ""), + })() + for cs in merged.get("code_systems", []) + if isinstance(cs, dict) and "id" in cs + } errors, warnings, valid_codes, invalid_codes, skipped_codes = [], [], [], [], [] de_checked = vs_checked = 0 - for cs in model.code_systems: - if cs.id in SKIP_VERSION_CHECK: - continue - try: - live_v = get_remote_version(cs.id) - except Exception as e: - warnings.append(f"{cs.id}: could not fetch live version ({e})") - continue - if live_v != cs.version: - warnings.append(f"{cs.id}: version drift – model={cs.version}, live={live_v}") - - for de in model.data_elements: - sys_id = de.elementCode.system - raw_code = de.elementCode.code - if sys_id not in VALIDATION_SYSTEMS: - continue - if "=" in str(raw_code): - skipped_codes.append(f"{sys_id}:{raw_code}") - continue - code = clean_code(raw_code) - de_checked += 1 - cs = cs_map[sys_id] - try: - label_live = get_remote_label(sys_id, code, cs.namespace_iri) - except requests.HTTPError: - label_live = None - - curie = f"{sys_id}:{raw_code}" - if not label_live: - errors.append(f"DE {de.ordinal} {de.elementName}: missing term {curie}") - invalid_codes.append(curie) - else: - valid_codes.append(curie) - label0 = getattr(de.elementCode, "label", None) - if label0 and label_live != label0: - warnings.append(f"DE {de.ordinal} {de.elementName}: label drift – {curie}: model='{label0}', live='{label_live}'") + # Version drift check + code_systems = [ + cs for cs in merged.get("code_systems", []) + if isinstance(cs, dict) and cs.get("id") not in SKIP_VERSION_CHECK + ] + with tqdm(code_systems, desc="Checking code system versions", unit="cs") as pbar: + for cs_dict in pbar: + cs_id = cs_dict.get("id", "") + pbar.set_postfix(cs=cs_id) + try: + live_v = get_remote_version(cs_id) + except Exception as e: + warnings.append(f"{cs_id}: could not fetch live version ({e})") + continue + model_v = cs_dict.get("version", "") + if live_v != model_v: + warnings.append( + f"{cs_id}: version drift – model={model_v}, live={live_v}" + ) + + # DataElement code validation + data_elements = [ + de for de in merged.get("data_elements", []) + if isinstance(de, dict) + ] + with tqdm(data_elements, desc="Validating data elements", unit="de") as pbar: + for de in pbar: + element_code = de.get("elementCode", {}) or {} + sys_id = element_code.get("system") + raw_code = element_code.get("code") + de_name = de.get("elementName", "") + ordinal = de.get("ordinal", "") + pbar.set_postfix(de=f"{ordinal} {de_name[:20]}") - yaml_s = ruamel.yaml.YAML(typ="safe") - with open(full_path, "r", encoding="utf-8") as fh: - merged = yaml_s.load(fh) or {} + if sys_id not in VALIDATION_SYSTEMS: + continue + if "=" in str(raw_code): + skipped_codes.append(f"{sys_id}:{raw_code}") + continue + code = clean_code(raw_code) + de_checked += 1 + cs = cs_map.get(sys_id) + if not cs: + warnings.append(f"DE {ordinal}: unknown code system '{sys_id}'") + continue + try: + label_live = get_remote_label(sys_id, code, cs.namespace_iri) + except requests.HTTPError: + label_live = None - for vs in merged.get("value_sets", []): - vs_id = vs.get("id", "") - for c in vs.get("codes", []): + curie = f"{sys_id}:{raw_code}" + if not label_live: + errors.append(f"DE {ordinal} {de_name}: missing term {curie}") + invalid_codes.append(curie) + else: + valid_codes.append(curie) + label0 = element_code.get("label") + if label0 and label_live != label0: + warnings.append( + f"DE {ordinal} {de_name}: label drift – " + f"{curie}: model='{label0}', live='{label_live}'" + ) + + # ValueSet code validation + value_sets = merged.get("value_sets", []) + all_vs_codes = [ + (vs.get("id", ""), c) + for vs in value_sets + for c in vs.get("codes", []) + ] + with tqdm(all_vs_codes, desc="Validating value set codes", unit="code") as pbar: + for vs_id, c in pbar: if isinstance(c, dict): sys_id = c.get("system") raw_code = c.get("code") @@ -131,9 +131,11 @@ def main(): sys_id, raw_code = c.split(":", 1) label0 = None else: - errors.append(f"VS {vs_id}: bad code entry {c}") + errors.append(f"VS {vs_id}: bad code entry {c!r}") continue + pbar.set_postfix(vs=vs_id[:20], code=str(raw_code)[:15]) + if sys_id not in VALIDATION_SYSTEMS: continue if raw_code is None or "=" in str(raw_code): @@ -142,7 +144,10 @@ def main(): code = clean_code(raw_code) vs_checked += 1 - cs = cs_map[sys_id] + cs = cs_map.get(sys_id) + if not cs: + warnings.append(f"VS {vs_id}: unknown code system '{sys_id}'") + continue try: label_live = get_remote_label(sys_id, code, cs.namespace_iri) except requests.HTTPError: @@ -155,15 +160,20 @@ def main(): else: valid_codes.append(curie) if label0 and label_live != label0: - warnings.append(f"VS {vs_id}: label drift – {curie}: model='{label0}', live='{label_live}'") - - print("\n=== RD‐CDM VALIDATION SUMMARY ===") - print(f" DataElements checked: {de_checked}") + warnings.append( + f"VS {vs_id}: label drift – " + f"{curie}: model='{label0}', live='{label_live}'" + ) + + # Summary + rd_cdm_version = merged.get("rd_cdm_version", "unknown") + print(f"\n=== RD-CDM VALIDATION SUMMARY (model version: {rd_cdm_version}) ===") + print(f" DataElements checked : {de_checked}") print(f" ValueSet members checked: {vs_checked}") - print(f" Valid terms: {len(valid_codes)}") - print(f" Invalid (missing) terms: {len(invalid_codes)}") - print(f" Skipped terms: {len(skipped_codes)}") - print(f" Warnings: {len(warnings)}\n") + print(f" Valid terms : {len(valid_codes)}") + print(f" Invalid (missing) terms : {len(invalid_codes)}") + print(f" Skipped terms : {len(skipped_codes)}") + print(f" Warnings : {len(warnings)}\n") if errors: print("Errors:") @@ -176,5 +186,6 @@ def main(): sys.exit(1 if errors else 0) + if __name__ == "__main__": main() diff --git a/src/rd_cdm/utils/versioning.py b/src/rd_cdm/utils/versioning.py index 4a235dc..8d62784 100644 --- a/src/rd_cdm/utils/versioning.py +++ b/src/rd_cdm/utils/versioning.py @@ -11,91 +11,13 @@ except ModuleNotFoundError: # pragma: no cover import tomli as tomllib # type: ignore[no-redef] -def _read_project_version(pyproject_path: Path) -> Optional[str]: - if not pyproject_path.exists(): - return None - with pyproject_path.open("rb") as f: - data = tomllib.load(f) - - # Poetry-style - v = ( - data.get("tool", {}) - .get("poetry", {}) - .get("version") - ) - # PEP 621 fallback ([project].version) - if not v: - v = data.get("project", {}).get("version") - return str(v) if v else None - -def version_to_tag(version: str) -> str: - """ - Map "2.0.1" or "v2.0.1" or "v2_0_1" -> "v2_0_1". - """ - v = version.strip() - v = re.sub(r"^[vV]", "", v) - v = v.replace(".", "_") - return f"v{v}" - -def normalize_dir_to_version(name: str) -> Optional[str]: - """ - Map "v2_0_1" -> "2.0.1" (used for sorting dirs). - """ - n = re.sub(r"^[vV]", "", name) - n = n.replace("_", ".") - if re.fullmatch(r"\d+(\.\d+){1,}", n): - return n - return None +def get_model_version() -> Optional[str]: + root = Path(__file__).resolve().parents[2] + return _read_project_version(root / "pyproject.toml") def resolve_instances_dir(version: Optional[str] = None) -> Path: - """ - Determine the instances directory: - 1) explicit `version` arg, or - 2) env RDCDM_VERSION, or - 3) pyproject version, or - 4) latest directory found by scanning. - """ - # repo root: rd_cdm/util/versioning.py -> .../src/rd_cdm/util -> up 2 root = Path(__file__).resolve().parents[2] base = root / "rd_cdm" / "instances" - - # 1/2/3: choose version - chosen_version = ( - version - or os.getenv("RDCDM_VERSION") - or _read_project_version(root / "pyproject.toml") - ) - - # 3a) Use chosen version if present - if chosen_version: - vtag = version_to_tag(chosen_version) - candidate = base / vtag - if candidate.is_dir(): - return candidate - - # 4) Fallback: pick latest by scanning - try: - from packaging.version import Version - except Exception: - Version = None # type: ignore - - best = None - for d in base.iterdir(): - if d.is_dir(): - norm = normalize_dir_to_version(d.name) - if not norm: - continue - if Version: - try: - key = Version(norm) - except Exception: - continue - else: - key = tuple(int(x) for x in norm.split(".")) # naive fallback - if not best or key > best[0]: - best = (key, d) - - if best: - return best[1] - - raise FileNotFoundError(f"No instances directory found in {base}") + if not base.is_dir(): + raise FileNotFoundError(f"No instances directory found at {base}") + return base \ No newline at end of file diff --git a/tests/test_csv_parsing.py b/tests/test_csv_parsing.py index 3951fca..28cd60c 100644 --- a/tests/test_csv_parsing.py +++ b/tests/test_csv_parsing.py @@ -1,32 +1,49 @@ -import types +# tests/test_csv_parsing.py +import csv +import ruamel.yaml import rd_cdm.utils.csv_parsing as cp +from rd_cdm.utils.config import PathsConfig + def test_csv_parsing_writes_all_and_combined(tmp_path, monkeypatch): - version_tag = "v2_0_1" - src_dir = tmp_path / "src" - inst_dir = src_dir / "rd_cdm" / "instances" / version_tag - out_dir = inst_dir / "csvs" + """main() should write per-section CSVs and a combined rd_cdm.csv + with a _metadata row carrying rd_cdm_version.""" + + inst_dir = tmp_path / "src" / "rd_cdm" / "instances" inst_dir.mkdir(parents=True, exist_ok=True) - # minimal source YAMLs - (inst_dir / "code_systems.yaml").write_text("code_systems:\n - {id: HP, version: v1}\n") - (inst_dir / "data_elements.yaml").write_text("data_elements:\n - {elementName: E, elementCode: {system: HP, code: '0000118'}}\n") - (inst_dir / "value_sets.yaml").write_text("value_sets:\n - {id: VS1, codes: ['HP:0000118']}\n") + # write a minimal merged rd_cdm.yaml + merged_data = { + "rd_cdm_version": "2.0.3", + "rd_cdm_date": "2025-03-24", + "code_systems": [{"id": "HP", "version": "v1"}], + "data_elements": [{"elementName": "E", "elementCode": {"system": "HP", "code": "0000118"}}], + "value_sets": [{"id": "VS1", "codes": ["HP:0000118"]}], + } + yaml = ruamel.yaml.YAML() + with (inst_dir / "rd_cdm.yaml").open("w") as f: + yaml.dump(merged_data, f) - # point resolver to our temp folder - monkeypatch.setattr(cp, "resolve_instances_dir", lambda ver=None: inst_dir) - # avoid ruamel dependency variability: use safe loader behavior - import ruamel.yaml - yaml = ruamel.yaml.YAML(typ="safe") - monkeypatch.setattr(cp, "ruamel", types.SimpleNamespace(yaml=types.SimpleNamespace(YAML=lambda: yaml))) + src_root = tmp_path / "src" + monkeypatch.setattr( + cp, + "resolve_paths", + lambda: PathsConfig(src_root=src_root, instances_dir=inst_dir), + ) - rc = cp.write_csvs_from_instances(None) + rc = cp.main() assert rc == 0 - # per-list CSVs - assert (out_dir / "code_systems.csv").exists() - assert (out_dir / "data_elements.csv").exists() - assert (out_dir / "value_sets.csv").exists() + csv_dir = inst_dir / "csvs" + assert (csv_dir / "code_systems.csv").exists() + assert (csv_dir / "data_elements.csv").exists() + assert (csv_dir / "value_sets.csv").exists() + assert (csv_dir / "rd_cdm.csv").exists() + + # check _metadata row carries the version + with (csv_dir / "rd_cdm.csv").open(newline="", encoding="utf-8") as f: + rows = list(csv.DictReader(f)) - # combined file follows v-tag style (e.g., rd_cdm_v2_0_1.csv) - assert (out_dir / "rd_cdm_v2_0_1.csv").exists() \ No newline at end of file + metadata_rows = [r for r in rows if r.get("_section") == "_metadata"] + assert len(metadata_rows) == 1 + assert metadata_rows[0]["rd_cdm_version"] == "2.0.3" \ No newline at end of file diff --git a/tests/test_json_parsing.py b/tests/test_json_parsing.py index 0eb133b..f76b30e 100644 --- a/tests/test_json_parsing.py +++ b/tests/test_json_parsing.py @@ -1,45 +1,43 @@ +# tests/test_json_parsing.py import json -from pathlib import Path -import types - +import ruamel.yaml import rd_cdm.utils.json_parsing as jp +from rd_cdm.utils.config import PathsConfig -def test_json_parsing_skips_merged_and_writes_combined(tmp_path, monkeypatch): - version_tag = "v2_0_1" - src_dir = tmp_path / "src" - inst_dir = src_dir / "rd_cdm" / "instances" / version_tag - json_dir = inst_dir / "jsons" - inst_dir.mkdir(parents=True, exist_ok=True) - - # create part YAMLs + a merged YAML that must be skipped in the loop - (inst_dir / "code_systems.yaml").write_text("dummy") - (inst_dir / "data_elements.yaml").write_text("dummy") - (inst_dir / "value_sets.yaml").write_text("dummy") - (inst_dir / "rd_cdm_v2_0_1.yaml").write_text("dummy") # must be skipped - - # monkeypatch instance resolver - monkeypatch.setattr(jp, "resolve_instances_dir", lambda ver=None: inst_dir) +def test_json_parsing_reads_merged_and_writes_json(tmp_path, monkeypatch): + """main() should read rd_cdm.yaml and write jsons/rd_cdm.json.""" - # monkeypatch loader + dumper to avoid LinkML dependency - monkeypatch.setattr(jp, "yaml_loader", types.SimpleNamespace( - load=lambda path, target_class: {"loaded_from": Path(path).name} - )) - monkeypatch.setattr(jp, "json_dumper", types.SimpleNamespace( - dumps=lambda obj: json.dumps(obj) - )) + inst_dir = tmp_path / "src" / "rd_cdm" / "instances" + inst_dir.mkdir(parents=True, exist_ok=True) - rc = jp.main(None) + # write a minimal merged rd_cdm.yaml (as merge step would produce) + merged_data = { + "rd_cdm_version": "2.0.3", + "rd_cdm_date": "2025-03-24", + "code_systems": [{"id": "HP", "version": "v1"}], + "data_elements": [{"elementName": "E"}], + "value_sets": [{"id": "VS1"}], + } + yaml = ruamel.yaml.YAML() + with (inst_dir / "rd_cdm.yaml").open("w") as f: + yaml.dump(merged_data, f) + + src_root = tmp_path / "src" + monkeypatch.setattr( + jp, + "resolve_paths", + lambda: PathsConfig(src_root=src_root, instances_dir=inst_dir), + ) + + rc = jp.main() assert rc == 0 - # per-file JSONs (no rd_cdm_v*.json from the loop itself) - assert (json_dir / "code_systems.json").exists() - assert (json_dir / "data_elements.json").exists() - assert (json_dir / "value_sets.json").exists() - assert (json_dir / "rd_cdm_v2_0_1.json").exists() - - # combined file present with v-tag in name - combined = json_dir / "rd_cdm_v2_0_1.json" - assert combined.exists() - data = json.loads(combined.read_text()) - assert set(data.keys()) == {"code_systems", "data_elements", "value_sets"} \ No newline at end of file + out_file = inst_dir / "jsons" / "rd_cdm.json" + assert out_file.exists() + + data = json.loads(out_file.read_text()) + assert data["rd_cdm_version"] == "2.0.3" + assert "code_systems" in data + assert "data_elements" in data + assert "value_sets" in data \ No newline at end of file diff --git a/tests/test_merge_instances.py b/tests/test_merge_instances.py index ea6d76d..45fcd0a 100644 --- a/tests/test_merge_instances.py +++ b/tests/test_merge_instances.py @@ -1,31 +1,54 @@ +# tests/test_merge_instances.py import ruamel.yaml +import rd_cdm.utils.merge_instances as merge_mod +from rd_cdm.utils.config import PathsConfig -import rd_cdm.utils.merge_instances as merge_mod -def test_merge_instances_writes_rd_cdm_v_tag_yaml(tmp_path, monkeypatch): - # fake repo skeleton: src/rd_cdm/instances/v2_0_1 with the 3 parts - version_tag = "v2_0_1" - inst_dir = tmp_path / "src" / "rd_cdm" / "instances" / version_tag +def test_merge_instances_writes_rd_cdm_yaml(tmp_path, monkeypatch): + """main() should merge the three part YAMLs into rd_cdm.yaml + with rd_cdm_version and rd_cdm_date from the schema.""" + + # flat instances dir (no version subdir) + inst_dir = tmp_path / "src" / "rd_cdm" / "instances" inst_dir.mkdir(parents=True, exist_ok=True) - (inst_dir / "code_systems.yaml").write_text("code_systems:\n - {id: HP, version: v1}\n") - (inst_dir / "data_elements.yaml").write_text("data_elements:\n - {elementName: E, elementCode: {system: HP, code: '0000118'}}\n") - (inst_dir / "value_sets.yaml").write_text("value_sets:\n - {id: VS1, codes: ['HP:0000118']}\n") + schema_dir = tmp_path / "src" / "rd_cdm" / "schema" + schema_dir.mkdir(parents=True, exist_ok=True) + + # minimal part YAMLs + (inst_dir / "code_systems.yaml").write_text( + "code_systems:\n - {id: HP, version: v1}\n" + ) + (inst_dir / "data_elements.yaml").write_text( + "data_elements:\n - {elementName: E, elementCode: {system: HP, code: '0000118'}}\n" + ) + (inst_dir / "value_sets.yaml").write_text( + "value_sets:\n - {id: VS1, codes: ['HP:0000118']}\n" + ) + + # minimal schema with version and date + (schema_dir / "rd_cdm.yaml").write_text( + "id: https://example.org/rd-cdm\nversion: 2.0.3\ndate: '2025-03-24'\n" + ) - # point resolve_instances_dir() to our temp instance dir + # patch resolve_paths to return our tmp dirs + src_root = tmp_path / "src" monkeypatch.setattr( - merge_mod, "resolve_instances_dir", - lambda ver=None: inst_dir + merge_mod, + "resolve_paths", + lambda: PathsConfig(src_root=src_root, instances_dir=inst_dir), ) - # run main() - rc = merge_mod.main(None) + rc = merge_mod.main() assert rc == 0 - out_file = inst_dir / f"rd_cdm_{version_tag}.yaml" + out_file = inst_dir / "rd_cdm.yaml" assert out_file.exists() - # sanity: merged keys present yaml = ruamel.yaml.YAML(typ="safe") merged = yaml.load(out_file.read_text()) - assert "code_systems" in merged and "data_elements" in merged and "value_sets" in merged + assert "code_systems" in merged + assert "data_elements" in merged + assert "value_sets" in merged + assert merged["rd_cdm_version"] == "2.0.3" + assert str(merged["rd_cdm_date"]) == "2025-03-24" \ No newline at end of file diff --git a/tests/test_versioning.py b/tests/test_versioning.py index b2024a7..d2dbf54 100644 --- a/tests/test_versioning.py +++ b/tests/test_versioning.py @@ -1,35 +1,27 @@ +# tests/test_versioning.py from pathlib import Path import rd_cdm.utils.versioning as ver -def test_version_to_tag_and_normalize(): - assert ver.version_to_tag("2.0.1") == "v2_0_1" - assert ver.version_to_tag("v2.0.1") == "v2_0_1" - assert ver.normalize_dir_to_version("v2_0_1") == "2.0.1" - assert ver.normalize_dir_to_version("garbage") is None - -def test_resolve_instances_dir_with_env_and_existing_dir(tmp_path, monkeypatch): - # Build temp structure that matches expected: /rd_cdm/instances/v2_0_1 +def test_resolve_instances_dir_returns_instances_path(tmp_path, monkeypatch): + """resolve_instances_dir should return src/rd_cdm/instances/ directly.""" root = tmp_path / "src" - inst = root / "rd_cdm" / "instances" / "v2_0_1" + inst = root / "rd_cdm" / "instances" inst.mkdir(parents=True, exist_ok=True) - # Monkeypatch Path(__file__).resolve().parents[2] -> root - class FakePath(Path): - _flavour = Path(".")._flavour # required for subclassing Path - def resolve(self): return self - @property - def parents(self): - # return something whose [2] is our `root` - class _Parents(list): - pass - p = _Parents([self.parent, self.parent.parent, root]) - return p + # Patch Path(__file__).resolve().parents[2] -> root + import rd_cdm.utils.versioning as ver_mod + monkeypatch.setattr(ver_mod, "__file__", str(root / "rd_cdm" / "utils" / "versioning.py")) + + resolved = ver.resolve_instances_dir() + assert resolved == inst + - monkeypatch.setattr(ver, "Path", FakePath) +def test_resolve_instances_dir_raises_when_missing(tmp_path, monkeypatch): + """Should raise FileNotFoundError if instances dir does not exist.""" + import rd_cdm.utils.versioning as ver_mod + monkeypatch.setattr(ver_mod, "__file__", str(tmp_path / "rd_cdm" / "utils" / "versioning.py")) - # Set env so it uses 2.0.1 - monkeypatch.setenv("RDCDM_VERSION", "2.0.1") - resolved = ver.resolve_instances_dir(None) - # Using our FakePath, resolved should be a FakePath pointing at inst - assert str(resolved).endswith("rd_cdm/instances/v2_0_1") + import pytest + with pytest.raises(FileNotFoundError): + ver.resolve_instances_dir() \ No newline at end of file